ABC@home

1. Martin, Greg and Winnie Miao. abc triples. (2014). DOI: 10.48550/ARXIV.1409.2974.

AQUA@home

1. Karimi, Kamran, Neil Dickson and Firas Hamze. High-performance Physics Simulations Using Multi-core CPUs and GPGPUs in a Volunteer Computing Context. The International Journal of High Performance Computing Applications (2011). DOI: 10.1177/1094342010372928.
2. Hamze, Firas, Neil Dickson and Kamran Karimi. Robust Parameter Selection for Parallel Tempering. (2010). DOI: 10.48550/ARXIV.1004.2840.
3. Dickson, Neil G., Kamran Karimi and Firas Hamze. Importance of Explicit Vectorization for CPU and GPU Software Performance. (2010). DOI: 10.48550/ARXIV.1004.0024.
4. Karimi, Kamran, Neil G. Dickson, Firas Hamze et al. Investigating the Performance of an Adiabatic Quantum Optimization Processor. (2010). DOI: 10.48550/ARXIV.1006.4147.

Acoustics@home

1. Zaikin, Oleg, Pavel Petrov, Mikhail Posypkin, Vadim Bulavintsev and Ilya Kurochkin. A Volunteer Computing Project for Solving Geoacoustic Inversion Problems. Open Engineering (2017). DOI: 10.1515/eng-2017-0040.
2. Zaikin, O. and P. Petrov. Application of iterative hill climbing to the sound speed profile inversion in underwater acoustics. IOP Conference Series: Materials Science and Engineering (2017). DOI: 10.1088/1757-899X/173/1/012022.

AndersonAttack@home

1. Bulavintsev, Vadim, Alexander Semenov, Oleg Zaikin and Stepan Kochemazov. A Bitslice Implementation of Anderson’s Attack on A5/1. Open Engineering (2018). DOI: 10.1515/eng-2018-0002.

Asteroids@home

1. Ďurech, Josef, Michael Vávra, Radim Vančo and Nicolas Erasmus. Rotation Periods of Asteroids Determined With Bootstrap Convex Inversion From ATLAS Photometry. Frontiers in Astronomy and Space Sciences (2022). DOI: 10.3389/fspas.2022.809771.
2. Durech, J., J. Tonry, N. Erasmus, L. Denneau, A. N. Heinze, H. Flewelling and R. Vanco. Asteroid models reconstructed from ATLAS photometry. (2020). DOI: 10.48550/ARXIV.2010.01820.
3. Durech, Josef, Josef Hanus and Radim Vanco. Inversion of asteroid photometry from Gaia DR2 and the Lowell Observatory photometric database. (2019). DOI: 10.48550/ARXIV.1909.09395.
4. Durech, Josef, Josef Hanus and Victor Ali-Lagoa. Asteroid models reconstructed from the Lowell Photometric Database and WISE data. (2018). DOI: 10.48550/ARXIV.1807.02083.
5. Hanuš, J., J. Ďurech, D. A. Oszkiewicz et al. New and updated convex shape models of asteroids based on optical data from a large collaboration network. Astronomy & Astrophysics (2016). DOI: 10.1051/0004-6361/201527441.
6. Durech, J., J. Hanus, D. Oszkiewicz and R. Vanco. Asteroid models from the Lowell Photometric Database. (2016). DOI: 10.48550/ARXIV.1601.02909.
7. Cibulková, H., J. Ďurech, D. Vokrouhlický, M. Kaasalainen and D. A. Oszkiewicz. Distribution of spin-axes longitudes and shape elongations of main-belt asteroids. Astronomy & Astrophysics (2016). DOI: 10.1051/0004-6361/201629192.
8. Ďurech, J., J. Hanuš and R. Vančo. Asteroids@home—A BOINC distributed computing project for asteroid shape reconstruction. Astronomy and Computing (2015). DOI: 10.1016/j.ascom.2015.09.004.
9. Durech, J., B. Carry, M. Delbo, M. Kaasalainen and M. Viikinkoski. Asteroid Models from Multiple Data Sources. (2015). DOI: 10.48550/ARXIV.1502.04816.
10. Durech, Josef, J. Hanus, R. Vanco, D. Oszkiewicz and E. Bowell. New Asteroid Shape Models Derived from the Lowell Photometric Database. (2013).

BOINC-MR

1. Costa, Fernando, Luís Veiga and Paulo Ferreira. BOINC-MR: MapReduce in a Volunteer Environment. On the Move to Meaningful Internet Systems: OTM 2012 (2012).
2. Costa, Fernando, Luis Silva and Michael Dahlin. Volunteer Cloud Computing: MapReduce over the Internet. Distributed Processing, Workshops and Phd Forum (IPDPSW) (2011). DOI: 10.1109/IPDPS.2011.345.

BOINC@TACC

1. Redondo, Carlos and Ritu Arora. Greyfish: An Out-of-the-Box, Reusable, Portable Cloud Storage Service. PEARC '19: Practice and Experience in Advanced Research Computing (2019). DOI: 10.1145/3332186.3333055.
2. Arora, Ritu, Carlos Redondo and Gerald Joshua. Scalable Software Infrastructure for Integrating Supercomputing with Volunteer Computing and Cloud Computing. Software Challenges to Exascale Computing (2019).
3. Wilson, Lucas A and David P Anderson. VAST: Integrating Volunteer Computing into Existing Cyberinfrastructure. (2017). DOI: 10.13140/RG.2.2.28139.64805.

BRaTS@Home

1. Coss, David. Weak shear study of galaxy clusters by simulated gravitational lensing. (2010).
2. Coss, David Raymond and R. Flores. BRaTS@Home and BOINC Distributed Computing for Parallel Computation. (2008).

BealF@Home

1. Świerczewski, Łukasz. Testowanie przypuszczenia Beal’a z wykorzystaniem superkomputerów oraz platformy do obliczeń rozproszonych BOINC. (2015).

Big and Ugly Rendering Project (BURP)

1. Kantert, Jan, Christian Reinbold, Sven Tomforde and Christian Muller-Schloer. An Evaluation of Two Trust-Based Autonomic/Organic Grid Computing Systems for Volunteer-Based Distributed Rendering. 2016 IEEE International Conference on Autonomic Computing (ICAC) (2016). DOI: 10.1109/ICAC.2016.55.
2. Kantert, Jan, Henning Spiegelberg, Sven Tomforde, Jorg Hahner and Christian Muller-Schloer. Distributed Rendering in an Open Self-Organised Trusted Desktop Grid. 2015 IEEE International Conference on Autonomic Computing (ICAC) (2015). DOI: 10.1109/ICAC.2015.66.

Charity Engine

1. Brown, Nico, Carson Cheng, Tanner Jacobi, Maia Karpovich, Matthias Merzenich, David Raucci and Mitchell Riley. Conway's Game of Life is Omniperiodic. (2023). DOI: 10.48550/ARXIV.2312.02799.
2. Booker, Andrew R. and Andrew V. Sutherland. On a question of Mordell. Proceedings of the National Academy of Sciences (2021). DOI: 10.1073/pnas.2022377118.

Citizen Science Grid

1. Desell, Travis. Large Scale Evolution of Convolutional Neural Networks Using Volunteer Computing. (2017). DOI: 10.48550/arXiv.1703.05422.

Climateprediction.net

1. Hatton, Luke, René Bañares-Alcántara, Sarah Sparrow, Fraser Lott and Nicholas Salmon. Assessing the impact of climate change on the cost of production of green ammonia from offshore wind. International Journal of Hydrogen Energy (2024). DOI: 10.1016/j.ijhydene.2023.10.117.
2. Ye, Kunhui, Tim Woollings, Sarah N. Sparrow, Peter A. G. Watson and James A. Screen. Response of winter climate and extreme weather to projected Arctic sea-ice loss in very large-ensemble climate model simulations. npj Climate and Atmospheric Science (2024). DOI: 10.1038/s41612-023-00562-5.
3. Miranda, Nicole, Jesus Lizana, Sarah Sparrow, Miriam Zachau-Walker, David Wallom, Radhika Khosla and Malcolm McCulloch. From 1.5ºC to 2.0ºC: the global increase in cooling degree days. (2023).
4. Miranda, Nicole D., Jesus Lizana, Sarah N. Sparrow, Miriam Zachau-Walker, Peter A. G. Watson, David C. H. Wallom, Radhika Khosla and Malcolm McCulloch. Change in cooling degree days with global mean temperature rise increasing from 1.5 °C to 2.0 °C. Nature Sustainability (2023). DOI: 10.1038/s41893-023-01155-z.
5. Lee, Donghyun, Sarah N Sparrow, Seung-Ki Min, Sang-Wook Yeh and Myles R Allen. Physically based equation representing the forcing-driven precipitation in climate models. Environmental Research Letters (2023). DOI: 10.1088/1748-9326/acf50f.
6. Higgins, Timothy B., Aneesh C. Subramanian, Andre Graubner et al. Using Deep Learning for an Analysis of Atmospheric Rivers in a High‐Resolution Large Ensemble Climate Data Set. Journal of Advances in Modeling Earth Systems (2023). DOI: 10.1029/2022MS003495.
7. Fallon, James C., Hannah C. Bloomfield, David J. Brayshaw et al. Understanding Climate Risk in Future Energy Systems: An Energy–Climate Data Hackathon. Bulletin of the American Meteorological Society (2022). DOI: 10.1175/BAMS-D-21-0305.1.
8. Calafat, Francisco M., Thomas Wahl, Michael Getachew Tadesse and Sarah N. Sparrow. Trends in Europe storm surge extremes match the rate of sea-level rise. Nature (2022). DOI: 10.1038/s41586-022-04426-5.
9. Rimi, Ruksana H., Karsten Haustein, Emily J. Barbour, Sarah N. Sparrow, Sihan Li, David C. H. Wallom and Myles R. Allen. Risks of seasonal extreme rainfall events in Bangladesh under 1.5 and 2.0 °C warmer worlds – how anthropogenic aerosols change the story. Hydrology and Earth System Sciences (2022). DOI: 10.5194/hess-26-5737-2022.
10. Li, Sihan, Sami Rifai, Liana O. Anderson and Sarah Sparrow. Identifying local‐scale meteorological conditions favorable to large fires in Brazil. Climate Resilience and Sustainability (2022). DOI: 10.1002/cli2.11.
11. Allen, M., B. Booth, David Frame, J. Gregory, J. Kettleborough and Leonard Smith. Observational constraints on future climate: distinguishing robust from model-dependent statements of uncertainty in climate forecasting. (2022).
12. Leach, Nicholas J., Peter A.G. Watson, Sarah N. Sparrow, David C.H. Wallom and David M.H. Sexton. Generating samples of extreme winters to support climate adaptation. Weather and Climate Extremes (2022). DOI: 10.1016/j.wace.2022.100419.
13. Pham, Hoa X., Asaad Y. Shamseldin and Bruce W. Melville. Projection of future extreme precipitation: a robust assessment of downscaled daily precipitation. Natural Hazards (2021). DOI: 10.1007/s11069-021-04584-1.
14. Di Capua, G., S. Sparrow, K. Kornhuber, E. Rousi, S. Osprey, D. Wallom, B. van den Hurk and D. Coumou. Drivers behind the summer 2010 wave train leading to Russian heatwave and Pakistan flooding. npj Climate and Atmospheric Science (2021). DOI: 10.1038/s41612-021-00211-9.
15. Aengenheyster, Matthias, Sarah Sparrow, Peter Watson, David Wallom, Laure Zanna and Myles Allen. Impact of sub-seasonal atmosphere-ocean interactions on extreme event statistics. (2021).
16. Andrews, Timothy, Christopher J. Smith, Gunnar Myhre, Piers M. Forster, Robin Chadwick and Duncan Ackerley. Effective Radiative Forcing in a GCM With Fixed Surface Temperatures. Journal of Geophysical Research: Atmospheres (2021). DOI: 10.1029/2020JD033880.
17. Sparrow, Sarah, Andrew Bowery, Glenn D. Carver, Marcus O. Köhler, Pirkka Ollinaho, Florian Pappenberger, David Wallom and Antje Weisheimer. OpenIFS@home version 1: a citizen science project for ensemble weather and climate forecasting. Geoscientific Model Development (2021). DOI: 10.5194/gmd-14-3473-2021.
18. Li, Sihan, Sarah N Sparrow, Friederike E L Otto et al. Anthropogenic climate change contribution to wildfire-prone weather conditions in the Cerrado and Arc of deforestation. Environmental Research Letters (2021). DOI: 10.1088/1748-9326/ac1e3a.
19. Bevacqua, Emanuele, Theodore G. Shepherd, Peter A. G. Watson, Sarah Sparrow, David Wallom and Dann Mitchell. Larger Spatial Footprint of Wintertime Total Precipitation Extremes in a Warmer Climate. Geophysical Research Letters (2021). DOI: 10.1029/2020GL091990.
20. van Oldenborgh, Geert Jan, Folmer Krikken, Sophie Lewis et al. Attribution of the Australian bushfire risk to anthropogenic climate change. Natural Hazards and Earth System Sciences (2021). DOI: 10.5194/nhess-21-941-2021.
21. Undorf, S., K. Allen, J. Hagg, S. Li, F. C. Lott, M. J. Metzger, S. N. Sparrow and S. F. B. Tett. Learning from the 2018 heatwave in the context of climate change: are high-temperature extremes important for adaptation in Scotland?. Environmental Research Letters (2020). DOI: 10.1088/1748-9326/ab6999.
22. Li, Sihan, Friederike E L Otto, Luke J Harrington, Sarah N Sparrow and David C H Wallom. A pan-South-America assessment of avoided exposure to dangerous extreme precipitation by limiting to 1.5 °C warming. Environmental Research Letters (2020). DOI: 10.1088/1748-9326/ab50a2.
23. Montes, Diego, Juan A. Añel, David C. H. Wallom, Peter Uhe, Pablo V. Caderno and Tomás F. Pena. Cloud Computing for Climate Modelling: Evaluation, Challenges and Benefits. Computers (2020). DOI: 10.3390/computers9020052.
24. Di Capua, Giorgia, Kai Kornhuber, Eftychia Rousi, Sarah Sparrow, David Wallom and Dim Coumou. Wave-resonance fingerprint in the 2010 summer: a modelling experiment. (2020).
25. Leach, Nicholas J., Sihan Li, Sarah Sparrow, Geert Jan van Oldenborgh, Fraser C. Lott, Antje Weisheimer and Myles R. Allen. Anthropogenic Influence on the 2018 Summer Warm Spell in Europe: The Impact of Different Spatio-Temporal Scales. Bulletin of the American Meteorological Society (2020). DOI: 10.1175/BAMS-D-19-0201.1.
26. Tozer, Carly R., James S. Risbey, Michael Grose et al. A 1-Day Extreme Rainfall Event in Tasmania: Process Evaluation and Long Tail Attribution. Bulletin of the American Meteorological Society (2020). DOI: 10.1175/BAMS-D-19-0219.1.
27. Fučkar, Neven Stjepan, Friederike E.L. Otto, Flavio Lehner, Izidine Pinto, Sarah Sparrow, Sihan Li and David Wallom. On High Precipitation in Mozambique, Zimbabwe and Zambia in February 2018. Bulletin of the American Meteorological Society (2020). DOI: 10.1175/BAMS-D-19-0162.1.
28. Naveau, Philippe, Alexis Hannart and Aurélien Ribes. Statistical Methods for Extreme Event Attribution in Climate Science. Annual Review of Statistics and Its Application (2020). DOI: 10.1146/annurev-statistics-031219-041314.
29. Iyyanki, Murali Krishna V. and Prisilla Jayanthi. The Impact of Climate Change on Human Eyes. Urban Health Risk and Resilience in Asian Cities (2020).
30. Bussi, Gianbattista and Paul G. Whitehead. Impacts of droughts on low flows and water quality near power stations. Hydrological Sciences Journal (2020). DOI: 10.1080/02626667.2020.1724295.
31. Min, Seung-Ki, Yeon-Hee Kim, Sang-Min Lee, Sarah Sparrow, Sihan Li, Fraser C. Lott and Peter A. Stott. Quantifying Human Impact on the 2018 Summer Longest Heat Wave in South Korea. Bulletin of the American Meteorological Society (2020). DOI: 10.1175/BAMS-D-19-0151.1.
32. Rimi, Ruksana, Karsten Haustein, Emily Barbour, Sarah Sparrow, Sihan Li, David Wallom and Myles Allen. A Multi-model Assessment of the Changing Risks of Extreme Rainfall Events in Bangladesh under 1.5 and 2.0 degrees’ warmer worlds. (2020).
33. Watson, Peter, Sarah Sparrow, William Ingram et al. Multi-thousand member ensemble atmospheric simulations with global 60km resolution using climateprediction.net. (2020).
34. Gaupp, Franziska, Jim Hall, Dann Mitchell and Simon Dadson. Increasing risks of multiple breadbasket failure under 1.5 and 2 °C global warming. Agricultural Systems (2019). DOI: 10.1016/j.agsy.2019.05.010.
35. Lo, Y. T. Eunice, Daniel M. Mitchell, Antonio Gasparrini et al. Increasing mitigation ambition to meet the Paris Agreement’s temperature goal avoids substantial heat-related mortality in U.S. cities. Science Advances (2019). DOI: 10.1126/sciadv.aau4373.
36. Marthews, T. R., R. G. Jones, S. J. Dadson, F. E. L. Otto, D. Mitchell, B. P. Guillod and M. R. Allen. The Impact of Human‐Induced Climate Change on Regional Drought in the Horn of Africa. Journal of Geophysical Research: Atmospheres (2019). DOI: 10.1029/2018JD030085.
37. Wehner, Michael F., Colin Zarzycki and Christina Patricola. Estimating the Human Influence on Tropical Cyclone Intensity as the Climate Changes. Hurricane Risk (2019).
38. Baker, Hugh S., Tim Woollings, Cheikh Mbengue, Myles R. Allen, Christopher H. O’Reilly, Hideo Shiogama and Sarah Sparrow. Forced summer stationary waves: the opposing effects of direct radiative forcing and sea surface warming. Climate Dynamics (2019). DOI: 10.1007/s00382-019-04786-1.
39. Lawal, Kamoru A. and Dáithí A. Stone. On the Co-Variability between Climate Indices and the Potential Spread of Seasonal Climate Simulations over South African Provinces. Atmospheric and Climate Sciences (2019). DOI: 10.4236/acs.2019.93027.
40. Rimi, Ruksana H., Karsten Haustein, Emily J. Barbour, Richard G. Jones, Sarah N. Sparrow and Myles R. Allen. Evaluation of a large ensemble regional climate modelling system for extreme weather events analysis over Bangladesh. International Journal of Climatology (2019). DOI: 10.1002/joc.5931.
41. Chen, Yang, Wei Chen, Qin Su et al. Anthropogenic Warming has Substantially Increased the Likelihood of July 2017–Like Heat Waves over Central Eastern China. Bulletin of the American Meteorological Society (2019). DOI: 10.1175/BAMS-D-18-0087.1.
42. de Abreu, Rafael C., Christopher Cunningham, Conrado M. Rudorff et al. Contribution of Anthropogenic Climate Change to April–May 2017 Heavy Precipitation over the Uruguay River Basin. Bulletin of the American Meteorological Society (2019). DOI: 10.1175/BAMS-D-18-0102.1.
43. Huntingford, Chris, Dann Mitchell, Kai Kornhuber, Dim Coumou, Scott Osprey and Myles Allen. Assessing changes in risk of amplified planetary waves in a warming world. Atmospheric Science Letters (2019). DOI: 10.1002/asl.929.
44. Li, Sihan, David E. Rupp, Linnia Hawkins et al. Reducing climate model biases by exploring parameter space with large ensembles of climate model simulations and statistical emulation. Geoscientific Model Development (2019). DOI: 10.5194/gmd-12-3017-2019.
45. Min, Seung-Ki, Yeon-Hee Kim, In-Hong Park, Donghyun Lee, Sarah Sparrow, David Wallom and Dáithí Stone. Anthropogenic Contribution to the 2017 Earliest Summer Onset in South Korea. Bulletin of the American Meteorological Society (2019). DOI: 10.1175/BAMS-D-18-0096.1.
46. Baker, Hugh S., Tim Woollings, Chris E. Forest and Myles R. Allen. The Linear Sensitivity of the North Atlantic Oscillation and Eddy-Driven Jet to SSTs. Journal of Climate (2019). DOI: 10.1175/JCLI-D-19-0038.1.
47. Hawkins, Linnia R., David E. Rupp, Doug J. McNeall, Sihan Li, Richard A. Betts, Philip W. Mote, Sarah N. Sparrow and David C. H. Wallom. Parametric Sensitivity of Vegetation Dynamics in the TRIFFID Model and the Associated Uncertainty in Projected Climate Change Impacts on Western U.S. Forests. Journal of Advances in Modeling Earth Systems (2019). DOI: 10.1029/2018MS001577.
48. Philip, Sjoukje, Sarah Sparrow, Sarah F. Kew et al. Attributing the 2017 Bangladesh floods from meteorological and hydrological perspectives. Hydrology and Earth System Sciences (2019). DOI: 10.5194/hess-23-1409-2019.
49. Hirsch, Annette L., Benoit P. Guillod, Sonia I. Seneviratne et al. Biogeophysical Impacts of Land-Use Change on Climate Extremes in Low-Emission Scenarios: Results From HAPPI-Land. Earth's Future (2018). DOI: 10.1002/2017EF000744.
50. Sparrow, Sarah, Qin Su, Fangxing Tian et al. Attributing human influence on the July 2017 Chinese heatwave: the influence of sea-surface temperatures. Environmental Research Letters (2018). DOI: 10.1088/1748-9326/aae356.
51. Schaller, Nathalie, Sarah N. Sparrow, Neil R. Massey, Andy Bowery, Jonathan Miller, Simon Wilson, David C. H. Wallom and Friederike E. L. Otto. Ensemble of European regional climate simulations for the winter of 2013 and 2014 from HadAM3P-RM3P. Scientific Data (2018). DOI: 10.1038/sdata.2018.57.
52. Freychet, N., S. Sparrow, S. F. B. Tett, M. J. Mineter, G. C. Hegerl and D. C. H. Wallom. Impacts of Anthropogenic Forcings and El Niño on Chinese Extreme Temperatures. Advances in Atmospheric Sciences (2018). DOI: 10.1007/s00376-018-7258-8.
53. Coxon, Gemma, Benoit Guillod, Jim Freer, Simon Dadson, Richard Jones, Thorsten Wagener, Ross Woods and Nicholas Howden. Projecting future changes in hydrological droughts in the UK : the impacts of bias correction and uncertainty in model predictions. (2018).
54. Harrington, Luke J. and Friederike E. L. Otto. Changing population dynamics and uneven temperature emergence combine to exacerbate regional exposure to heat extremes under 1.5 °C and 2 °C of warming. Environmental Research Letters (2018). DOI: 10.1088/1748-9326/aaaa99.
55. Philip, Sjoukje Y., Sarah F. Kew, Mathias Hauser, Benoit P. Guillod, Adriaan J. Teuling, Kirien Whan, Peter Uhe and Geert Jan van Oldenborgh. Western US high June 2015 temperatures and their relation to global warming and soil moisture. Climate Dynamics (2018). DOI: 10.1007/s00382-017-3759-x.
56. Li, Sihan, David E. Rupp, Linnia Hawkins et al. Improving climate model accuracy by exploring parameter space with an O(10⁵) member ensemble and emulator. (2018).
57. Uhe, Peter, Sjoukje Philip, Sarah Kew et al. Attributing drivers of the 2016 Kenyan drought: 2016 KENYAN DROUGHT. International Journal of Climatology (2018). DOI: 10.1002/joc.5389.
58. Philip, Sjoukje, Sarah Sparrow, Sarah F. Kew et al. Attributing the 2017 Bangladesh floods from meteorological andhydrological perspectives. (2018).
59. Kay, Alison L., Naomi Booth, Rob Lamb, Emma Raven, Nathalie Schaller and Sarah Sparrow. Flood event attribution and damage estimation using national-scale grid-based modelling: Winter 2013/2014 in Great Britain. International Journal of Climatology (2018). DOI: 10.1002/joc.5721.
60. Baker, Hugh S., Richard J. Millar, David J. Karoly et al. Higher CO2 concentrations increase extreme event risk in a 1.5 °C world. Nature Climate Change (2018). DOI: 10.1038/s41558-018-0190-1.
61. Otto, Friederike E L, Piotr Wolski, Flavio Lehner et al. Anthropogenic influence on the drivers of the Western Cape drought 2015–2017. Environmental Research Letters (2018). DOI: 10.1088/1748-9326/aae9f9.
62. Sparrow, Sarah, Richard J. Millar, Kuniko Yamazaki et al. Finding Ocean States That Are Consistent with Observations from a Perturbed Physics Parameter Ensemble. Journal of Climate (2018). DOI: 10.1175/JCLI-D-17-0514.1.
63. Guillod, Benoit P., Richard G. Jones, Simon J. Dadson et al. A large set of potential past, present and future hydro-meteorological time series for the UK. Hydrology and Earth System Sciences (2018). DOI: 10.5194/hess-22-611-2018.
64. Parker, Hannah R, Fraser C Lott, Rosalind J Cornforth, Daniel M Mitchell, Sarah Sparrow and David Wallom. A comparison of model ensembles for attributing 2012 West African rainfall. Environmental Research Letters (2017). DOI: 10.1088/1748-9326/aa5386.
65. Mulholland, David P., Keith Haines, Sarah N. Sparrow and David Wallom. Climate model forecast biases assessed with a perturbed physics ensemble. Climate Dynamics (2017). DOI: 10.1007/s00382-016-3407-x.
66. Rupp, David E. and Sihan Li. Less warming projected during heavy winter precipitation in the Cascades and Sierra Nevada: LESS WARMING DURING HEAVY PRECIPITATION. International Journal of Climatology (2017). DOI: 10.1002/joc.4963.
67. Rupp, David E., Sihan Li, Philip W. Mote, Neil Massey, Sarah N. Sparrow and David C. H. Wallom. Influence of the Ocean and Greenhouse Gases on Severe Drought Likelihood in the Central United States in 2012. Journal of Climate (2017). DOI: 10.1175/JCLI-D-16-0294.1.
68. Mitchell, Daniel, Paolo Davini, Ben Harvey et al. Assessing mid-latitude dynamics in extreme event attribution systems. Climate Dynamics (2017). DOI: 10.1007/s00382-016-3308-z.
69. Rupp, David E., Sihan Li, Philip W. Mote, Karen M. Shell, Neil Massey, Sarah N. Sparrow, David C. H. Wallom and Myles R. Allen. Seasonal spatial patterns of projected anthropogenic warming in complex terrain: a modeling study of the western US. Climate Dynamics (2017). DOI: 10.1007/s00382-016-3200-x.
70. Montes, Diego, Juan A. Añel, Tomás F. Pena, Peter Uhe and David C. H. Wallom. Enabling BOINC in infrastructure as a service cloud system. Geoscientific Model Development (2017). DOI: 10.5194/gmd-10-811-2017.
71. Guillod, Benoit P., Richard G. Jones, Alison L. Kay, Neil R. Massey, Sarah Sparrow, David C. H. Wallom and Simon S. Wilson. Managing the Risks, Impacts and Uncertainties of drought and water Scarcity (MaRIUS) project: Large set of potential past and future climate time series for the UK from the weather@home2 model. (2017). DOI: 10.5285/0CEA8D7ACA57427FAE92241348AE9B03.
72. Guillod, Benoit P., Richard G. Jones, Andy Bowery et al. weather@home 2: validation of an improved global–regional climate modelling system. Geoscientific Model Development (2017). DOI: 10.5194/gmd-10-1849-2017.
73. Parker, Hannah R., Emily Boyd, Rosalind J. Cornforth, Rachel James, Friederike E. L. Otto and Myles R. Allen. Stakeholder perceptions of event attribution in the loss and damage debate. Climate Policy (2017). DOI: 10.1080/14693062.2015.1124750.
74. Añel, Juan, Tomas Pena, David Wallom and Diego Perez Montes. Enabling BOINC in Cloud Services: CPDN as Example. (2016).
75. van Oldenborgh, Geert Jan, Friederike E. L. Otto, Karsten Haustein and Krishna AchutaRao. The Heavy Precipitation Event of December 2015 in Chennai, India. Bulletin of the American Meteorological Society (2016). DOI: 10.1175/BAMS-D-16-0129.1.
76. Uhe, P., F. E. L. Otto, K. Haustein, G. J. van Oldenborgh, A. D. King, D. C. H. Wallom, M. R. Allen and H. Cullen. Comparison of methods: Attributing the 2014 record European temperatures to human influences: COMPARING ATTRIBUTION, EUROPE 2014 TEMPERATURE. Geophysical Research Letters (2016). DOI: 10.1002/2016GL069568.
77. Stott, Peter A., Nikolaos Christidis, Friederike E. L. Otto et al. Attribution of extreme weather and climate‐related events. WIREs Climate Change (2016). DOI: 10.1002/wcc.380.
78. Hannart, A., J. Pearl, F. E. L. Otto, P. Naveau and M. Ghil. Causal Counterfactual Theory for the Attribution of Weather and Climate-Related Events. Bulletin of the American Meteorological Society (2016). DOI: 10.1175/BAMS-D-14-00034.1.
79. Karoly, David J., Mitchell T. Black, Andrew D. King and Michael R. Grose. The Roles of Climate Change and El Niño in the Record Low Rainfall in October 2015 in Tasmania, Australia. Bulletin of the American Meteorological Society (2016). DOI: 10.1175/BAMS-D-16-0139.1.
80. Black, Mitchell T. and David J. Karoly. Southern Australia’s Warmest October on Record: The Role of ENSO and Climate Change. Bulletin of the American Meteorological Society (2016). DOI: 10.1175/BAMS-D-16-0124.1.
81. Black, Mitchell T., David J. Karoly, Suzanne M. Rosier et al. The weather@home regional climate modelling project for Australia and New Zealand. Geoscientific Model Development (2016). DOI: 10.5194/gmd-9-3161-2016.
82. Sippel, S., F. E. L. Otto, M. Forkel et al. A novel bias correction methodology for climate impact simulations. Earth System Dynamics (2016). DOI: 10.5194/esd-7-71-2016.
83. Schaller, Nathalie, Alison L. Kay, Rob Lamb et al. Human influence on climate in the 2014 southern England winter floods and their impacts. Nature Climate Change (2016). DOI: 10.1038/nclimate2927.
84. Haustein, K, F E L Otto, P Uhe et al. Real-time extreme weather event attribution with forecast seasonal SSTs. Environmental Research Letters (2016). DOI: 10.1088/1748-9326/11/6/064006.
85. Guillod, Benoit P., Neil Massey, Friederike E. L. Otto, Myles R. Allen, Richard Jones and Jim W. Hall. Synthetic drought event sets: thousands of meteorological drought events for risk-based management under present and future conditions. (2016).
86. Mote, Philip W., Myles R. Allen, Richard G. Jones, Sihan Li, Roberto Mera, David E. Rupp, Ahmed Salahuddin and Dean Vickers. Superensemble Regional Climate Modeling for the Western United States. Bulletin of the American Meteorological Society (2016). DOI: 10.1175/BAMS-D-14-00090.1.
87. Otto, Friederike E. L. The art of attribution. Nature Climate Change (2016). DOI: 10.1038/nclimate2971.
88. Mitchell, Daniel, Clare Heaviside, Sotiris Vardoulakis et al. Attributing human mortality during extreme heat waves to anthropogenic climate change. Environmental Research Letters (2016). DOI: 10.1088/1748-9326/11/7/074006.
89. Mote, Philip W., David E. Rupp, Sihan Li et al. Perspectives on the causes of exceptionally low 2015 snowpack in the western United States. Geophysical Research Letters (2016). DOI: 10.1002/2016GL069965.
90. Vautard, R, P Yiou, F Otto, P Stott, N Christidis, G J van Oldenborgh and N Schaller. Attribution of human-induced dynamical and thermodynamical contributions in extreme weather events. Environmental Research Letters (2016). DOI: 10.1088/1748-9326/11/11/114009.
91. Thompson, Allen and Friederike E. L. Otto. Ethical and normative implications of weather event attribution for policy discussions concerning loss and damage. Climatic Change (2015). DOI: 10.1007/s10584-015-1433-z.
92. Wesselink, Anna, Andrew Juan Challinor, James Watson et al. Equipped to deal with uncertainty in climate and impacts predictions: lessons from internal peer review. Climatic Change (2015). DOI: 10.1007/s10584-014-1213-1.
93. Otto, Friederike E. L., Karsten Haustein, Peter Uhe et al. Factors Other Than Climate Change, Main Drivers of 2014/15 Water Shortage in Southeast Brazil. Bulletin of the American Meteorological Society (2015). DOI: 10.1175/BAMS-D-15-00120.1.
94. Sippel, Sebastian, Jakob Zscheischler, Martin Heimann, Friederike E. L. Otto, Jonas Peters and Miguel D. Mahecha. Quantifying changes in climate variability and extremes: Pitfalls and their overcoming. Geophysical Research Letters (2015). DOI: 10.1002/2015GL066307.
95. Li, Sihan, Philip W. Mote, David E. Rupp, Dean Vickers, Roberto Mera and Myles Allen. Evaluation of a Regional Climate Modeling Effort for the Western United States Using a Superensemble from Weather@home. Journal of Climate (2015). DOI: 10.1175/JCLI-D-14-00808.1.
96. Lawal, Kamoru A., Dáithí A. Stone, Tolu Aina, Cameron Rye and Babatunde J. Abiodun. Trends in the potential spread of seasonal climate simulations over South Africa. International Journal of Climatology (2015). DOI: 10.1002/joc.4234.
97. Massey, N., R. Jones, F. E. L. Otto et al. weather@home—development and validation of a very large ensemble modelling system for probabilistic event attribution. Quarterly Journal of the Royal Meteorological Society (2015). DOI: 10.1002/qj.2455.
98. Rupp, David E., Sihan Li, Neil Massey, Sarah N. Sparrow, Philip W. Mote and Myles Allen. Anthropogenic influence on the changing likelihood of an exceptionally warm summer in Texas, 2011: Changing likelihood of warm summers.. Geophysical Research Letters (2015). DOI: 10.1002/2014GL062683.
99. Volunteer Crowd Computing and Federated Cloud developments. (2015).
100. Mera, Roberto, Neil Massey, David E. Rupp, Philip Mote, Myles Allen and Peter C. Frumhoff. Climate change, climate justice and the application of probabilistic event attribution to summer heat extremes in the California Central Valley. Climatic Change (2015). DOI: 10.1007/s10584-015-1474-3.
101. Sippel, Sebastian, Peter Walton and Friederike E. L. Otto. Stakeholder Perspectives on the Attribution of Extreme Weather Events: An Explorative Enquiry. Weather, Climate, and Society (2015). DOI: 10.1175/WCAS-D-14-00045.1.
102. Otto, Friederike E. L., David J. Frame, Alexander Otto and Myles R. Allen. Embracing uncertainty in climate change policy. Nature Climate Change (2015). DOI: 10.1038/nclimate2716.
103. Otto, Friederike E. L., Suzanne M. Rosier, Myles R. Allen, Neil R. Massey, Cameron J. Rye and Jara Imbers Quintana. Attribution analysis of high precipitation events in summer in England and Wales over the last decade. Climatic Change (2015). DOI: 10.1007/s10584-014-1095-2.
104. Otto, Friederike E. L., Emily Boyd, Richard G. Jones, Rosalind J. Cornforth, Rachel James, Hannah R. Parker and Myles R. Allen. Attribution of extreme weather events in Africa: a preliminary exploration of the science and policy implications. Climatic Change (2015). DOI: 10.1007/s10584-015-1432-0.
105. Rosier, Suzanne, Sam Dean, Stephen Stuart, Trevor Carey-Smith, Mitchell T. Black and Neil Massey. Extreme Rainfall in Early July 2014 in Northland, New Zealand—Was There an Anthropogenic Influence?. Bulletin of the American Meteorological Society (2015). DOI: 10.1175/BAMS-D-15-00105.1.
106. Sippel, Sebastian, Dann Mitchell, Mitchell T. Black, Andrea J. Dittus, Luke Harrington, Nathalie Schaller and Friederike E.L. Otto. Combining large model ensembles with extreme value statistics to improve attribution statements of rare events. Weather and Climate Extremes (2015). DOI: 10.1016/j.wace.2015.06.004.
107. Hannart, A., C. Vera, B. Cerne and F. E. L. Otto. Causal Influence of Anthropogenic Forcings on the Argentinian Heat Wave of December 2013. Bulletin of the American Meteorological Society (2015). DOI: 10.1175/BAMS-D-15-00137.1.
108. Otto, Friederike E. L. Attribution of extreme weather. Nature Geoscience (2015). DOI: 10.1038/ngeo2484.
109. Sippel, Sebastian and F E. L. Otto. Beyond climatological extremes - assessing how the odds of hydrometeorological extreme events in South-East Europe change in a warming climate. Climatic Change (2014). DOI: 10.1007/s10584-014-1153-9.
110. Huntingford, Chris, Terry Marsh, Adam A. Scaife et al. Potential influences on the United Kingdom's floods of winter 2013/14. Nature Climate Change (2014). DOI: 10.1038/nclimate2314.
111. Peterson, Thomas C., Martin P. Hoerling, Peter A. Stott and Stephanie C. Herring. Explaining Extreme Events of 2012 from a Climate Perspective. Bulletin of the American Meteorological Society (2013). DOI: 10.1175/BAMS-D-13-00085.1.
112. Otto, Friederike E. L., Richard G. Jones, Kate Halladay and Myles R. Allen. Attribution of changes in precipitation patterns in African rainforests. Philosophical Transactions of the Royal Society B: Biological Sciences (2013). DOI: 10.1098/rstb.2012.0299.
113. Rowlands, Daniel J., David J. Frame, Duncan Ackerley et al. Broad range of 2050 warming from an observationally constrained large climate model ensemble. Nature Geoscience (2012). DOI: 10.1038/ngeo1430.
114. Peterson, Thomas C., Peter A. Stott and Stephanie Herring. Explaining Extreme Events of 2011 from a Climate Perspective. Bulletin of the American Meteorological Society (2012). DOI: 10.1175/BAMS-D-12-00021.1.
115. Otto, F. E. L., N. Massey, G. J. van Oldenborgh, R. G. Jones and M. R. Allen. Reconciling two approaches to attribution of the 2010 Russian heat wave: RUSSIAN HEAT WAVE 2010. Geophysical Research Letters (2012). DOI: 10.1029/2011GL050422.
116. Ricke, Katharine L., Daniel J. Rowlands, William J. Ingram, David W. Keith and M. Granger Morgan. Effectiveness of stratospheric solar-radiation management as a function of climate sensitivity. Nature Climate Change (2012). DOI: 10.1038/nclimate1328.
117. Kay, A.L., S.M. Crooks, P. Pall and D.A. Stone. Attribution of Autumn/Winter 2000 flood risk in England to anthropogenic climate change: A catchment-based study. Journal of Hydrology (2011). DOI: 10.1016/j.jhydrol.2011.06.006.
118. Pall, Pardeep, Tolu Aina, Dáithí A. Stone, Peter A. Stott, Toru Nozawa, Arno G. J. Hilberts, Dag Lohmann and Myles R. Allen. Anthropogenic greenhouse gas contribution to flood risk in England and Wales in autumn 2000. Nature (2011). DOI: 10.1038/nature09762.
119. Sanderson, Benjamin M., Karen M. Shell and William Ingram. Climate feedbacks determined using radiative kernels in a multi-thousand member ensemble of AOGCMs. Climate Dynamics (2010). DOI: 10.1007/s00382-009-0661-1.
120. Fowler, Hayley J., Daniel Cooley, Stephan R. Sain and Milo Thurston. Detecting change in UK extreme precipitation using results from the climateprediction.net BBC climate change experiment. Extremes (2010). DOI: 10.1007/s10687-010-0101-y.
121. Ricke, Katharine L., M. Granger Morgan and Myles R. Allen. Regional climate response to solar-radiation management. Nature Geoscience (2010). DOI: 10.1038/ngeo915.
122. Frame, D.J, T Aina, C.M Christensen et al. The climate prediction .net BBC climate change experiment: design of the coupled model ensemble. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences (2009). DOI: 10.1098/rsta.2008.0240.
123. Stone, Dáithí A., Myles R. Allen, Peter A. Stott, Pardeep Pall, Seung-Ki Min, Toru Nozawa and Seiji Yukimoto. The Detection and Attribution of Human Influence on Climate. Annual Review of Environment and Resources (2009). DOI: 10.1146/annurev.environ.040308.101032.
124. Lopez, Ana, Fai Fung, Mark New, Glenn Watts, Alan Weston and Robert L. Wilby. From climate model ensembles to climate change impacts and adaptation: A case study of water resource management in the southwest of England. Water Resources Research (2009). DOI: 10.1029/2008WR007499.
125. Ackerley, Duncan, Eleanor J. Highwood and David J. Frame. Quantifying the effects of perturbing the physics of an interactive sulfur scheme using an ensemble of GCMs on the climateprediction.net platform: SULFUR CYCLE UNCERTAINTY QUANTIFICATION. Journal of Geophysical Research: Atmospheres (2009). DOI: 10.1029/2008JD010532.
126. Allen, Myles R., David J. Frame and Charles F. Mason. The case for mandatory sequestration. Nature Geoscience (2009). DOI: 10.1038/ngeo709.
127. Sanderson, Benjamin M., C. Piani, W. J. Ingram, D. A. Stone and M. R. Allen. Towards constraining climate sensitivity by linear analysis of feedback patterns in thousands of perturbed-physics GCM simulations. Climate Dynamics (2008). DOI: 10.1007/s00382-007-0280-7.
128. Knutti, Reto, Stefan Krähenmann, David J. Frame and Myles R. Allen. Comment on “Heat capacity, time constant, and sensitivity of Earth's climate system” by S. E. Schwartz. Journal of Geophysical Research (2008). DOI: 10.1029/2007JD009473.
129. Sanderson, Benjamin M., R. Knutti, T. Aina et al. Constraints on Model Response to Greenhouse Gas Forcing and the Role of Subgrid-Scale Processes. Journal of Climate (2008). DOI: 10.1175/2008JCLI1869.1.
130. Knight, Christopher G., Sylvia H. E. Knight, Neil Massey et al. Association of parameter, software, and hardware variation with large-scale behavior across 57,000 climate models. Proceedings of the National Academy of Sciences (2007). DOI: 10.1073/pnas.0608144104.
131. New, Mark, Ana Lopez, Suraje Dessai and Rob Wilby. Challenges in using probabilistic climate change information for impact assessments: an example from the water sector. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences (2007). DOI: 10.1098/rsta.2007.2080.
132. Collins, Mat. Ensembles and probabilities: a new era in the prediction of climate change. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences (2007). DOI: 10.1098/rsta.2007.2068.
133. Schwartz, Stephen E. Heat capacity, time constant, and sensitivity of Earth's climate system. Journal of Geophysical Research (2007). DOI: 10.1029/2007JD008746.
134. Frame, D.J, N.E Faull, M.M Joshi and M.R Allen. Probabilistic climate forecasts and inductive problems. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences (2007). DOI: 10.1098/rsta.2007.2069.
135. Pall, P., M. R. Allen and D. A. Stone. Testing the Clausius–Clapeyron constraint on changes in extreme precipitation under CO2 warming. Climate Dynamics (2007). DOI: 10.1007/s00382-006-0180-2.
136. Allen, Myles R. and David J. Frame. Call Off the Quest. Science (2007). DOI: 10.1126/science.1149988.
137. Piani, C., B. Sanderson, F. Giorgi, D. J. Frame, C. Christensen and M. R. Allen. Regional probabilistic climate forecasts from a multithousand, multimodel ensemble of simulations. Journal of Geophysical Research: Atmospheres (2007). DOI: 10.1029/2007JD008712.
138. Knutti, Reto, Gerald A. Meehl, Myles R. Allen and David A. Stainforth. Constraining Climate Sensitivity from the Seasonal Cycle in Surface Temperature. Journal of Climate (2006). DOI: 10.1175/JCLI3865.1.
139. Allen, Myles, David Frame, Jamie Kettleborough and David Stainforth. Model error in weather and climate forecasting. Predictability of Weather and Climate (2006).
140. Schellnhuber, Hans Joachim, Wolfgang Cramer, Wolfgang P. Cramer, Nebojsa Nakicenovic, Gary Yohe and Tom Wigley. Avoiding Dangerous Climate Change. (2006).
141. Hegerl, Gabriele C., Thomas J. Crowley, William T. Hyde and David J. Frame. Climate sensitivity constrained by temperature reconstructions over the past seven centuries. Nature (2006). DOI: 10.1038/nature04679.
142. Frame, D. J., B. B. B. Booth, J. A. Kettleborough, D. A. Stainforth, J. M. Gregory, M. Collins and M. R. Allen. Constraining climate forecasts: The role of prior assumptions. Geophysical Research Letters (2005). DOI: 10.1029/2004GL022241.
143. Christensen, C., T. Aina and D. Stainforth. The Challenge of Volunteer Computing with Lengthy Climate Model Simulations. First International Conference on e-Science and Grid Computing (e-Science'05) (2005). DOI: 10.1109/E-SCIENCE.2005.76.
144. Piani, C., D. J. Frame, D. A. Stainforth and M. R. Allen. Constraints on climate change from a multi-thousand member ensemble of simulations. Geophysical Research Letters (2005). DOI: 10.1029/2005GL024452.
145. Stainforth, D. A., T. Aina, C. Christensen et al. Uncertainty in predictions of the climate response to rising levels of greenhouse gases. Nature (2005). DOI: 10.1038/nature03301.
146. Stott, Peter A., D. A. Stone and M. R. Allen. Human contribution to the European heatwave of 2003. Nature (2004). DOI: 10.1038/nature03089.
147. Environmental Online Communication. Advanced Information and Knowledge Processing (2004).
148. Murphy, James M., David M. H. Sexton, David N. Barnett, Gareth S. Jones, Mark J. Webb, Matthew Collins and David A. Stainforth. Quantification of modelling uncertainties in a large ensemble of climate change simulations. Nature (2004). DOI: 10.1038/nature02771.
149. Allen, Myles R. and Richard Lord. The blame game. Nature (2004). DOI: 10.1038/432551a.
150. Stainforth, David A., Myles R. Allen, David Frame, Jamie Kettleborough, Carl Christensen, Tolu Aina and Matthew Collins. Climateprediction.net: A Global Community for Research in Climate Physics. Environmental Online Communication (2004).
151. Joughin, Ian, Waleed Abdalati and Mark Fahnestock. Large fluctuations in speed on Greenland's Jakobshavn Isbræ glacier. Nature (2004). DOI: 10.1038/nature03130.
152. Stainforth, D.A., D. Frame and J.P.R.B. Walton. Visualization For Public-Resource Climate Modeling. Eurographics / IEEE VGTC Symposium on Visualization (2004). DOI: 10.2312/VISSYM/VISSYM04/103-108.

Collatz Conjecture

1. Barina, David. Convergence verification of the Collatz problem. The Journal of Supercomputing (2021). DOI: 10.1007/s11227-020-03368-x.

ComsolGrid

1. Christian Benjamin Ries and Christian Schröder. ComsolGrid – A framework for performing large-scale parameter studies using COMSOL Multiphysics and the Berkeley Open Infrastructure for Network Computing (BOINC). COMSOL Conference 2010 (2008).

Correlizer

1. Knoch, Tobias A. Simulation of different three-dimensional polymer models of interphase chromosomes compared to experiments–an evaluation and review framework of the 3D genome organization. Seminars in Cell & Developmental Biology (2019). DOI: 10.1016/j.semcdb.2018.07.012.
2. Knoch, Tobias A. A Guided Protocol for Array Based T2C : A High-Quality Selective High-Resolution High-Throughput Chromosome Interaction Capture. Current Protocols in Human Genetics (2018). DOI: 10.1002/cphg.55.
3. Rivero, Alejandro and Dario Ferrer. ISDEP, a fusion application deployed in the EDGeS project.. … workshop 30 March … (2010).
4. Knoch, Tobias, Volkmar Baumgärtner, Luc de Zeeuw, Frank Grosveld and Kurt Egger. Large-scale resource sharing at public funded organizations. e-Human "Grid" Ecology.. (2009).
5. Knoch, Tobias A., Markus Göker, Rudolf Lohner, Anis Abuseiris and Frank G. Grosveld. Fine-structured multi-scaling long-range correlations in completely sequenced genomes—features, origin, and classification. European Biophysics Journal (2009). DOI: 10.1007/s00249-009-0489-y.

Cosmology@Home

1. Leclercq, F., B. Faure, G. Lavaux, B. D. Wandelt, A. H. Jaffe, A. F. Heavens and W. J. Percival. Perfectly parallel cosmological simulations using spatial comoving Lagrangian acceleration. Astronomy & Astrophysics (2020). DOI: 10.1051/0004-6361/202037995.
2. Aghanim, N., Y. Akrami, M. Ashdown et al. Planck intermediate results - LI. Features in the cosmic microwave background temperature power spectrum and shifts in cosmological parameters. Astronomy & Astrophysics (2017). DOI: 10.1051/0004-6361/201629504.
3. DockerCon EU 2015: Finding a Theory of the Universe with Docker and V…. (2015).
4. Fendt, William A. and Benjamin D. Wandelt. Pico: Parameters for the Impatient Cosmologist. The Astrophysical Journal (2007). DOI: 10.1086/508342.
5. Fendt, William A. and Benjamin D. Wandelt. Computing High Accuracy Power Spectra with Pico. (2007). DOI: 10.48550/ARXIV.0712.0194.

Crystal Search

1. Thielmann, Yvonne, Thorsten Luft, Norbert Zint and Juergen Koepke. Crystal search – feasibility study of a real-time deep learning process for crystallization well images. Acta Crystallographica Section A Foundations and Advances (2023). DOI: 10.1107/S2053273323001948.

DENIS@home

1. Gómez Gómez, Marta, Jesús Carro, Violeta Monasterio and Esther Pueyo. Investigación in silico sobre el papel de los canales SK en miocitos ventriculares de pacientes con insuficiencia cardiaca. Jornada de Jóvenes Investigadores del I3A (2022). DOI: 10.26754/jjii3a.20227021.
2. Gomez, "Marta, Jesús Carro, Esther Pueyo and Violeta Monasterio". An in Silico Investigation into the Role of SK Channels in Failing Ventricular Myocytes. 2022 Computing in Cardiology Conference (2022). DOI: 10.22489/CinC.2022.228.
3. Carro, Jesús. New Methodologies for the Development and Validation of Electrophysiological Models. (2019).
4. Monasterio, Violeta, Joel Castro-Mur and Jesús Carro. DENIS: Solving cardiac electrophysiological simulations with volunteer computing. PLOS ONE (2018). DOI: 10.1371/journal.pone.0205568.
5. Carro, Jesús, José F Rodríguez-Matas and Esther Pueyo. A Methodology to Improve Human Ventricular Models for the Investigation of Cardiac Arrhythmias. Biophysical Journal (2017). DOI: 10.1016/j.bpj.2016.11.2183.
6. Castro, Joel, Violeta Monasterio and Jesus Carro. Volunteer Computing Approach for the Collaborative Simulation of Electrophysiological Models. 2016 IEEE 25th International Conference on Enabling Technologies: Infrastructure for Collaborative Enterprises (WETICE) (2016). DOI: 10.1109/WETICE.2016.34.

DNA@Home

1. Zarns, Kristopher, Travis Desell, Sergei Nechaev and Archana Dhasarathy. Searching the Human Genome for Snail and Slug with DNA@Home. 2015 IEEE 11th International Conference on e-Science (e-Science) (2015). DOI: 10.1109/eScience.2015.27.
2. Desell, Travis, Lee A. Newberg, Malik Magdon-Ismail, Boleslaw K. Szymanski and William Thompson. Finding Protein Binding Sites Using Volunteer Computing Grids. Proceedings of the 2011 2nd International Congress on Computer Applications and Computational Science (2012).

DistributedDataMining

1. Nico Schlitter and Joerg Laessig. Distributed Data Analytics using RapidMiner and BOINC. RapidMiner Community Meeting and Conference, RCOMM 2013 (2013).

Docking@home

1. Zhang, Boyu, Trilce Estrada, Pietro Cicotti, Pavan Balaji and Michela Taufer. Enabling scalable and accurate clustering of distributed ligand geometries on supercomputers. Parallel Computing (2017). DOI: 10.1016/j.parco.2017.02.005.
2. Zhang, Boyu, Trilce Estrada, Pietro Cicotti and Michela Taufer. On Efficiently Capturing Scientific Properties in Distributed Big Data without Moving the Data: A Case Study in Distributed Structural Biology Using MapReduce. 2013 IEEE 16th International Conference on Computational Science and Engineering (CSE) (2013). DOI: 10.1109/CSE.2013.28.
3. Estrada, Trilce, Kathleen L. Pusecker, Manuel R. Torres, Joanne Cohoon and Michela Taufer. Benchmarking Gender Differences in Volunteer Computing Projects. 2013 IEEE 9th International Conference on eScience (eScience) (2013). DOI: 10.1109/eScience.2013.29.
4. ExSciTecH: Expanding Volunteer Computing to Explore Science, Technology, and Health. (2012).
5. Estrada, T., B. Zhang, P. Cicotti, R.S. Armen and M. Taufer. A scalable and accurate method for classifying protein–ligand binding geometries using a MapReduce approach. Computers in Biology and Medicine (2012). DOI: 10.1016/j.compbiomed.2012.05.001.
6. Estrada, Trilce, Boyu Zhang, Michela Taufer, Pietro Cicotti and Roger Armen. Reengineering High-throughput Molecular Datasets for Scalable Clustering Using MapReduce. 2012 IEEE 14th Int'l Conf. on High Performance Computing and Communication (HPCC) & 2012 IEEE 9th Int'l Conf. on Embedded Software and Systems (ICESS) (2012). DOI: 10.1109/HPCC.2012.54.
7. Rahaman, Obaidur, Trilce P. Estrada, Douglas J. Doren, Michela Taufer, Charles L. Brooks and Roger S. Armen. Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein–Ligand Binding Geometry and Free Energy. Journal of Chemical Information and Modeling (2011). DOI: 10.1021/ci1003009.
8. Estrada, Trilce and Michela Taufer. Providing Quality of Science in Volunteer Computing. Communication (HPCC) (2011). DOI: 10.1109/HPCC.2011.19.
9. Estrada, Trlce, Roger Armen and Michela Taufer. Automatic selection of near-native protein-ligand conformations using a hierarchical clustering and volunteer computing. the First ACM International Conference (2010). DOI: 10.1145/1854776.1854807.
10. Luo, Wenjia, Jianfeng Pei and Yushan Zhu. A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity. Journal of Molecular Modeling (2010). DOI: 10.1007/s00894-009-0598-7.
11. Taufer, M., R. Armen, Jianhan Chen, P. Teller and C. Brooks. Computational multiscale modeling in protein--ligand docking. IEEE Engineering in Medicine and Biology Magazine (2009). DOI: 10.1109/MEMB.2009.931789.
12. Atlas, James, Trilce Estrada, Keith Decker and Michela Taufer. Balancing Scientist Needs and Volunteer Preferences in Volunteer Computing Using Constraint Optimization. Computational Science – ICCS 2009 (2009).
13. Estrada, Trilce, Michela Taufer and David P. Anderson. Performance Prediction and Analysis of BOINC Projects: An Empirical Study with EmBOINC. Journal of Grid Computing (2009). DOI: 10.1007/s10723-009-9126-3.
14. Estrada, Trilce, Michela Taufer, Kevin Reed and David P. Anderson. EmBOINC: An emulator for performance analysis of BOINC projects. Distributed Processing (IPDPS) (2009). DOI: 10.1109/IPDPS.2009.5161135.
15. Estrada, Trilce, Michela Taufer and Kevin Reed. Modeling Job Lifespan Delays in Volunteer Computing Projects. 2009 9th IEEE/ACM International Symposium on Cluster Computing and the Grid (2009). DOI: 10.1109/CCGRID.2009.69.
16. Estrada, Trilce, Olac Fuentes and Michela Taufer. A distributed evolutionary method to design scheduling policies for volunteer computing. the 2008 conference (2008). DOI: 10.1145/1366230.1366282.
17. Lopez, Guillermo A., Michela Taufer and Patricia J. Teller. Evaluation of IEEE 754 floating-point arithmetic compliance across a wide range of heterogeneous computers. the 2007 conference (2007). DOI: 10.1145/1347787.1347793.
18. Taufer, M., A. Kerstens, T. P. Estrada, D. A. Flores, R. Zamudio, P. J. Teller, R. Armen and C. L. Brooks. Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling. 2007 IEEE International Parallel and Distributed Processing Symposium (2007). DOI: 10.1109/IPDPS.2007.370668.
19. Taufer, Michela, Andre Kerstens, Trilce Estrada, David Flores and Patricia J. Teller. SimBA: A Discrete Event Simulator for Performance Prediction of Volunteer Computing Projects. 21st International Workshop on Principles of Advanced and Distributed Simulation (2007). DOI: 10.1109/PADS.2007.27.
20. Estrada, Trilce, David A. Flores, Michela Taufer, Patricia J. Teller, Andre Kerstens and David P. Anderson. The Effectiveness of Threshold-Based Scheduling Policies in BOINC Projects. 2006 Second IEEE International Conference on e-Science and Grid Computing (2006). DOI: 10.1109/E-SCIENCE.2006.261172.

EDGeS@Home

1. Kacsuk, P., Zoltan Farkas, József Kovács et al. Desktop grid in the era of cloud computing. (2015).
2. Fedak, Gilles. Contributions to Desktop Grid Computing. (2015).
3. Delamare, Simon, Gilles Fedak, Derrick Kondo and Oleg Lodygensky. SpeQuloS: a QoS service for hybrid and elastic computing infrastructures. Cluster Computing (2014). DOI: 10.1007/s10586-013-0283-6.
4. Visegrádi, Ádám, József Kovács and Peter Kacsuk. Efficient extension of gLite VOs with BOINC based desktop grids. Future Generation Computer Systems (2014). DOI: 10.1016/j.future.2013.10.012.
5. Marosi, Attila, József Kovács and Peter Kacsuk. Towards a volunteer cloud system. Future Generation Computer Systems (2013). DOI: 10.1016/j.future.2012.03.013.
6. Delamare, Simon, Gilles Fedak, Derrick Kondo, Oleg Lodygensky, Péter Kacsuk, Jozsef Kovacs and Filipe Araujo. Advanced QoS Prototype for the EDGI Infrastructure. (2013).
7. Delamare, Simon, Gilles Fedak, Derrick Kondo, O. Lodygensky, Péter Kacsuk, József Kovács and Filipe Araujo. Intermediate QoS Prototype for the EDGI Infrastructure. (2013).
8. Terstyanszky, Gabor, Tamas Kiss, Tamas Kukla, Zsolt Lichtenberger, Stephen Winter, Pamela Greenwell, Sharron McEldowney and Hans Heindl. Application repository and science gateway for running molecular docking and dynamics simulations. Studies in Health Technology and Informatics (2012).
9. Kacsuk, P., Z. Farkas and Z. Balaton. EDGeS Bridge Technologies to Interconnect Service and Desktop Grids. Remote Instrumentation Services on the e-Infrastructure (2011).
10. Velasco, J. L., F. Castejón and A. Tarancón. Finite orbit width effect in ion collisional transport in TJ-II. Physics of Plasmas (2009). DOI: 10.1063/1.3126583.
11. Fedak, Gilles, Haiwu He, Oleg Lodygensky et al. EDGeS: A Bridge between Desktop Grids and Service Grids. 2008 Third ChinaGrid Annual Conference (CHINAGRID) (2008). DOI: 10.1109/ChinaGrid.2008.44.
12. Antolí, B., Francisco Castejón, A. Giner et al. ZIVIS: A City Computing Platform Based on Volunteer Computing. (2007).

EOn

1. Chill, Samuel T, Matthew Welborn, Rye Terrell, Liang Zhang, Jean-Claude Berthet, Andreas Pedersen, Hannes Jónsson and Graeme Henkelman. EON: software for long time simulations of atomic scale systems. Modelling and Simulation in Materials Science and Engineering (2014). DOI: 10.1088/0965-0393/22/5/055002.
2. Pedersen, Andreas, Graeme Henkelman, Jakob Schiøtz and Hannes Jónsson. Long time scale simulation of a grain boundary in copper. New Journal of Physics (2009). DOI: 10.1088/1367-2630/11/7/073034.
3. Mei, Donghai, Lijun Xu and Graeme Henkelman. Potential Energy Surface of Methanol Decomposition on Cu(110). The Journal of Physical Chemistry C (2009). DOI: 10.1021/jp808211q.
4. Xu, Lijun, Donghai Mei and Graeme Henkelman. Adaptive kinetic Monte Carlo simulation of methanol decomposition on Cu(100). The Journal of Chemical Physics (2009). DOI: 10.1063/1.3281688.
5. Xu, Lijun and Graeme Henkelman. Adaptive kinetic Monte Carlo for first-principles accelerated dynamics. The Journal of Chemical Physics (2008). DOI: 10.1063/1.2976010.
6. Henkelman, Graeme and Hannes Jónsson. Multiple Time Scale Simulations of Metal Crystal Growth Reveal the Importance of Multiatom Surface Processes. Physical Review Letters (2003). DOI: 10.1103/PhysRevLett.90.116101.

Einstein@Home

1. Ming, J., M. A. Papa, H.-B. Eggenstein, B. Beheshtipour, B. Machenschalk, R. Prix, B. Allen and M. Bensch. Deep Einstein@Home Search for Continuous Gravitational Waves from the Central Compact Objects in the Supernova Remnants Vela Jr. and G347.3-0.5 Using LIGO Public Data. The Astrophysical Journal (2024). DOI: 10.3847/1538-4357/ad8b9e.
2. Smith, D. A., S. Abdollahi, M. Ajello et al. The Third Fermi Large Area Telescope Catalog of Gamma-Ray Pulsars. The Astrophysical Journal (2023). DOI: 10.3847/1538-4357/acee67.
3. Steltner, Benjamin. Large-Scale surveys for continuous gravitational waves: from data preparation to multi-stage hierarchical follow-ups. (2023). DOI: 10.15488/13266.
4. Steltner, B., M. A. Papa, H. -B. Eggenstein, R. Prix, M. Bensch and B. Machenschalk. Deep Einstein@Home all-sky search for continuous gravitational waves in LIGO O3 public data. (2023). DOI: 10.48550/ARXIV.2303.04109.
5. Parent, E., H. Sewalls, P. C. C. Freire et al. Study of 72 Pulsars Discovered in the PALFA Survey: Timing Analysis, Glitch Activity, Emission Variability, and a Pulsar in an Eccentric Binary. The Astrophysical Journal (2022). DOI: 10.3847/1538-4357/ac375d.
6. Ming, J., M. A. Papa, H.-B. Eggenstein, B. Machenschalk, B. Steltner, R. Prix, B. Allen and O. Behnke. Results From an Einstein@Home Search for Continuous Gravitational Waves From G347.3 at Low Frequencies in LIGO O2 Data. The Astrophysical Journal (2022). DOI: 10.3847/1538-4357/ac35cb.
7. Steltner, B., M. A. Papa, H.-B. Eggenstein et al. Einstein@Home All-sky Search for Continuous Gravitational Waves in LIGO O2 Public Data. The Astrophysical Journal (2021). DOI: 10.3847/1538-4357/abc7c9.
8. Nieder, L., C. J. Clark, D. Kandel et al. Discovery of a Gamma-Ray Black Widow Pulsar by GPU-accelerated Einstein@Home. The Astrophysical Journal Letters (2020). DOI: 10.3847/2041-8213/abbc02.
9. Papa, M. A., J. Ming, E. V. Gotthelf et al. Search for Continuous Gravitational Waves from the Central Compact Objects in Supernova Remnants Cassiopeia A, Vela Jr., and G347.3–0.5. The Astrophysical Journal (2020). DOI: 10.3847/1538-4357/ab92a6.
10. Nieder, L., B. Allen, C. J. Clark and H. J. Pletsch. Exploiting Orbital Constraints from Optical Data to Detect Binary Gamma-Ray Pulsars. The Astrophysical Journal (2020). DOI: 10.3847/1538-4357/abaf53.
11. Clark, C. J., L. Nieder, G. Voisin et al. Einstein@Home Discovery of the Gamma-ray Millisecond Pulsar PSR J2039-5617 Confirms Its Predicted Redback Nature. (2020). DOI: 10.48550/ARXIV.2007.14849.
12. Ming, J., M. A. Papa, A. Singh et al. Results from an Einstein@Home search for continuous gravitational waves from Cassiopeia A, Vela Jr., and G347.3. Physical Review D (2019). DOI: 10.1103/PhysRevD.100.024063.
13. Walsh, Sinéad, Karl Wette, Maria Alessandra Papa and Reinhard Prix. Optimizing the choice of analysis method for all-sky searches for continuous gravitational waves with Einstein@Home. Physical Review D (2019). DOI: 10.1103/PhysRevD.99.082004.
14. Ming, Jing, Maria Alessandra Papa, Badri Krishnan et al. Optimally setting up directed searches for continuous gravitational waves in Advanced LIGO O1 data. Physical Review D (2018). DOI: 10.1103/PhysRevD.97.024051.
15. Clark, Colin J., Holger J. Pletsch, Jason Wu et al. Einstein@Home discovers a radio-quiet gamma-ray millisecond pulsar. Science Advances (2018). DOI: 10.1126/sciadv.aao7228.
16. Wu, J., C. J. Clark, H. J. Pletsch et al. The Einstein@Home Gamma-ray Pulsar Survey. II. Source Selection, Spectral Analysis, and Multiwavelength Follow-up. The Astrophysical Journal (2018). DOI: 10.3847/1538-4357/aaa411.
17. Singh, Avneet, Maria Alessandra Papa, Heinz-Bernd Eggenstein and Sinéad Walsh. Adaptive clustering procedure for continuous gravitational wave searches. Physical Review D (2017). DOI: 10.1103/PhysRevD.96.082003.
18. Zhu, Sylvia J., Maria Alessandra Papa and Sinéad Walsh. New veto for continuous gravitational wave searches. Physical Review D (2017). DOI: 10.1103/PhysRevD.96.124007.
19. Zhu, Sylvia J., Maria Alessandra Papa and Sinéad Walsh. A new veto for continuous gravitational wave searches. (2017). DOI: 10.48550/ARXIV.1707.05268.
20. Lyne, A. G., B. W. Stappers, S. Bogdanov et al. TIMING OF 29 PULSARS DISCOVERED IN THE PALFA SURVEY. The Astrophysical Journal (2017). DOI: 10.3847/1538-4357/834/2/137.
21. Abbott, B. P., R. Abbott, T. D. Abbott et al. First low-frequency Einstein@Home all-sky search for continuous gravitational waves in Advanced LIGO data. Physical Review D (2017). DOI: 10.1103/PhysRevD.96.122004.
22. Clark, C. J., J. Wu, H. J. Pletsch et al. THE EINSTEIN@HOME GAMMA-RAY PULSAR SURVEY. I. SEARCH METHODS, SENSITIVITY, AND DISCOVERY OF NEW YOUNG GAMMA-RAY PULSARS. The Astrophysical Journal (2017). DOI: 10.3847/1538-4357/834/2/106.
23. Zhu, Sylvia J., Maria Alessandra Papa, Heinz-Bernd Eggenstein et al. An Einstein@home search for continuous gravitational waves from Cassiopeia A. (2016). DOI: 10.48550/ARXIV.1608.07589.
24. Zhu, Sylvia J., Maria Alessandra Papa, Heinz-Bernd Eggenstein et al. Einstein@Home search for continuous gravitational waves from Cassiopeia A. Physical Review D (2016). DOI: 10.1103/PhysRevD.94.082008.
25. Abbott, B. P., R. Abbott, T. D. Abbott et al. Results of the deepest all-sky survey for continuous gravitational waves on LIGO S6 data running on the Einstein@Home volunteer distributed computing project. Physical Review D (2016). DOI: 10.1103/PhysRevD.94.102002.
26. Singh, Avneet, Maria Alessandra Papa, Heinz-Bernd Eggenstein et al. Results of an all-sky high-frequency Einstein@Home search for continuous gravitational waves in LIGO’s fifth science run. Physical Review D (2016). DOI: 10.1103/PhysRevD.94.064061.
27. Papa, Maria Alessandra, Heinz-Bernd Eggenstein, Sinéad Walsh et al. Hierarchical follow-up of subthreshold candidates of an all-sky Einstein@Home search for continuous gravitational waves on LIGO sixth science run data. Physical Review D (2016). DOI: 10.1103/PhysRevD.94.122006.
28. Clark, C. J., H. J. Pletsch, J. Wu et al. THE BRAKING INDEX OF A RADIO-QUIET GAMMA-RAY PULSAR. The Astrophysical Journal (2016). DOI: 10.3847/2041-8205/832/1/L15.
29. Lazarus, P., P. C. C. Freire, B. Allen et al. EINSTEIN@HOME DISCOVERY OF A DOUBLE NEUTRON STAR BINARY IN THE PALFA SURVEY. The Astrophysical Journal (2016). DOI: 10.3847/0004-637X/831/2/150.
30. Knispel, B., A. G. Lyne, B. W. Stappers et al. Einstein@Home DISCOVERY OF A PALFA MILLISECOND PULSAR IN AN ECCENTRIC BINARY ORBIT. The Astrophysical Journal (2015). DOI: 10.1088/0004-637X/806/1/140.
31. Clark, C. J., H. J. Pletsch, J. Wu et al. PSR J1906+0722: AN ELUSIVE GAMMA-RAY PULSAR. The Astrophysical Journal (2015). DOI: 10.1088/2041-8205/809/1/L2.
32. Shaltev, M., P. Leaci, M. A. Papa and R. Prix. Fully coherent follow-up of continuous gravitational-wave candidates: An application to Einstein@Home results. Physical Review D (2014). DOI: 10.1103/PhysRevD.89.124030.
33. Aasi, J., J. Abadie, B. P. Abbott et al. Einstein@Home all-sky search for periodic gravitational waves in LIGO S5 data. Physical Review D (2013). DOI: 10.1103/PhysRevD.87.042001.
34. Allen, B., B. Knispel, J. M. Cordes et al. THE EINSTEIN@HOME SEARCH FOR RADIO PULSARS AND PSR J2007+2722 DISCOVERY. The Astrophysical Journal (2013). DOI: 10.1088/0004-637X/773/2/91.
35. Pletsch, H. J., L. Guillemot, B. Allen et al. EINSTEIN@HOME DISCOVERY OF FOUR YOUNG GAMMA-RAY PULSARS IN FERMI LAT DATA. The Astrophysical Journal (2013). DOI: 10.1088/2041-8205/779/1/L11.
36. Knispel, B., R. P. Eatough, H. Kim et al. EINSTEIN@HOME DISCOVERY OF 24 PULSARS IN THE PARKES MULTI-BEAM PULSAR SURVEY. The Astrophysical Journal (2013). DOI: 10.1088/0004-637X/774/2/93.
37. Knispel, B., P. Lazarus, B. Allen et al. ARECIBO PALFA SURVEY AND EINSTEIN@HOME: BINARY PULSAR DISCOVERY BY VOLUNTEER COMPUTING. The Astrophysical Journal (2011). DOI: 10.1088/2041-8205/732/1/L1.
38. Knispel, B., B. Allen, J. M. Cordes et al. Pulsar Discovery by Global Volunteer Computing. Science (2010). DOI: 10.1126/science.1195253.
39. Abbott, B. P., R. Abbott, R. Adhikari et al. Einstein@Home search for periodic gravitational waves in early S5 LIGO data. Physical Review D (2009). DOI: 10.1103/PhysRevD.80.042003.
40. Abbott, B., R. Abbott, R. Adhikari et al. Einstein@Home search for periodic gravitational waves in LIGO S4 data. Physical Review D (2009). DOI: 10.1103/PhysRevD.79.022001.
41. Pletsch, Holger J. and Bruce Allen. Exploiting Large-Scale Correlations to Detect Continuous Gravitational Waves. Physical Review Letters (2009). DOI: 10.1103/PhysRevLett.103.181102.
42. Breitbart, Jens and Gaurav Khanna. An Exploration of CUDA and CBEA for a Gravitational Wave Data- Analysis Application (Einstein@Home). The Open Astronomy Journal (2009). DOI: 10.2174/1874381101004010154.

Enigma@Home

1. Girard, Daniel J. Breaking “Tirpitz”: Cryptanalysis of the Japanese-German joint naval cipher. Cryptologia (2016). DOI: 10.1080/01611194.2015.1087073.
2. Campbell, MacGregor. Uncrackable codes: The second world war's last Enigma. New Scientist (2011). DOI: 10.1016/S0262-4079(11)61202-5.

GPUGrid.net

1. Doerr, Stefan, Maciej Majewski, Adrià Pérez, Andreas Krämer, Cecilia Clementi, Frank Noe, Toni Giorgino and Gianni De Fabritiis. TorchMD: A Deep Learning Framework for Molecular Simulations. Journal of Chemical Theory and Computation (2021). DOI: 10.1021/acs.jctc.0c01343.
2. Bollati, Michela, Luisa Diomede, Toni Giorgino et al. A novel hotspot of gelsolin instability triggers an alternative mechanism of amyloid aggregation. Computational and Structural Biotechnology Journal (2021). DOI: 10.1016/j.csbj.2021.11.025.
3. Herrera-Nieto, Pablo, Adrià Pérez and Gianni De Fabritiis. Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations. Scientific Reports (2020). DOI: 10.1038/s41598-020-69322-2.
4. Herrera-Nieto, Pablo, Adrià Pérez and Gianni De Fabritiis. Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations. Journal of Chemical Information and Modeling (2020). DOI: 10.1021/acs.jcim.0c00381.
5. Cossu, Federica, Luca Sorrentino, Elisa Fagnani, Mattia Zaffaroni, Mario Milani, Toni Giorgino and Eloise Mastrangelo. Computational and Experimental Characterization of NF023, A Candidate Anticancer Compound Inhibiting cIAP2/TRAF2 Assembly. Journal of Chemical Information and Modeling (2020). DOI: 10.1021/acs.jcim.0c00518.
6. Martinez-Rosell, Gerard, Silvia Lovera, Zara A. Sands and Gianni De Fabritiis. PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations. Journal of Chemical Information and Modeling (2020). DOI: 10.1021/acs.jcim.9b01209.
7. Rodríguez-Espigares, Ismael, Mariona Torrens-Fontanals, Johanna K. S. Tiemann et al. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nature Methods (2020). DOI: 10.1038/s41592-020-0884-y.
8. Wang, Jiang, Simon Olsson, Christoph Wehmeyer, Adrià Pérez, Nicholas E. Charron, Gianni de Fabritiis, Frank Noé and Cecilia Clementi. Machine Learning of Coarse-Grained Molecular Dynamics Force Fields. ACS Central Science (2019). DOI: 10.1021/acscentsci.8b00913.
9. Martinez-Rosell, Gerard, Matt J. Harvey and Gianni De Fabritiis. Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors. Journal of Chemical Information and Modeling (2018). DOI: 10.1021/acs.jcim.7b00625.
10. Ferruz, Noelia, Stefan Doerr, Michelle A. Vanase-Frawley et al. Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs. Scientific Reports (2018). DOI: 10.1038/s41598-018-19345-7.
11. Pérez, Adrià, Gerard Martínez-Rosell and Gianni De Fabritiis. Simulations meet machine learning in structural biology. Current Opinion in Structural Biology (2018). DOI: 10.1016/j.sbi.2018.02.004.
12. Kapoor, Abhijeet, Gerard Martinez-Rosell, Davide Provasi, Gianni de Fabritiis and Marta Filizola. Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity. Scientific Reports (2017). DOI: 10.1038/s41598-017-11483-8.
13. Plattner, Nuria, Stefan Doerr, Gianni De Fabritiis and Frank Noé. Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. Nature Chemistry (2017). DOI: 10.1038/nchem.2785.
14. Doerr, Stefan, Toni Giorgino, Gerard Martínez-Rosell, João M. Damas and Gianni De Fabritiis. High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD. Journal of Chemical Theory and Computation (2017). DOI: 10.1021/acs.jctc.7b00480.
15. Doerr, Stefan, Igor Ariz-Extreme, Matthew J. Harvey and Gianni De Fabritiis. Dimensionality reduction methods for molecular simulations. (2017). DOI: 10.48550/ARXIV.1710.10629.
16. Martínez-Rosell, Gerard, Toni Giorgino, Matt J. Harvey and Gianni de Fabritiis. Drug Discovery and Molecular Dynamics: Methods, Applications and Perspective Beyond the Second Timescale. Current Topics in Medicinal Chemistry (2017). DOI: 10.2174/1568026617666170414142549.
17. Ferruz, Noelia, Gary Tresadern, Antonio Pineda-Lucena and Gianni De Fabritiis. Multibody cofactor and substrate molecular recognition in the myo-inositol monophosphatase enzyme. Scientific Reports (2016). DOI: 10.1038/srep30275.
18. Doerr, S., M. J. Harvey, Frank Noé and G. De Fabritiis. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery. Journal of Chemical Theory and Computation (2016). DOI: 10.1021/acs.jctc.6b00049.
19. Stanley, Nathaniel, Leonardo Pardo and Gianni De Fabritiis. The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor. Scientific Reports (2016). DOI: 10.1038/srep22639.
20. Stanley, Nathaniel, Santiago Esteban-Martín and Gianni De Fabritiis. Progress in studying intrinsically disordered proteins with atomistic simulations. Progress in Biophysics and Molecular Biology (2015). DOI: 10.1016/j.pbiomolbio.2015.03.003.
21. Ferruz, Noelia, Matthew J. Harvey, Jordi Mestres and Gianni De Fabritiis. Insights from Fragment Hit Binding Assays by Molecular Simulations. Journal of Chemical Information and Modeling (2015). DOI: 10.1021/acs.jcim.5b00453.
22. Doerr, S. and G. De Fabritiis. On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations. Journal of Chemical Theory and Computation (2014). DOI: 10.1021/ct400919u.
23. Dainese, Enrico, Gianni De Fabritiis, Annalaura Sabatucci et al. Membrane lipids are key modulators of the endocannabinoid-hydrolase FAAH. Biochemical Journal (2014). DOI: 10.1042/BJ20130960.
24. Stanley, Nathaniel, Santiago Esteban-Martín and Gianni De Fabritiis. Kinetic modulation of a disordered protein domain by phosphorylation. Nature Communications (2014). DOI: 10.1038/ncomms6272.
25. Huang, Xuhui and Gianni De Fabritiis. Understanding Molecular Recognition by Kinetic Network Models Constructed from Molecular Dynamics Simulations. An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation (2014).
26. Bisignano, P., S. Doerr, M. J. Harvey, A. D. Favia, A. Cavalli and G. De Fabritiis. Kinetic Characterization of Fragment Binding in AmpC β-Lactamase by High-Throughput Molecular Simulations. Journal of Chemical Information and Modeling (2014). DOI: 10.1021/ci4006063.
27. Lauro, G., N. Ferruz, S. Fulle, M. J. Harvey, P. W. Finn and G. De Fabritiis. Reranking Docking Poses Using Molecular Simulations and Approximate Free Energy Methods. Journal of Chemical Information and Modeling (2014). DOI: 10.1021/ci500309a.
28. Venken, Tom, Arnout Voet, Marc De Maeyer, Gianni De Fabritiis and S. Kashif Sadiq. Rapid Conformational Fluctuations of Disordered HIV-1 Fusion Peptide in Solution. Journal of Chemical Theory and Computation (2013). DOI: 10.1021/ct300856r.
29. Pérez-Hernández, Guillermo, Fabian Paul, Toni Giorgino, Gianni De Fabritiis and Frank Noé. Identification of slow molecular order parameters for Markov model construction. The Journal of Chemical Physics (2013). DOI: 10.1063/1.4811489.
30. Harvey, Matthew J. and Gianni De Fabritiis. High-throughput molecular dynamics: the powerful new tool for drug discovery. Drug Discovery Today (2012). DOI: 10.1016/j.drudis.2012.03.017.
31. Giorgino, T., I. Buch and G. De Fabritiis. Visualizing the Induced Binding of SH2-Phosphopeptide. Journal of Chemical Theory and Computation (2012). DOI: 10.1021/ct300003f.
32. Bruno, Agostino, Gabriele Costantino, Gianni de Fabritiis, Manuel Pastor and Jana Selent. Membrane-Sensitive Conformational States of Helix 8 in the Metabotropic Glu2 Receptor, a Class C GPCR. PLoS ONE (2012). DOI: 10.1371/journal.pone.0042023.
33. Harvey, M. J. and Gianni De Fabritiis. A survey of computational molecular science using graphics processing units: Survey of computational molecular science on GPUs. Wiley Interdisciplinary Reviews: Computational Molecular Science (2012). DOI: 10.1002/wcms.1101.
34. Wright, David W., S. Kashif Sadiq, Gianni De Fabritiis and Peter V. Coveney. Thumbs Down for HIV: Domain Level Rearrangements Do Occur in the NNRTI-Bound HIV-1 Reverse Transcriptase. Journal of the American Chemical Society (2012). DOI: 10.1021/ja301565k.
35. Sadiq, S. Kashif, Frank Noé and Gianni De Fabritiis. Kinetic characterization of the critical step in HIV-1 protease maturation. Proceedings of the National Academy of Sciences (2012). DOI: 10.1073/pnas.1210983109.
36. Buch, Ignasi, S. Kashif Sadiq and Gianni De Fabritiis. Optimized Potential of Mean Force Calculations for Standard Binding Free Energies. Journal of Chemical Theory and Computation (2011). DOI: 10.1021/ct2000638.
37. Buch, Ignasi, Toni Giorgino and Gianni De Fabritiis. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proceedings of the National Academy of Sciences (2011). DOI: 10.1073/pnas.1103547108.
38. Giorgino, Toni and Gianni De Fabritiis. A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A. Journal of Chemical Theory and Computation (2011). DOI: 10.1021/ct100707s.
39. Giorgino, Toni, M.J. Harvey and Gianni de Fabritiis. Distributed computing as a virtual supercomputer: Tools to run and manage large-scale BOINC simulations. Computer Physics Communications (2010). DOI: 10.1016/j.cpc.2010.04.007.
40. Buch, I., M. J. Harvey, T. Giorgino, D. P. Anderson and G. De Fabritiis. High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing. Journal of Chemical Information and Modeling (2010). DOI: 10.1021/ci900455r.
41. De Lomana, Adrián López García, Qasim K. Beg, G. De Fabritiis and Jordi Villà-Freixa. Statistical Analysis of Global Connectivity and Activity Distributions in Cellular Networks. Journal of Computational Biology (2010). DOI: 10.1089/cmb.2008.0240.
42. Selent, Jana, Ferran Sanz, Manuel Pastor and Gianni De Fabritiis. Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors. PLoS Computational Biology (2010). DOI: 10.1371/journal.pcbi.1000884.
43. Sadiq, S. Kashif and Gianni De Fabritiis. Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing. Proteins: Structure, Function, and Bioinformatics (2010). DOI: 10.1002/prot.22806.
44. Harvey, M. J. and G. De Fabritiis. An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware. Journal of Chemical Theory and Computation (2009). DOI: 10.1021/ct900275y.
45. Guix, Francesc X., Gerard Ill-Raga, Ramona Bravo et al. Amyloid-dependent triosephosphate isomerase nitrotyrosination induces glycation and tau fibrillation. Brain (2009). DOI: 10.1093/brain/awp023.
46. Harvey, M. J., G. Giupponi and G. De Fabritiis. ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale. Journal of Chemical Theory and Computation (2009). DOI: 10.1021/ct9000685.
47. Harvey, M. J., G. De Fabritiis and G. Giupponi. Accuracy of the lattice-Boltzmann method using the Cell processor. Physical Review E (2008). DOI: 10.1103/PhysRevE.78.056702.
48. De Fabritiis, G., P. V. Coveney and J. Villà-Freixa. Energetics of K+ permeability through Gramicidin A by forward-reverse steered molecular dynamics. Proteins: Structure, Function, and Bioinformatics (2008). DOI: 10.1002/prot.22036.
49. Giupponi, G., M.J. Harvey and G. De Fabritiis. The impact of accelerator processors for high-throughput molecular modeling and simulation. Drug Discovery Today (2008). DOI: 10.1016/j.drudis.2008.08.001.
50. Fabritiis, Gianni De, Sebastien Geroult, Peter V. Coveney and Gabriel Waksman. Insights from the energetics of water binding at the domain-ligand interface of the Src SH2 domain. Proteins: Structure, Function, and Bioinformatics (2008). DOI: 10.1002/prot.22027.
51. Delgado-Buscalioni, R, P V Coveney and G De Fabritiis. Towards multi-scale modelling of complex liquids using hybrid particle—continuum schemes. Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science (2008). DOI: 10.1243/09544062JMES746.
52. Lloyd, Sharon, Dave Gavaghan, Andrew Simpson et al. Integrative Biology — the challenges of developing a collaborative research environment for heart and cancer modelling. Future Generation Computer Systems (2007). DOI: 10.1016/j.future.2006.07.002.
53. De Fabritiis, G. Performance of the Cell processor for biomolecular simulations. Computer Physics Communications (2007). DOI: 10.1016/j.cpc.2007.02.107.

Gerasim@home

1. Vatutin, Eduard, Alexey Belyshev, Natalia Nikitina and Maxum Manzuk. USE OF X-BASED DIAGONAL FILLINGS AND ESODLS CMS SCHEMES FOR ENUMERATION OF MAIN CLASSES OF DIAGONAL LATIN SQUARES. Telecommunications (2023). DOI: 10.31044/1684-2588-2023-0-1-2-16.
2. Vatutin, Eduard, Oleg Zaikin, Maxim Manzyuk and Natalia Nikitina. Searching for Orthogonal Latin Squares via Cells Mapping and BOINC-Based Cube-and-Conquer. Supercomputing (2021).
3. Vatutin, Eduard and Alexey Belyshev. Enumerating the Orthogonal Diagonal Latin Squares of Small Order for Different Types of Orthogonality. Supercomputing (2020).
4. Vatutin, Eduard, Alexey Belyshev, Natalia Nikitina and Maxim Manzuk. Evaluation of Efficiency of Using Simple Transformations When Searching for Orthogonal Diagonal Latin Squares of Order 10. High-Performance Computing Systems and Technologies in Scientific Research, Automation of Control and Production (2020).
5. Vatutin, Eduard, Alexey Belyshev, Stepan Kochemazov, Oleg Zaikin and Natalia Nikitina. Enumeration of Isotopy Classes of Diagonal Latin Squares of Small Order Using Volunteer Computing. Supercomputing (2019).
6. Southwest State University, Eduard Vatutin, Stepan Kochemazov et al. CENTRAL SYMMETRY PROPERTIES FOR DIAGONAL LATIN SQUARES. Problems of Information Technology (2019). DOI: 10.25045/jpit.v10.i2.01.
7. Vatutin, Eduard, Oleg Zaikin, Stepan Kochemazov and Sergey Valyaev. Using Volunteer Computing to Study Some Features of Diagonal Latin Squares. Open Engineering (2017). DOI: 10.1515/eng-2017-0052.
8. Vatutin, Eduard. Comparison of Decisions Quality of Heuristic Methods with Limited Depth-First Search Techniques in the Graph Shortest Path Problem. Open Engineering (2017). DOI: 10.1515/eng-2017-0041.
9. Vatutin, Eduard, Vitaly Titov and Alexander Belyaev. On the Selection of Optimal Structure Organization of Logic Multicontrollers. MATEC Web of Conferences (2016). DOI: 10.1051/matecconf/20167901084.

GridRepublic

1. Mario-Vasquez, Jorge E., Ujwal R. Bagal, Elijah Lowe et al. Finding Candida auris in public metagenomic repositories. (2023).

HashClash

1. Stevens, Marc, Elie Bursztein, Pierre Karpman, Ange Albertini and Yarik Markov. The First Collision for Full SHA-1. Advances in Cryptology – CRYPTO 2017 (2017).
2. Stevens, Marc, Pierre Karpman and Thomas Peyrin. Freestart Collision for Full SHA-1. (2016). DOI: 10.1007/978-3-662-49890-3_18.
3. Karpman, Pierre, Thomas Peyrin and Marc Stevens. Practical Free-Start Collision Attacks on 76-step SHA-1. (2015). DOI: 10.1007/978-3-662-47989-6_30.
4. Stevens, Marc. Fast Collision Attack on MD5. (2013).
5. Stevens, M. M. J. Attacks on hash functions and applications. (2012).
6. Stevens, Marc. Single-block collision attack on MD5. Cryptology ePrint Archive (2012).
7. Stevens, Marc, Arjen K. Lenstra and Benne De Weger. Chosen-prefix collisions for MD5 and applications. International Journal of Applied Cryptography (2012). DOI: 10.1504/IJACT.2012.048084.
8. Stevens, Marc, Alexander Sotirov, Jacob Appelbaum, Arjen Lenstra, David Molnar, Dag Arne Osvik and Benne de Weger. Short Chosen-Prefix Collisions for MD5 and the Creation of a Rogue CA Certificate. (2009). DOI: 10.1007/978-3-642-03356-8_4.
9. Stevens, M. On Collisions for MD5. International Journal of Human-computer Studies / International Journal of Man-machine Studies - IJMMS (2007).
10. Stevens, Marc, Arjen Lenstra and Benne de Weger. Chosen-Prefix Collisions for MD5 and Colliding X.509 Certificates for Different Identities. (2007). DOI: 10.1007/978-3-540-72540-4_1.
11. Stevens, Marc, Arjen Lenstra and Benne de Weger. Target Collisions for MD5 and Colliding X.509 Certificates for Different Identities. (2006).

IThena

1. iThena Project: Distributed measurements and analysis of the global Internet – BOINC (Berkeley Open Infrastructure for Network Computing) and Big Data environment​. (2020).

Ibercivis

1. Martínez de Salazar, Pablo, Javier Ramos, Victor L. Cruz, Rosa Polo, Julia del Amo and Javier Martínez-Salazar. Tenofovir and remdesivir ensemble docking with the SARS-CoV-2 polymerase and template-nascent RNA. (2020). DOI: 10.22541/au.160133726.63184055.
2. Jorge, Miguel. Predicting hydrophobic solvation by molecular simulation: 2. New united-atom model for alkanes, alkenes, and alkynes. Journal of Computational Chemistry (2017). DOI: 10.1002/jcc.24689.
3. Jorge, Miguel, Nuno M. Garrido, Carlos J. V. Simões, Cândida G. Silva and Rui M. M. Brito. Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models. Journal of Computational Chemistry (2017). DOI: 10.1002/jcc.24690.
4. Sagarra, Oleguer, Mario Gutiérrez-Roig, Isabelle Bonhoure and Josep Perelló. Citizen Science Practices for Computational Social Science Research: The Conceptualization of Pop-Up Experiments. Frontiers in Physics (2016). DOI: 10.3389/fphy.2015.00093.
5. Silva, Cândida, Antonio Jose Monteiro, Caroline Manahl et al. Cell Spotting: educational and motivational outcomes of cell biology citizen science project in the classroom. Journal of Science Communication (2016). DOI: 10.22323/2.15010202.
6. Ponciano, Lesandro and Francisco Brasileiro. Finding Volunteers' Engagement Profiles in Human Computation for Citizen Science Projects. (2015). DOI: 10.48550/ARXIV.1501.02134.
7. Guerrero, Ginés D., Baldomero Imbernón, Horacio Pérez-Sánchez, Francisco Sanz, José M. García and José M. Cecilia. A Performance/Cost Evaluation for a GPU-Based Drug Discovery Application on Volunteer Computing. BioMed Research International (2014). DOI: 10.1155/2014/474219.
8. Silva, Cândida. SOCIENTIZE participatory experiments, dissemination and networking activities in perspective. Human Computation (2014). DOI: 10.15346/hc.v1i2.4.
9. Fernandez, L. A., A. Gordillo-Guerrero, V. Martin-Mayor and J. J. Ruiz-Lorenzo. Numerical test of the Cardy-Jacobsen conjecture in the site-diluted Potts model in three dimensions. Physical Review B (2012). DOI: 10.1103/PhysRevB.86.184428.
10. Camjayi, Alberto and Liliana Arrachea. Conductance of a quantum dot in the Kondo regime connected to dirty wires. Physical Review B (2012). DOI: 10.1103/PhysRevB.86.235143.
11. Gracia-Lázaro, Carlos, Alfredo Ferrer, Gonzalo Ruiz, Alfonso Tarancón, José A. Cuesta, Angel Sánchez and Yamir Moreno. Heterogeneous networks do not promote cooperation when humans play a Prisoner’s Dilemma. Proceedings of the National Academy of Sciences (2012). DOI: 10.1073/pnas.1206681109.
12. Cruz, Victor L., Javier Ramos and Javier Martinez-Salazar. Assessment of the Intrinsic Conformational Preferences of Dipeptide Amino Acids in Aqueous Solution by Combined Umbrella Sampling/MBAR Statistics. A Comparison with Experimental Results. The Journal of Physical Chemistry B (2012). DOI: 10.1021/jp206757j.
13. Cruz, Víctor, Javier Ramos and Javier Martínez-Salazar. Water-Mediated Conformations of the Alanine Dipeptide as Revealed by Distributed Umbrella Sampling Simulations, Quantum Mechanics Based Calculations, and Experimental Data. The Journal of Physical Chemistry B (2011). DOI: 10.1021/jp2022727.
14. Garcia, Luis Isaac Ramos and Julio F Almansa. Technical Note: An algorithm to calculate the tissue phantom ratio from depth dose in radiosurgery: Calculation of the tissue phantom ratio from depth dose. Medical Physics (2011). DOI: 10.1118/1.3570575.
15. Bustos, A., F. Castejón, L.A. Fernández, J. García, V. Martin-Mayor, J.M. Reynolds, R. Seki and J.L. Velasco. Impact of 3D features on ion collisional transport in ITER. Nuclear Fusion (2010). DOI: 10.1088/0029-5515/50/12/125007.
16. Martínez-Mendoza, A. J., J. A. Méndez-Bermúdez, Imre Varga, Moises Martinez-Mares and Jose A. Moreno-Razo. Conductance statistics for the power-law banded random matrix model. CONDENSED MATTER PHYSICS: IV Mexican Meeting on Experimental and Theoretical Physics: Symposium on Condensed Matter Physics (2010). DOI: 10.1063/1.3536612.
17. Simões, Carlos J. V., Trishna Mukherjee, Rui M. M. Brito and Richard M. Jackson. Toward the Discovery of Functional Transthyretin Amyloid Inhibitors: Application of Virtual Screening Methods. Journal of Chemical Information and Modeling (2010). DOI: 10.1021/ci100250z.
18. Velasco, J. L., F. Castejón and A. Tarancón. Finite orbit width effect in ion collisional transport in TJ-II. Physics of Plasmas (2009). DOI: 10.1063/1.3126583.

LHC@home (ATLAS@home)

1. Elmsheuser, Johannes, Alessandro Di Girolamo, Andrej Filipcic, Antonio Limosani, Markus Schulz, David Smith, Andrea Sciaba and Andrea Valassi. ATLAS Grid Workflow Performance Optimization. EPJ Web of Conferences (2019). DOI: 10.1051/epjconf/201921403021.
2. Wu, Wenjing and David Cameron. Backfilling the Grid with Containerized BOINC in the ATLAS computing. EPJ Web of Conferences (2019). DOI: 10.1051/epjconf/201921407015.
3. Wu, Wenjing, David Cameron and Di Qing. Using ATLAS@Home to Exploit Extra CPU from Busy Grid Sites. Computing and Software for Big Science (2019). DOI: 10.1007/s41781-019-0023-6.
4. Cameron, David, Alexander Bogdanchikov, Riccardo-Maria Bianchi and Wenjing Wu. Advances in ATLAS@Home towards a major ATLAS computing resource. (2018).
5. Furano, Fabrizio, Oliver Keeble and Laurence Field. Dynamic federation of grid and cloud storage. Physics of Particles and Nuclei Letters (2016). DOI: 10.1134/S1547477116050186.
6. Alonso-Monsalve, Saúl, Félix García-Carballeira and Alejandro Calderón. Improving the Performance of Volunteer Computing with Data Volunteers: A Case Study with the ATLAS@home Project. Algorithms and Architectures for Parallel Processing (2016).
7. Tomás, R., M. Giovannozzi and R. de Maria. Nonlinear correction schemes for the phase 1 LHC insertion region upgrade and dynamic aperture studies. Physical Review Special Topics - Accelerators and Beams (2009). DOI: 10.1103/PhysRevSTAB.12.011002.

LHC@home (CMS@Home)

1. Pérez-Calero Yzquierdo, Antonio, Maria Acosta Flechas, Diego Davila Foyo et al. Evolution of the CMS Global Submission Infrastructure for the HL-LHC Era. EPJ Web of Conferences (2020). DOI: 10.1051/epjconf/202024503016.
2. Dykstra, Dave, Brian Bockelman, Jakob Blomer and Laurence Field. The Open High Throughput Computing Content Delivery Network. EPJ Web of Conferences (2019). DOI: 10.1051/epjconf/201921404023.
3. Field, L., D. Spiga, I. Reid, H. Riahi and L. Cristella. CMS@home: Integrating the Volunteer Cloud and High-Throughput Computing. Computing and Software for Big Science (2018). DOI: 10.1007/s41781-018-0006-z.
4. Cheung, Kwong Tat, Laurence Field and Fabrizio Furano. A world-wide databridge supported by a commercial cloud provider. Journal of Physics: Conference Series (2017). DOI: 10.1088/1742-6596/898/6/062041.
5. Berzano, D, J Blomer, P Buncic, I Charalampidis, G Ganis and R Meusel. Status and Roadmap of CernVM. Journal of Physics: Conference Series (2015). DOI: 10.1088/1742-6596/664/2/022018.
6. Field, L, H Borras, D Spiga and H Riahi. CMS@home: Enabling Volunteer Computing Usage for CMS. Journal of Physics: Conference Series (2015). DOI: 10.1088/1742-6596/664/2/022017.

LHC@home (SixTrack)

1. D'Andrea, Marco, Alessio Mereghetti, Daniele Mirarchi, Veronica Olsen and Stefano Redaelli. Release of Crystal Routine for Multi-Turn Proton Simulations within SixTrack v5. 12th International Particle Accelerator Conference (IPAC'21), Campinas, SP, Brazil, 24-28 May 2021 (2021). DOI: 10.18429/JACoW-IPAC2021-WEPAB024.
2. De Maria, Riccardo, Joel Andersson, Laurence Field et al. SixTrack Project: Status, Runtime Environment, and New Developments. Proceedings of the 13th Int. Computational Accelerator Physics Conf. (2019). DOI: 10.18429/JACOW-ICAP2018-TUPAF02.
3. De Maria, R., J. Andersson, V. K. Berglyd Olsen et al. SixTrack V and runtime environment. International Journal of Modern Physics A (2019). DOI: 10.1142/S0217751X19420351.
4. De Maria, Riccardo, Nils Hoimyr, Joel Andersson et al. JACoW : SixTrack project: Status, runtime environment, and new developments. CERN Document Server (2019).
5. Maclean, E. H., M. Giovannozzi and R. B. Appleby. Innovative method to measure the extent of the stable phase-space region of proton synchrotrons. Physical Review Accelerators and Beams (2019). DOI: 10.1103/PhysRevAccelBeams.22.034002.
6. De Maria, R., J. Andersson, V.K. Berglyd Olsen et al. SixTrack Version 5: Status and New Developments. Journal of Physics: Conference Series (2019). DOI: 10.1088/1742-6596/1350/1/012129.
7. Kaltchev, Dobrin, Nikolaos Karastathis, Yannis Papaphilippou and Dario Pellegrini. Extended-Domain Tune-Scans for the HL-LHC Dynamic Aperture in Presence of Beam-Beam Effects. Proceedings of the 9th Int. Particle Accelerator Conf. (2018). DOI: 10.18429/JACOW-IPAC2018-TUPAL064.
8. Kaltchev, Dobrin, Nikolaos Karastathis, Dario Pellegrini, E. McIntosh and Yannis Papaphilippou. JACoW : Extended-Domain Tune-Scans for the HL-LHC Dynamic Aperture in Presence of Beam-Beam Effects. CERN Document Server (2018).
9. Sjobak, Kyrre, Javier Barranco García, Riccardo De Maria, Miriam Fitterer, Vikas Gupta, Eric McIntosh, Alessio Mereghetti and James Molson. New Features of the 2017 SixTrack Release. Proceedings of the 8th Int. Particle Accelerator Conf. (2017). DOI: 10.18429/JACOW-IPAC2017-THPAB047.
10. Høimyr, N, J Blomer, P Buncic et al. BOINC service for volunteer cloud computing. Journal of Physics: Conference Series (2012). DOI: 10.1088/1742-6596/396/3/032057.
11. Harutyunyan, A, J Blomer, P Buncic et al. CernVM Co-Pilot: an Extensible Framework for Building Scalable Computing Infrastructures on the Cloud. Journal of Physics: Conference Series (2012). DOI: 10.1088/1742-6596/396/3/032054.
12. E. McIntosh,, F. Schmidt and F. d. Dinechin. Massive Tracking on Heterogeneous Platforms. 9th International Computational Accelerator Physics Conference, 2006 (2006).
13. Herr, Werner, D Kaltchev, E McIntosh and F Schmidt. Large Scale Beam-beam Simulations for the CERN LHC using Distributed Computing. 10th European Particle Accelerator Conference (2006).

LHC@home (Test4Theory)

1. Jueid, Adil. Studying QCD modeling of uncertainties in particle spectra from dark-matter annihilation into jets. Journal of Physics: Conference Series (2021). DOI: 10.1088/1742-6596/2156/1/012057.
2. Jueid, Adil, Simone Amoroso, Sascha Caron, Peter Skands and Roberto Ruiz de austri. Particle spectra from dark matter annihilation: physics modelling and QCD uncertainties. Tools for High Energy Physics and Cosmology (2021). DOI: 10.22323/1.392.0028.
3. d'Enterria, David and Cynthia Yan. Revised QCD effects on the Z $\to b\bar{b}$ forward-backward asymmetry. (2020).
4. Hunt-Smith, Nicholas and Peter Skands. String fragmentation with a time-dependent tension. The European Physical Journal C (2020). DOI: 10.1140/epjc/s10052-020-08654-9.
5. Bierlich, Christian, Andy Buckley, Christian Holm Christensen et al. Confronting experimental data with heavy-ion models: Rivet for heavy ions. The European Physical Journal C (2020). DOI: 10.1140/epjc/s10052-020-8033-4.
6. Duncan, Cody B and Peter Skands. Fragmentation of two repelling Lund strings. SciPost Physics (2020). DOI: 10.21468/SciPostPhys.8.5.080.
7. Soyez, Grégory. Pileup mitigation at the LHC: A theorist’s view. Physics Reports (2019). DOI: 10.1016/j.physrep.2019.01.007.
8. Cameron, David, Laurence Field, Nikolas Giannakis and Nils Høimyr. Extending CERN computing to volunteers - LHC@home consolidation and outlook. EPJ Web of Conferences (2019). DOI: 10.1051/epjconf/201921403016.
9. The FCC Collaboration, A. Abada, M. Abbrescia et al. FCC Physics Opportunities: Future Circular Collider Conceptual Design Report Volume 1. The European Physical Journal C (2019). DOI: 10.1140/epjc/s10052-019-6904-3.
10. Acharya, S., D. Adamová, A. Adler et al. Charged jet cross section and fragmentation in proton-proton collisions at s = 7 TeV. Physical Review D (2019). DOI: 10.1103/PhysRevD.99.012016.
11. Bartalini, Paolo and Jonathan Richard Gaunt. Multiple Parton Interactions at the LHC. Advanced Series on Directions in High Energy Physics (2018).
12. Corcella, Gennaro, Roberto Franceschini and Doojin Kim. Fragmentation uncertainties in hadronic observables for top-quark mass measurements. Nuclear Physics B (2018). DOI: 10.1016/j.nuclphysb.2018.02.012.
13. Grosse-Oetringhaus, Jan Fiete. Phenomenology of Soft QCD: The Role of Minimum-Bias Measurements. Advanced Series on Directions in High Energy Physics (2018).
14. Adam, J., L. Adamczyk, J. R. Adams et al. Longitudinal double-spin asymmetries for π 0 s in the forward direction for 510 GeV polarized p p collisions. Physical Review D (2018). DOI: 10.1103/PhysRevD.98.032013.
15. Tanabashi, M., K. Hagiwara, K. Hikasa et al. Review of Particle Physics. Physical Review D (2018). DOI: 10.1103/PhysRevD.98.030001.
16. Sjöstrand, Torbjörn. The Development of MPI Modeling in Pythia. Advanced Series on Directions in High Energy Physics (2018).
17. Skands, Peter and David d’Enterria. QCD studies at FCC-ee. 38th International Conference on High Energy Physics (2017). DOI: 10.22323/1.282.1156.
18. Barranco, Javier, Yunhai Cai, David Cameron et al. LHC@Home: a BOINC-based volunteer computing infrastructure for physics studies at CERN. Open Engineering (2017). DOI: 10.1515/eng-2017-0042.
19. Mangano Et Al., M. L. Chapter 1: Standard Model Processes. CERN Yellow Reports: Monographs (2017). DOI: 10.23731/CYRM-2017-003.1.
20. Gras, Philippe, Stefan Höche, Deepak Kar et al. Systematics of quark/gluon tagging. Journal of High Energy Physics (2017). DOI: 10.1007/JHEP07(2017)091.
21. Richardson, Peter. Parton Showers since LEP. (2017).
22. Akiba, K, M Akbiyik, M Albrow et al. LHC forward physics. Journal of Physics G: Nuclear and Particle Physics (2016). DOI: 10.1088/0954-3899/43/11/110201.
23. Martin, T., P. Skands and S. Farrington. Probing collective effects in hadronisation with the extremes of the underlying event. The European Physical Journal C (2016). DOI: 10.1140/epjc/s10052-016-4135-4.
24. Fox, Patrick J. and David Tucker-Smith. Exotic decays of heavy B quarks. Journal of High Energy Physics (2016). DOI: 10.1007/JHEP01(2016)038.
25. Sjöstrand, Torbjörn, Stefan Ask, Jesper R. Christiansen et al. An introduction to PYTHIA 8.2. Computer Physics Communications (2015). DOI: 10.1016/j.cpc.2015.01.024.
26. Grebenyuk, A., D. Kar and A. Siodmok. Outlook on MPI and MC models. (2015).
27. Astalos, R. and others. Proceedings of the Sixth International Workshop on Multiple Partonic Interactions at the Large Hadron Collider. (2015).
28. Heß, Benjamin Andreas. Particle Identification in Jets and High-Multiplicity pp Events with the ALICE TPC. (2015).
29. Cacciari, Matteo, Gavin P. Salam and Gregory Soyez. SoftKiller, a particle-level pileup removal method. The European Physical Journal C (2015). DOI: 10.1140/epjc/s10052-015-3267-2.
30. Høimyr, N, M Marquina, T Asp, P Jones, A Gonzalez and L Field. Towards a Production Volunteer Computing Infrastructure for HEP. Journal of Physics: Conference Series (2015). DOI: 10.1088/1742-6596/664/2/022023.
31. Kalaydzhyan, Tigran and Edward Shuryak. Collective flow in high-multiplicity proton-proton collisions. Physical Review C (2015). DOI: 10.1103/PhysRevC.91.054913.
32. Bierlich, Christian, Gösta Gustafson, Leif Lönnblad and Andrey Tarasov. Effects of overlapping strings in pp collisions. Journal of High Energy Physics (2015). DOI: 10.1007/JHEP03(2015)148.
33. Christiansen, Jesper R. and Peter Z. Skands. String formation beyond leading colour. Journal of High Energy Physics (2015). DOI: 10.1007/JHEP08(2015)003.
34. Seidel, Markus. Precise measurement of the top-quark mass at the CMS experiment using the ideogram method. (2015).
35. Charalampidis, I., D. Berzano, J. Blomer, P. Buncic, G. Ganis, R. Meusel and B. Segal. CernVM WebAPI - Controlling Virtual Machines from the Web. Journal of Physics: Conference Series (2015). DOI: 10.1088/1742-6596/664/2/022010.
36. Barletta, William, Marco Battaglia, Markus Klute, Michelangelo Mangano, Soren Prestemon, Lucio Rossi and Peter Skands. Future hadron colliders: From physics perspectives to technology R&D. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment (2014). DOI: 10.1016/j.nima.2014.07.010.
37. Skands, P., S. Carrazza and J. Rojo. Tuning PYTHIA 8.1: the Monash 2013 tune. The European Physical Journal C (2014). DOI: 10.1140/epjc/s10052-014-3024-y.
38. Fischer, N., S. Gieseke, S. Plätzer and P. Skands. Revisiting radiation patterns in $$e^+e^-$$ e + e - collisions. The European Physical Journal C (2014). DOI: 10.1140/epjc/s10052-014-2831-5.
39. Karneyeu, A., L. Mijovic, S. Prestel and P. Z. Skands. MCPLOTS: a particle physics resource based on volunteer computing. The European Physical Journal C (2014). DOI: 10.1140/epjc/s10052-014-2714-9.
40. Hartgring, L., E. Laenen and P. Skands. Antenna showers with one-loop matrix elements. Journal of High Energy Physics (2013). DOI: 10.1007/JHEP10(2013)127.
41. Katzy, Judith M. QCD Monte-Carlo model tunes for the LHC. Progress in Particle and Nuclear Physics (2013). DOI: 10.1016/j.ppnp.2013.08.002.
42. Sjöstrand, Torbjörn. Colour reconnection and its effects on precise measurements at the LHC. (2013).
43. Barletta, William, Marco Battaglia, Markus Klute, Michelangelo Mangano, Soren Prestemon, Lucio Rossi and Peter Skands. Working Group Report: Hadron Colliders. (2013).
44. Skands, Peter Z. Soft-QCD and UE spectra in pp collisions at very high CM energies (a Snowmass white paper). (2013).

Leiden Classical

1. Wijzenbroek, Mark, Darcey Helstone, Jörg Meyer and Geert-Jan Kroes. Dynamics of H2 dissociation on the close-packed (111) surface of the noblest metal: H2 + Au(111). The Journal of Chemical Physics (2016). DOI: 10.1063/1.4964486.
2. Wijzenbroek, M. and M. F. Somers. Static surface temperature effects on the dissociation of H ₂ and D ₂ on Cu(111). The Journal of Chemical Physics (2012). DOI: 10.1063/1.4738956.

MLC@Home

1. Clemens, John. MLDS: A Dataset for Weight-Space Analysis of Neural Networks. (2021). DOI: 10.48550/ARXIV.2104.10555.

Malariacontrol.net

1. Penny, Melissa A., Robert Verity, Caitlin A. Bever et al. Public health impact and cost-effectiveness of the RTS,S/AS01 malaria vaccine: a systematic comparison of predictions from four mathematical models. The Lancet (2016). DOI: 10.1016/S0140-6736(15)00725-4.
2. Cameron, Ewan, Katherine E. Battle, Samir Bhatt et al. Defining the relationship between infection prevalence and clinical incidence of Plasmodium falciparum malaria. Nature Communications (2015). DOI: 10.1038/ncomms9170.
3. Penny, Melissa A., Nicolas Maire, Caitlin A. Bever, Peter Pemberton-Ross, Olivier J. T. Briët, David L. Smith, Peter W. Gething and Thomas A. Smith. Distribution of malaria exposure in endemic countries in Africa considering country levels of effective treatment. Malaria Journal (2015). DOI: 10.1186/s12936-015-0864-3.
4. Penny, Melissa A, Katya Galactionova, Michael Tarantino, Marcel Tanner and Thomas A Smith. The public health impact of malaria vaccine RTS,S in malaria endemic Africa: country-specific predictions using 18 month follow-up Phase III data and simulation models. BMC Medicine (2015). DOI: 10.1186/s12916-015-0408-2.
5. Stuckey, Erin M., Jennifer Stevenson, Katya Galactionova et al. Modeling the Cost Effectiveness of Malaria Control Interventions in the Highlands of Western Kenya. PLoS ONE (2014). DOI: 10.1371/journal.pone.0107700.
6. Briët, Olivier JT and Melissa A Penny. Repeated mass distributions and continuous distribution of long-lasting insecticidal nets: modelling sustainability of health benefits from mosquito nets, depending on case management. Malaria Journal (2013). DOI: 10.1186/1475-2875-12-401.
7. Briët, Olivier JT and Nakul Chitnis. Effects of changing mosquito host searching behaviour on the cost effectiveness of a mass distribution of long-lasting, insecticidal nets: a modelling study. Malaria Journal (2013). DOI: 10.1186/1475-2875-12-215.
8. Nunes, Julia K, Vicky Cárdenas, Christian Loucq, Nicolas Maire, Thomas Smith, Craig Shaffer, Kårstein Måseide and Alan Brooks. Modeling the public health impact of malaria vaccines for developers and policymakers. BMC Infectious Diseases (2013). DOI: 10.1186/1471-2334-13-295.
9. Briët, Olivier JT, Melissa A Penny, Diggory Hardy et al. Effects of pyrethroid resistance on the cost effectiveness of a mass distribution of long-lasting insecticidal nets: a modelling study. Malaria Journal (2013). DOI: 10.1186/1475-2875-12-77.
10. Briët, Olivier JT, Diggory Hardy and Thomas A Smith. Importance of factors determining the effective lifetime of a mass, long-lasting, insecticidal net distribution: a sensitivity analysis. Malaria Journal (2012). DOI: 10.1186/1475-2875-11-20.
11. Crowell, Valerie, Diggory Hardy, Olivier Briët, Nakul Chitnis, Nicolas Maire and Thomas Smith. Can we depend on case management to prevent re-establishment of P. falciparum malaria, after local interruption of transmission?. Epidemics (2012). DOI: 10.1016/j.epidem.2011.10.003.
12. Stuckey, Erin M, Jennifer C Stevenson, Mary K Cooke et al. Simulation of malaria epidemiology and control in the highlands of western Kenya. Malaria Journal (2012). DOI: 10.1186/1475-2875-11-357.
13. Smith, Thomas, Amanda Ross, Nicolas Maire et al. Ensemble Modeling of the Likely Public Health Impact of a Pre-Erythrocytic Malaria Vaccine. PLoS Medicine (2012). DOI: 10.1371/journal.pmed.1001157.
14. Brooks, Alan, Olivier J. T. Briët, Diggory Hardy, Richard Steketee and Thomas A. Smith. Simulated Impact of RTS,S/AS01 Vaccination Programs in the Context of Changing Malaria Transmission. PLoS ONE (2012). DOI: 10.1371/journal.pone.0032587.
15. Maire, Nicolas, Samuel D. Shillcutt, Damian G. Walker, Fabrizio Tediosi and Thomas A. Smith. Cost-Effectiveness of the Introduction of a Pre-Erythrocytic Malaria Vaccine into the Expanded Program on Immunization in Sub-Saharan Africa: Analysis of Uncertainties Using a Stochastic Individual-Based Simulation Model of Plasmodium falciparum Malaria. Value in Health (2011). DOI: 10.1016/j.jval.2011.06.004.
16. Smith, Thomas A., Nakul Chitnis, Olivier J.T. Briët and Marcel Tanner. Uses of mosquito-stage transmission-blocking vaccines against Plasmodium falciparum. Trends in Parasitology (2011). DOI: 10.1016/j.pt.2010.12.011.
17. Ross, Amanda, Nicolas Maire, Elisa Sicuri, Thomas Smith and Lesong Conteh. Determinants of the Cost-Effectiveness of Intermittent Preventive Treatment for Malaria in Infants and Children. PLoS ONE (2011). DOI: 10.1371/journal.pone.0018391.
18. Bretscher, Michael T., Nicolas Maire, Nakul Chitnis, Ingrid Felger, Seth Owusu-Agyei and Tom Smith. The distribution of Plasmodium falciparum infection durations. Epidemics (2011). DOI: 10.1016/j.epidem.2011.03.002.
19. Carneiro, Ilona, Lucy Smith, Amanda Ross, Arantxa Roca-Feltrer, Brian Greenwood, Joanna Armstrong Schellenberg, Thomas Smith and David Schellenberg. Intermittent preventive treatment for malaria in infants: a decision-support tool for sub-Saharan Africa. Bulletin of the World Health Organization (2010). DOI: 10.2471/BLT.09.072397.
20. Ross, Amanda and Thomas Smith. Interpreting malaria age-prevalence and incidence curves: a simulation study of the effects of different types of heterogeneity. Malaria Journal (2010). DOI: 10.1186/1475-2875-9-132.
21. Krebs, Viola. Motivations of cybervolunteers in an applied distributed computing environment: MalariaControl.net as an example. First Monday (2010). DOI: 10.5210/fm.v15i2.2783.
22. Gosoniu, L., P. Vounatsou, N. Sogoba, N. Maire and T. Smith. Mapping malaria risk in West Africa using a Bayesian nonparametric non-stationary model. Computational Statistics & Data Analysis (2009). DOI: 10.1016/j.csda.2009.02.022.
23. Tediosi, Fabrizio, Nicolas Maire, Melissa Penny, Alain Studer and Thomas A Smith. Simulation of the cost-effectiveness of malaria vaccines. Malaria Journal (2009). DOI: 10.1186/1475-2875-8-127.
24. Penny, Melissa A., Nicolas Maire, Alain Studer, Allan Schapira and Thomas A. Smith. What Should Vaccine Developers Ask? Simulation of the Effectiveness of Malaria Vaccines. PLoS ONE (2008). DOI: 10.1371/journal.pone.0003193.
25. Smith, T., N. Maire, A. Ross et al. Towards a comprehensive simulation model of malaria epidemiology and control. Parasitology (2008). DOI: 10.1017/S0031182008000371.
26. Ross, Amanda, Melissa Penny, Nicolas Maire et al. Modelling the Epidemiological Impact of Intermittent Preventive Treatment against Malaria in Infants. PLoS ONE (2008). DOI: 10.1371/journal.pone.0002661.

Milkyway@home

1. Mendelsohn, Eric J., Heidi Jo Newberg, Siddhartha Shelton, Lawrence M. Widrow, Jeffery M. Thompson and Carl J. Grillmair. Estimate of the Mass and Radial Profile of the Orphan–Chenab Stream's Dwarf-galaxy Progenitor Using MilkyWay@home. The Astrophysical Journal (2022). DOI: 10.3847/1538-4357/ac498a.
2. Mendelsohn, E. J., H. J. Newberg, S. Shelton, L. Widrow, J. Thompson and C. Grillmair. Estimate of the Mass and Radial Profile of the Orphan Stream's Dwarf Galaxy Progenitor Using MilkyWay@home. (2021).
3. Donlon, T., H. Newberg, J. Weiss, A. Guffey and J. Thompson. A Trifurcated Sagittarius Stream in the South. (2021).
4. Shelton, Siddhartha, Heidi Jo Newberg, Jake Weiss et al. An Algorithm for Reconstructing the Orphan Stream Progenitor with MilkyWay@home Volunteer Computing. (2021). DOI: 10.48550/ARXIV.2102.07257.
5. Donlon, Thomas, Heidi Jo Newberg, Robyn Sanderson and Lawrence M. Widrow. The Milky Way’s Shell Structure Reveals the Time of a Radial Collision. The Astrophysical Journal (2020). DOI: 10.3847/1538-4357/abb5f6.
6. Mendelsohn, E. J., H. J. Newberg, T. Donlon and J. M. Thompson. N-Body Simulations with MilkyWay@home. (2020).
7. Newberg, Heidi Jo, Siddhartha Shelton, Eric Mendelsohn et al. Streams and the Milky Way dark matter halo. Proceedings of the International Astronomical Union (2019). DOI: 10.1017/S174392131900855X.
8. Weiss, Jake, Heidi Jo Newberg, Matthew Newby and Travis Desell. Fitting the Density Substructure of the Stellar Halo with MilkyWay@home. The Astrophysical Journal Supplement Series (2018). DOI: 10.3847/1538-4365/aadb92.
9. Shelton, Siddhartha. Constraining Dwarf Galaxy Properties Using Tidal Streams. (2018).
10. Weiss, Jake. The Stellar Density of the Major Substructure in the Milky Way Halo. (2018).
11. Weiss, Jake, Heidi Jo Newberg and Travis Desell. A Tangle of Stellar Streams in the North Galactic Cap. The Astrophysical Journal (2018). DOI: 10.3847/2041-8213/aae5fc.
12. Desell, Travis, Malik Magdon-Ismail, Heidi Newberg, Lee A. Newberg, Boleslaw K. Szymanski and Carlos A. Varela. A Robust Asynchronous Newton Method for Massive Scale Computing Systems. (2017). DOI: 10.48550/ARXIV.1702.02204.
13. Dumas, Julie, Heidi J. Newberg, Bethany Niedzielski, Adam Susser, Jeffery M. Thompson, Jake Weiss and Kim M. Lewis. TESTING THE DARK MATTER CAUSTIC THEORY AGAINST OBSERVATIONS IN THE MILKY WAY. The Astrophysical Journal (2015). DOI: 10.1088/0004-637X/811/1/36.
14. Newberg, Heidi Jo, Matthew Newby, Travis Desell, Malik Magdon-Ismail, Boleslaw Szymanski and Carlos Varela. MilkyWay@home: Harnessing volunteer computers to constrain dark matter in the Milky Way. Proceedings of the International Astronomical Union (2013). DOI: 10.1017/S1743921313006273.
15. Newby, Matthew, Nathan Cole, Heidi Jo Newberg et al. A SPATIAL CHARACTERIZATION OF THE SAGITTARIUS DWARF GALAXY TIDAL TAILS. The Astronomical Journal (2013). DOI: 10.1088/0004-6256/145/6/163.
16. Newberg, Heidi Jo. Determining distances to stars statistically from photometry. Proceedings of the International Astronomical Union (2012). DOI: 10.1017/S174392131202114X.
17. Desell, Travis, Malik Magdon-Ismail, Boleslaw Szymanski, Carlos A. Varela, Benjamin A. Willett, Matthew Arsenault and Heidi Newberg. Evolving N-Body Simulations to Determine the Origin and Structure of the Milky Way Galaxy's Halo Using Volunteer Computing. Distributed Processing, Workshops and Phd Forum (IPDPSW) (2011). DOI: 10.1109/IPDPS.2011.346.
18. Desell, Travis, Anthony Waters, Malik Magdon-Ismail et al. Accelerating the MilkyWay@Home Volunteer Computing Project with GPUs. Parallel Processing and Applied Mathematics (2010).
19. Desell, Travis, David P. Anderson, Malik Magdon-Ismail, Heidi New, Boleslaw K. Szymanski and Carlos A. Varela. An analysis of massively distributed evolutionary algorithms. 2010 IEEE Congress on Evolutionary Computation (CEC) (2010). DOI: 10.1109/CEC.2010.5586073.
20. Desell, Travis, Malik Magdon-Ismail, Boleslaw Szymanski, Carlos A. Varela, Heidi Newberg and David P. Anderson. Validating Evolutionary Algorithms on Volunteer Computing Grids. Distributed Applications and Interoperable Systems (2010).
21. Cole, Nate, Travis Desell, Daniel Lombraña González, Francisco Fernández de Vega, Malik Magdon-Ismail, Heidi Newberg, Boleslaw Szymanski and Carlos Varela. Evolutionary Algorithms on Volunteer Computing Platforms: The MilkyWay@Home Project. Parallel and Distributed Computational Intelligence (2010).
22. Desell, Travis, Malik Magdon-Ismail, Boleslaw Szymanski, Carlos Varela, Heidi Newberg and Nathan Cole. Robust Asynchronous Optimization for Volunteer Computing Grids. 2009 5th IEEE International Conference on e-Science (e-Science) (2009). DOI: 10.1109/e-Science.2009.44.
23. Desell, Travis, Boleslaw Szymanski and Carlos Varela. Asynchronous genetic search for scientific modeling on large-scale heterogeneous environments. Distributed Processing Symposium (IPDPS) (2008). DOI: 10.1109/IPDPS.2008.4536169.
24. Szymanski, Boleslaw K., Travis Desell and Carlos Varela. The Effects of Heterogeneity on Asynchronous Panmictic Genetic Search. Parallel Processing and Applied Mathematics (2008).
25. Desell, Travis, Boleslaw Szymanski and Carlos Varela. An asynchronous hybrid genetic-simplex search for modeling the Milky Way galaxy using volunteer computing. the 10th annual conference (2008). DOI: 10.1145/1389095.1389273.
26. Cole, Nathan, Heidi Jo Newberg, Malik Magdon‐Ismail et al. Maximum Likelihood Fitting of Tidal Streams with Application to the Sagittarius Dwarf Tidal Tails. The Astrophysical Journal (2008). DOI: 10.1086/589681.
27. Desell, Travis, Nathan Cole, Malik Magdon-Ismail, Heidi Newberg, Boleslaw Szymanski and Carlos Varela. Distributed and Generic Maximum Likelihood Evaluation. Third IEEE International Conference on e-Science and Grid Computing (e-Science 2007) (2007). DOI: 10.1109/E-SCIENCE.2007.30.

MindModeling@Home

1. Godwin, Hayward J., Stephen C. Walenchok, Joseph W. Houpt, Michael C. Hout and Stephen D. Goldinger. Faster than the speed of rejection: Object identification processes during visual search for multiple targets.. Journal of Experimental Psychology: Human Perception and Performance (2015). DOI: 10.1037/xhp0000036.
2. Richard Moore, L. and Glenn Gunzelmann. An interpolation approach for fitting computationally intensive models. Cognitive Systems Research (2014). DOI: 10.1016/j.cogsys.2013.09.001.
3. Moore, L. Richard. Cognitive model exploration and optimization: a new challenge for computational science. Computational and Mathematical Organization Theory (2011). DOI: 10.1007/s10588-011-9092-8.
4. Moore, L. Richard, Matthew Kopala, Thomas Mielke, Michael Krusmark and Kevin A. Gluck. Simultaneous performance exploration and optimized search with volunteer computing. the 19th ACM International Symposium (2010). DOI: 10.1145/1851476.1851518.
5. Harris, Jack, Kevin A. Gluck, Thomas Mielke and L. Richard Moore. Mindmodeling@Home. . . and Anywhere Else You Have Idle Processors. (2009).
6. Gluck, Kevin, Matthias Scheutz, Glenn Gunzelmann, Jack Harris and Jeff Kershner. Combinatorics meets processing power: Large-scale computational resources for BRIMS. 16th Conference on Behavior Representation in Modeling and Simulation 2007, BRIMS (2007).

Najmanovich Research Group

1. Samish, I., P. E. Bourne and R. J. Najmanovich. Achievements and challenges in structural bioinformatics and computational biophysics. Bioinformatics (2015). DOI: 10.1093/bioinformatics/btu769.
2. Gaudreault, Francis and Rafael J. Najmanovich. FlexAID: Revisiting Docking on Non-Native-Complex Structures. Journal of Chemical Information and Modeling (2015). DOI: 10.1021/acs.jcim.5b00078.
3. Duchêne, Dominic, Eloïc Colombo, Antoine Désilets, Pierre-Luc Boudreault, Richard Leduc, Eric Marsault and Rafael Najmanovich. Analysis of Subpocket Selectivity and Identification of Potent Selective Inhibitors for Matriptase and Matriptase-2. Journal of Medicinal Chemistry (2014). DOI: 10.1021/jm5015633.

NanoHUB@Home

1. Gesing, Sandra, Michael Zentner, Steve Clark, Claire Stirm and Ben Haley. HUBzero®: Novel Concepts Applied to Established Computing Infrastructures to Address Communities' Needs. PEARC '19: Practice and Experience in Advanced Research Computing (2019). DOI: 10.1145/3332186.3332238.

NanoHive@Home

1. Allis, Damian G., Brian Helfrich, Robert A. Freitas and Ralph C. Merkle. Analysis of Diamondoid Mechanosynthesis Tooltip Pathologies Generated via a Distributed Computing Approach. Journal of Computational and Theoretical Nanoscience (2011). DOI: 10.1166/jctn.2011.1792.

Neurona@Home

1. Acedo, L., E. Lamprianidou, J.-A. Moraño, J. Villanueva-Oller and R.-J. Villanueva. Firing patterns in a random network cellular automata model of the brain. Physica A: Statistical Mechanics and its Applications (2015). DOI: 10.1016/j.physa.2015.05.017.
2. Acedo, L., J. Villanueva-Oller, J. A. Moraño and R.-J. Villanueva. The Neurona@Home project: Simulating a large-scale cellular automata brain in a distributed computing environment. PHYSICS, COMPUTATION, AND THE MIND - ADVANCES AND CHALLENGES AT INTERFACES: Proceedings of the 12th Granada Seminar on Computational and Statistical Physics (2013). DOI: 10.1063/1.4776528.

NumberFields@Home

1. Driver, Eric D. and John W. Jones. Computing septic number fields. Journal of Number Theory (2019). DOI: 10.1016/j.jnt.2019.02.022.
2. Driver, Eric D. and John W. Jones. Minimum Discriminants of Imprimitive Decic Fields. Experimental Mathematics (2010). DOI: 10.1080/10586458.2010.10390637.
3. Driver, Eric D. and John W. Jones. A targeted Martinet search. Mathematics of Computation (2009). DOI: 10.1090/S0025-5718-08-02178-9.

OProject

1. Swierczewski, Lukasz. The Distributed Computing Model Based on The Capabilities of The Internet. (2012).

Orbit@home

1. Tricarico, Pasquale. The near-Earth asteroid population from two decades of observations. Icarus (2017). DOI: 10.1016/j.icarus.2016.12.008.

POEM@HOME

1. Girrbach, Maria, Irene Meliciani, Björn Waterkotte et al. A fluorescence polarization assay for the experimental validation of an in silico model of the chemokine CXCL8 binding to receptor-derived peptides. Physical Chemistry Chemical Physics (2014). DOI: 10.1039/C3CP53850H.
2. Strunk, Timo, Moritz Wolf and Wolfgang Wenzel. Peptide structure prediction using distributed volunteer computing networks. Journal of Mathematical Chemistry (2012). DOI: 10.1007/s10910-011-9937-x.
3. Boeuf, Stephane, Tanja Throm, Beatrice Gutt et al. Engineering hydrophobin DewA to generate surfaces that enhance adhesion of human but not bacterial cells. Acta Biomaterialia (2012). DOI: 10.1016/j.actbio.2011.11.022.
4. Strunk, T., M. Wolf, M. Brieg et al. SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems. Journal of Computational Chemistry (2012). DOI: 10.1002/jcc.23089.
5. Meliciani, Irene, Konstantin Klenin, Timo Strunk, Katja Schmitz and Wolfgang Wenzel. Probing hot spots on protein-protein interfaces with all-atom free-energy simulation. The Journal of Chemical Physics (2009). DOI: 10.1063/1.3177008.

Predictor@Home

1. Taufer, M., Chahm An, A. Kerstens and C.L. Brooks III. Predictor@Home: A "Protein Structure Prediction Supercomputer' Based on Global Computing. IEEE Transactions on Parallel and Distributed Systems (2006). DOI: 10.1109/TPDS.2006.110.
2. Taufer, M., M. Crowley, D. J. Price, A. A. Chien and C. L. Brooks. Study of a highly accurate and fast protein-ligand docking method based on molecular dynamics. Concurrency and Computation: Practice and Experience (2005). DOI: 10.1002/cpe.949.
3. Taufer, M., D. Anderson, P. Cicotti and C.L. Brooks. Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing. 19th IEEE International Parallel and Distributed Processing Symposium (2005). DOI: 10.1109/IPDPS.2005.247.
4. Taufer, M., P.J. Teller, D.P. Anderson and C.L. Brooks. Metrics for effective resource management in global computing environments. First International Conference on e-Science and Grid Computing (e-Science'05) (2005). DOI: 10.1109/E-SCIENCE.2005.58.
5. Taufer, M., M. Crowley, D. Price, A.A. Chien and C.L. Brooks. Study of a highly accurate and fast protein-ligand docking algorithm based on molecular dynamics. 18th International Parallel and Distributed Processing Symposium, 2004. (2004). DOI: 10.1109/IPDPS.2004.1303203.

PrimeGrid

1. Bethune, Iain. PrimeGrid: a Volunteer Computing Platform for Number Theory. Annual International Conference on Computational Mathematics, Computational Geometry & Statistics (2015). DOI: 10.5176/2251-1911_CMCGS15.43.
2. Bethune, Iain Arthur and Yves Gallot. Genefer: Programs for Finding Large Probable Generalized Fermat Primes. Journal of Open Research Software (2015). DOI: 10.5334/jors.ca.
3. Bethune, Iain and Michael Goetz. Extending the Generalized Fermat Prime Number Search Beyond One Million Digits Using GPUs. Parallel Processing and Applied Mathematics (2014).

Proteins@home

1. Schmidt am Busch, Marcel, Audrey Sedano and Thomas Simonson. Computational Protein Design: Validation and Possible Relevance as a Tool for Homology Searching and Fold Recognition. PLoS ONE (2010). DOI: 10.1371/journal.pone.0010410.
2. Schmidt am Busch, Marcel, David Mignon and Thomas Simonson. Computational protein design as a tool for fold recognition. Proteins: Structure, Function, and Bioinformatics (2009). DOI: 10.1002/prot.22426.
3. Schmidt Am Busch, Marcel, Anne Lopes, David Mignon and Thomas Simonson. Computational protein design: Software implementation, parameter optimization, and performance of a simple model. Journal of Computational Chemistry (2008). DOI: 10.1002/jcc.20870.
4. am Busch, Marcel Schmidt, Anne Lopes, Najette Amara, Christine Bathelt and Thomas Simonson. Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design. BMC Bioinformatics (2008). DOI: 10.1186/1471-2105-9-148.

QMC@Home

1. Dohm, Sebastian, Eckhard Spohr and Martin Korth. Developing adaptive QM/MM computer simulations for electrochemistry. Journal of Computational Chemistry (2017). DOI: 10.1002/jcc.24513.
2. Husch, Tamara, Nusret Duygu Yilmazer, Andrea Balducci and Martin Korth. Large-scale virtual high-throughput screening for the identification of new battery electrolyte solvents: computing infrastructure and collective properties. Physical Chemistry Chemical Physics (2015). DOI: 10.1039/C4CP04338C.
3. Yilmazer, Nusret Duygu and Martin Korth. Comparison of Molecular Mechanics, Semi-Empirical Quantum Mechanical, and Density Functional Theory Methods for Scoring Protein–Ligand Interactions. The Journal of Physical Chemistry B (2013). DOI: 10.1021/jp402719k.
4. Korth, Martin, Stefan Grimme and Mike D. Towler. The Lithium–Thiophene Riddle Revisited. The Journal of Physical Chemistry A (2011). DOI: 10.1021/jp204132g.
5. Korth, Martin, Arne Lüchow and Stefan Grimme. Toward the Exact Solution of the Electronic Schrödinger Equation for Noncovalent Molecular Interactions: Worldwide Distributed Quantum Monte Carlo Calculations. The Journal of Physical Chemistry A (2008). DOI: 10.1021/jp077592t.
6. Bande, Annika and Arne Luechow. ChemInform Abstract: Vanadium Oxide Compounds with Quantum Monte Carlo. ChemInform (2008). DOI: 10.1002/chin.200839002.
7. Grimme, Stefan, Marc Steinmetz and Martin Korth. How to Compute Isomerization Energies of Organic Molecules with Quantum Chemical Methods. The Journal of Organic Chemistry (2007). DOI: 10.1021/jo062446p.

QuChemPedIA@home

1. Cauchy, Thomas, Jules Leguy and Benoit Da Mota. Definition and exploration of realistic chemical spaces using the connectivity and cyclic features of ChEMBL and ZINC. Digital Discovery (2023). DOI: 10.1039/D2DD00092J.
2. Leguy, Jules, Marta Glavatskikh, Thomas Cauchy and Benoit Da Mota. Scalable estimator of the diversity for de novo molecular generation resulting in a more robust QM dataset (OD9) and a more efficient molecular optimization. Journal of Cheminformatics (2021). DOI: 10.1186/s13321-021-00554-8.
3. Leguy, Jules, Thomas Cauchy, Marta Glavatskikh, Béatrice Duval and Benoit Da Mota. EvoMol: a flexible and interpretable evolutionary algorithm for unbiased de novo molecular generation. Journal of Cheminformatics (2020). DOI: 10.1186/s13321-020-00458-z.
4. Glavatskikh, Marta, Jules Leguy, Gilles Hunault, Thomas Cauchy and Benoit Da Mota. Dataset’s chemical diversity limits the generalizability of machine learning predictions. Journal of Cheminformatics (2019). DOI: 10.1186/s13321-019-0391-2.

Quake-Catcher Network

1. Chen, Kate Huihsuan, Wen-Tzong Liang, Chun-Hung Lin and Leon Yufeng Wu. Citizen Seismology in Taiwan: Development, Outreach, and Formative Assessment of Near-Real Time Earthquake Game Competition Activities. Frontiers in Earth Science (2020). DOI: 10.3389/feart.2020.00154.
2. Fu, Jihua, Zhitao Li, Hao Meng, Jianjun Wang and Xinjian Shan. Performance Evaluation of Low-Cost Seismic Sensors for Dense Earthquake Early Warning: 2018–2019 Field Testing in Southwest China. Sensors (2019). DOI: 10.3390/s19091999.
3. Liang, Wen-Tzong, Jian-Cheng Lee, Kate Huihsuan Chen, Nai-Chi Hsiao, Academia Sinica 128 Institute of Earth Sciences, National Taiwan Normal University Department of Earth Sciences and Central Weather Bureau Seismological Center. Citizen Earthquake Science in Taiwan: From Science to Hazard Mitigation. Journal of Disaster Research (2017). DOI: 10.20965/jdr.2017.p1174.
4. Dominguez, L. A., B. Yildirim, A. L. Husker, E. Cochran, C. Christensen, V. M. Cruz-Atienza and J. F. Lawrence. The Red Atrapa Sismos (Quake-Catcher Network in Mexico): Assessing Performance during Large and Damaging Earthquakes. Seismological Research Letters (2015). DOI: 10.1785/0220140171.
5. Dixit, Amod Mani, Adam T. Ringler, Danielle F. Sumy et al. Strong-Motion Observations of the M 7.8 Gorkha, Nepal, Earthquake Sequence and Development of the N-SHAKE Strong-Motion Network. Seismological Research Letters (2015). DOI: 10.1785/0220150146.
6. Chung, Angela I., Elizabeth S. Cochran, Anna E. Kaiser, Carl M. Christensen, Battalgazi Yildirim and Jesse F. Lawrence. Improved Rapid Magnitude Estimation for a Community‐Based, Low‐Cost MEMS Accelerometer Network. Bulletin of the Seismological Society of America (2015). DOI: 10.1785/0120140232.
7. Neighbors, C., E. J. Liao, E. S. Cochran et al. Investigation of the high-frequency attenuation parameter, κ (kappa), from aftershocks of the 2010 Mw 8.8 Maule, Chile earthquake. Geophysical Journal International (2015). DOI: 10.1093/gji/ggu390.
8. Yildirim, B., E. S. Cochran, A. Chung, C. M. Christensen and J. F. Lawrence. On the Reliability of Quake-Catcher Network Earthquake Detections. Seismological Research Letters (2015). DOI: 10.1785/0220140218.
9. Lawrence, J. F., E. S. Cochran, A. Chung et al. Rapid Earthquake Characterization Using MEMS Accelerometers and Volunteer Hosts Following the M 7.2 Darfield, New Zealand, Earthquake. Bulletin of the Seismological Society of America (2014). DOI: 10.1785/0120120196.
10. Benson, K., S. Schlachter, T. Estrada, M. Taufer, J. Lawrence and E. Cochran. On the powerful use of simulations in the Quake-Catcher Network to efficiently position low-cost earthquake sensors. Future Generation Computer Systems (2013). DOI: 10.1016/j.future.2013.04.012.
11. Chung, A. I., C. Neighbors, A. Belmonte et al. The Quake-Catcher Network Rapid Aftershock Mobilization Program Following the 2010 M 8.8 Maule, Chile Earthquake. Seismological Research Letters (2011). DOI: 10.1785/gssrl.82.4.526.
12. Cochran, Elizabeth S., Jesse F. Lawrence, Carl Christensen and Ravi S. Jakka. The Quake-Catcher Network: Citizen Science Expanding Seismic Horizons. Seismological Research Letters (2009). DOI: 10.1785/gssrl.80.1.26.
13. Cochran, Elizabeth, Jesse Lawrence, Carl Christensen and Angela Chung. A novel strong-motion seismic network for community participation in earthquake monitoring. IEEE Instrumentation & Measurement Magazine (2009). DOI: 10.1109/MIM.2009.5338255.

RNA World (beta)

1. Hoch, Philipp G., Olga Y. Burenina, Michael H.W. Weber, Daria A. Elkina, Mikhail V. Nesterchuk, Petr V. Sergiev, Roland K. Hartmann and Elena A. Kubareva. Phenotypic characterization and complementation analysis of Bacillus subtilis 6S RNA single and double deletion mutants. Biochimie (2015). DOI: 10.1016/j.biochi.2014.12.019.
2. Sinha, Akesh, Caroline Köhrer, Michael H.W. Weber, Isao Masuda, Vamsi K. Mootha, Ya-Ming Hou and Uttam L. RajBhandary. Biochemical Characterization of Pathogenic Mutations in Human Mitochondrial Methionyl-tRNA Formyltransferase. Journal of Biological Chemistry (2014). DOI: 10.1074/jbc.M114.610626.
3. Arora, Smriti, Satya Prathyusha Bhamidimarri, Michael H. W. Weber and Umesh Varshney. Role of the Ribosomal P-Site Elements of m ² G966, m ⁵ C967, and the S9 C-Terminal Tail in Maintenance of the Reading Frame during Translational Elongation in Escherichia coli. Journal of Bacteriology (2013). DOI: 10.1128/JB.00455-13.
4. Arora, S., S. P. Bhamidimarri, M. Bhattacharyya, A. Govindan, M. H. W. Weber, S. Vishveshwara and U. Varshney. Distinctive contributions of the ribosomal P-site elements m2G966, m5C967 and the C-terminal tail of the S9 protein in the fidelity of initiation of translation in Escherichia coli. Nucleic Acids Research (2013). DOI: 10.1093/nar/gkt175.
5. Seshadri, Anuradha, Badrinath Dubey, Michael H. W. Weber and Umesh Varshney. Impact of rRNA methylations on ribosome recycling and fidelity of initiation in Escherichia coli. Molecular Microbiology (2009). DOI: 10.1111/j.1365-2958.2009.06685.x.

Rakesearch

1. Vatutin, Eduard, Oleg Zaikin, Maxim Manzyuk and Natalia Nikitina. Searching for Orthogonal Latin Squares via Cells Mapping and BOINC-Based Cube-and-Conquer. (2021). DOI: 10.1007/978-3-030-92864-3_38.
2. Vatutin, Eduard and Alexey Belyshev. Enumerating the Orthogonal Diagonal Latin Squares of Small Order for Different Types of Orthogonality. (2020). DOI: 10.1007/978-3-030-64616-5_50.
3. Ivashko, Evgeny and Natalia Nikitina. Replication of “Tail” Computations in a Desktop Grid Project. (2020). DOI: 10.1007/978-3-030-64616-5_52.
4. Manzyuk, Maxim, Natalia Nikitina and Eduard Vatutin. Start-up and the Results of the Volunteer Computing Project RakeSearch. (2019). DOI: 10.1007/978-3-030-36592-9_59.

Rosetta@home

1. Roy, Anindya, Lei Shi, Ashley Chang et al. De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8. (2023).
2. Kim, David E., Davin R. Jensen, David Feldman et al. De novo design of small beta barrel proteins. Proceedings of the National Academy of Sciences (2023). DOI: 10.1073/pnas.2207974120.
3. Rettie, Stephen A., Katelyn V. Campbell, Asim K. Bera et al. Cyclic peptide structure prediction and design using AlphaFold. (2023).
4. Wu, Kejia, Hua Bai, Ya-Ting Chang et al. De novo design of modular peptide-binding proteins by superhelical matching. Nature (2023). DOI: 10.1038/s41586-023-05909-9.
5. Courbet, A., J. Hansen, Y. Hsia et al. Computational design of mechanically coupled axle-rotor protein assemblies. Science (2022). DOI: 10.1126/science.abm1183.
6. Hunt, Andrew C., James Brett Case, Young-Jun Park et al. Multivalent designed proteins protect against SARS-CoV-2 variants of concern. (2021). DOI: 10.1101/2021.07.07.451375.
7. Norn, Christoffer, Basile I. M. Wicky, David Juergens et al. Protein sequence design by conformational landscape optimization. Proceedings of the National Academy of Sciences (2021). DOI: 10.1073/pnas.2017228118.
8. Hsia, Yang, Rubul Mout, William Sheffler et al. Design of multi-scale protein complexes by hierarchical building block fusion. Nature Communications (2021). DOI: 10.1038/s41467-021-22276-z.
9. Quijano-Rubio, Alfredo, Hsien-Wei Yeh, Jooyoung Park et al. De novo design of modular and tunable protein biosensors. Nature (2021). DOI: 10.1038/s41586-021-03258-z.
10. Leman, Julia Koehler, Brian D. Weitzner, P. Douglas Renfrew et al. Better together: Elements of successful scientific software development in a distributed collaborative community. PLOS Computational Biology (2020). DOI: 10.1371/journal.pcbi.1007507.
11. Brunette, Tj, Matthew J. Bick, Jesse M. Hansen, Cameron M. Chow, Justin M. Kollman and David Baker. Modular repeat protein sculpting using rigid helical junctions. Proceedings of the National Academy of Sciences (2020). DOI: 10.1073/pnas.1908768117.
12. Wei, Kathy Y., Danai Moschidi, Matthew J. Bick et al. Computational design of closely related proteins that adopt two well-defined but structurally divergent folds. Proceedings of the National Academy of Sciences (2020). DOI: 10.1073/pnas.1914808117.
13. Mulligan, Vikram Khipple, Christine S. Kang, Michael R. Sawaya et al. Computational design of mixed chirality peptide macrocycles with internal symmetry. Protein Science (2020). DOI: 10.1002/pro.3974.
14. Cao, Longxing, Inna Goreshnik, Brian Coventry et al. De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Science (2020). DOI: 10.1126/science.abd9909.
15. Yang, Jianyi, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov and David Baker. Improved protein structure prediction using predicted interresidue orientations. Proceedings of the National Academy of Sciences (2020). DOI: 10.1073/pnas.1914677117.
16. Pyles, Harley, Shuai Zhang, James J. De Yoreo and David Baker. Controlling protein assembly on inorganic crystals through designed protein interfaces. Nature (2019). DOI: 10.1038/s41586-019-1361-6.
17. Silva, Daniel-Adriano, Shawn Yu, Umut Ulge et al. De novo design of potent and selective mimics of IL-2 and IL-15. Nature (2019). DOI: 10.1038/s41586-018-0830-7.
18. Cong, Qian, Ivan Anishchenko, Sergey Ovchinnikov and David Baker. Protein interaction networks revealed by proteome coevolution. Science (2019). DOI: 10.1126/science.aaw6718.
19. Shen, Hao, Jorge A. Fallas, Eric Lynch et al. De novo design of self-assembling helical protein filaments. Science (2018). DOI: 10.1126/science.aau3775.
20. Lu, Peilong, Duyoung Min, Frank DiMaio et al. Accurate computational design of multipass transmembrane proteins. Science (2018). DOI: 10.1126/science.aaq1739.
21. Dou, Jiayi, Anastassia A. Vorobieva, William Sheffler et al. De novo design of a fluorescence-activating β-barrel. Nature (2018). DOI: 10.1038/s41586-018-0509-0.
22. Ovchinnikov, Sergey, Hahnbeom Park, David E. Kim, Frank DiMaio and David Baker. Protein structure prediction using Rosetta in CASP12. Proteins: Structure, Function, and Bioinformatics (2018). DOI: 10.1002/prot.25390.
23. Marcos, Enrique, Tamuka M. Chidyausiku, Andrew C. McShan et al. De novo design of a non-local β-sheet protein with high stability and accuracy. Nature Structural & Molecular Biology (2018). DOI: 10.1038/s41594-018-0141-6.
24. Park, Hahnbeom, David E. Kim, Sergey Ovchinnikov, David Baker and Frank DiMaio. Automatic structure prediction of oligomeric assemblies using Robetta in CASP12. Proteins: Structure, Function, and Bioinformatics (2018). DOI: 10.1002/prot.25387.
25. Ovchinnikov, Sergey, Hahnbeom Park, Neha Varghese et al. Protein structure determination using metagenome sequence data. Science (2017). DOI: 10.1126/science.aah4043.
26. Hosseinzadeh, Parisa, Gaurav Bhardwaj, Vikram Khipple Mulligan et al. Comprehensive computational design of ordered peptide macrocycles. Science (2017). DOI: 10.1126/science.aap7577.
27. Rocklin, Gabriel J., Tamuka M. Chidyausiku, Inna Goreshnik et al. Global analysis of protein folding using massively parallel design, synthesis, and testing. Science (2017). DOI: 10.1126/science.aan0693.
28. Hsia, Yang, Jacob B. Bale, Shane Gonen et al. Design of a hyperstable 60-subunit protein icosahedron. Nature (2016). DOI: 10.1038/nature18010.
29. Ovchinnikov, Sergey, David E. Kim, Ray Yu-Ruei Wang, Yuan Liu, Frank DiMaio and David Baker. Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta. Proteins: Structure, Function, and Bioinformatics (2016). DOI: 10.1002/prot.24974.
30. Huang, Po-Ssu, Kaspar Feldmeier, Fabio Parmeggiani, D. Alejandro Fernandez Velasco, Birte Höcker and David Baker. De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nature Chemical Biology (2016). DOI: 10.1038/nchembio.1966.
31. Boyken, Scott E., Zibo Chen, Benjamin Groves et al. De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity. Science (2016). DOI: 10.1126/science.aad8865.
32. Bhardwaj, Gaurav, Vikram Khipple Mulligan, Christopher D. Bahl et al. Accurate de novo design of hyperstable constrained peptides. Nature (2016). DOI: 10.1038/nature19791.
33. Bale, Jacob B., Shane Gonen, Yuxi Liu et al. Accurate design of megadalton-scale two-component icosahedral protein complexes. Science (2016). DOI: 10.1126/science.aaf8818.
34. Antala, Sagar, Sergey Ovchinnikov, Hetunandan Kamisetty, David Baker and Robert E. Dempski. Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4 *. Journal of Biological Chemistry (2015). DOI: 10.1074/jbc.M114.617613.
35. Brunette, T. J., Fabio Parmeggiani, Po-Ssu Huang et al. Exploring the repeat protein universe through computational protein design. Nature (2015). DOI: 10.1038/nature16162.
36. Pearson, A. D., J. H. Mills, Y. Song, F. Nasertorabi, G. W. Han, D. Baker, R. C. Stevens and P. G. Schultz. Trapping a transition state in a computationally designed protein bottle. Science (2015). DOI: 10.1126/science.aaa2424.
37. Ovchinnikov, Sergey, Lisa Kinch, Hahnbeom Park et al. Large-scale determination of previously unsolved protein structures using evolutionary information. eLife (2015). DOI: 10.7554/eLife.09248.
38. Park, Keunwan, Betty W. Shen, Fabio Parmeggiani, Po-Ssu Huang, Barry L. Stoddard and David Baker. Control of repeat-protein curvature by computational protein design. Nature Structural & Molecular Biology (2015). DOI: 10.1038/nsmb.2938.
39. Siegel, Justin B., Amanda Lee Smith, Sean Poust et al. Computational protein design enables a novel one-carbon assimilation pathway. Proceedings of the National Academy of Sciences (2015). DOI: 10.1073/pnas.1500545112.
40. Parmeggiani, Fabio, Po-Ssu Huang, Sergey Vorobiev et al. A General Computational Approach for Repeat Protein Design. Journal of Molecular Biology (2015). DOI: 10.1016/j.jmb.2014.11.005.
41. King, Neil P., Jacob B. Bale, William Sheffler, Dan E. McNamara, Shane Gonen, Tamir Gonen, Todd O. Yeates and David Baker. Accurate design of co-assembling multi-component protein nanomaterials. Nature (2014). DOI: 10.1038/nature13404.
42. Strauch, Eva-Maria, Sarel J. Fleishman and David Baker. Computational design of a pH-sensitive IgG binding protein. Proceedings of the National Academy of Sciences (2014). DOI: 10.1073/pnas.1313605111.
43. Griss, Rudolf, Alberto Schena, Luc Reymond, Luc Patiny, Dominique Werner, Christine E. Tinberg, David Baker and Kai Johnsson. Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring. Nature Chemical Biology (2014). DOI: 10.1038/nchembio.1554.
44. Ovchinnikov, Sergey, Hetunandan Kamisetty and David Baker. Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information. eLife (2014). DOI: 10.7554/eLife.02030.
45. Baker, David. Protein folding, structure prediction and design. Biochemical Society Transactions (2014). DOI: 10.1042/BST20130055.
46. King, Chris, Esteban N. Garza, Ronit Mazor, Jonathan L. Linehan, Ira Pastan, Marion Pepper and David Baker. Removing T-cell epitopes with computational protein design. Proceedings of the National Academy of Sciences (2014). DOI: 10.1073/pnas.1321126111.
47. Huang, Po-Ssu, Gustav Oberdorfer, Chunfu Xu et al. High thermodynamic stability of parametrically designed helical bundles. Science (2014). DOI: 10.1126/science.1257481.
48. Kim, David E., Frank DiMaio, Ray Yu-Ruei Wang, Yifan Song and David Baker. One contact for every twelve residues allows robust and accurate topology-level protein structure modeling: Contact Guided Protein Structure Prediction. Proteins: Structure, Function, and Bioinformatics (2014). DOI: 10.1002/prot.24374.
49. Conway, Patrick, Michael D. Tyka, Frank DiMaio, David E. Konerding and David Baker. Relaxation of backbone bond geometry improves protein energy landscape modeling: Relaxation of Backbone Bond Geometry. Protein Science (2014). DOI: 10.1002/pro.2389.
50. Cherny, Izhack, Per Greisen, Yacov Ashani, Sagar D. Khare, Gustav Oberdorfer, Haim Leader, David Baker and Dan S. Tawfik. Engineering V-Type Nerve Agents Detoxifying Enzymes Using Computationally Focused Libraries. ACS Chemical Biology (2013). DOI: 10.1021/cb4004892.
51. Adams, Paul D., David Baker, Axel T. Brunger et al. Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems. Annual Review of Biophysics (2013). DOI: 10.1146/annurev-biophys-083012-130253.
52. Song, Yifan, Frank DiMaio, Ray Yu-Ruei Wang, David Kim, Chris Miles, T. J. Brunette, James Thompson and David Baker. High-Resolution Comparative Modeling with RosettaCM. Structure (2013). DOI: 10.1016/j.str.2013.08.005.
53. DiMaio, Frank, Nathaniel Echols, Jeffrey J. Headd, Thomas C. Terwilliger, Paul D. Adams and David Baker. Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nature Methods (2013). DOI: 10.1038/nmeth.2648.
54. King, Neil P., William Sheffler, Michael R. Sawaya et al. Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy. Science (2012). DOI: 10.1126/science.1219364.
55. Khare, Sagar D., Yakov Kipnis, Per Jr Greisen et al. Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nature Chemical Biology (2012). DOI: 10.1038/nchembio.777.
56. Azoitei, Mihai L., Yih-En Andrew Ban, Jean-Philippe Julien et al. Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope. Journal of Molecular Biology (2012). DOI: 10.1016/j.jmb.2011.10.003.
57. Terwilliger, Thomas C., Frank DiMaio, Randy J. Read et al. phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. Journal of Structural and Functional Genomics (2012). DOI: 10.1007/s10969-012-9129-3.
58. Tyka, Michael D., Kenneth Jung and David Baker. Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. Journal of Computational Chemistry (2012). DOI: 10.1002/jcc.23069.
59. Lange, Oliver F., Paolo Rossi, Nikolaos G. Sgourakis et al. Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. Proceedings of the National Academy of Sciences (2012). DOI: 10.1073/pnas.1203013109.
60. Wodak, Shoshana J. Next-generation protein engineering targets influenza. Nature Biotechnology (2012). DOI: 10.1038/nbt.2268.
61. Kellogg, Elizabeth H., Andrew Leaver-Fay and David Baker. Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins: Structure, Function, and Bioinformatics (2011). DOI: 10.1002/prot.22921.
62. Fleishman, Sarel J., Sagar D. Khare, Nobuyasu Koga and David Baker. Restricted sidechain plasticity in the structures of native proteins and complexes: Restricted Sidechain Plasticity. Protein Science (2011). DOI: 10.1002/pro.604.
63. Li, Mi, Frank DiMaio, Dongwen Zhou, Alla Gustchina, Jacek Lubkowski, Zbigniew Dauter, David Baker and Alexander Wlodawer. Crystal structure of XMRV protease differs from the structures of other retropepsins. Nature Structural & Molecular Biology (2011). DOI: 10.1038/nsmb.1964.
64. Chen, Dong-Hua, Matthew L. Baker, Corey F. Hryc et al. Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proceedings of the National Academy of Sciences (2011). DOI: 10.1073/pnas.1015739108.
65. Khersonsky, Olga, Daniela Röthlisberger, Andrew M. Wollacott et al. Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution. Journal of Molecular Biology (2011). DOI: 10.1016/j.jmb.2011.01.041.
66. Windbichler, Nikolai, Miriam Menichelli, Philippos Aris Papathanos et al. A synthetic homing endonuclease-based gene drive system in the human malaria mosquito. Nature (2011). DOI: 10.1038/nature09937.
67. Leaver-Fay, Andrew, Michael Tyka, Steven M. Lewis et al. Rosetta3. Methods in Enzymology (2011).
68. Tyka, Michael D., Daniel A. Keedy, Ingemar André, Frank DiMaio, Yifan Song, David C. Richardson, Jane S. Richardson and David Baker. Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping. Journal of Molecular Biology (2011). DOI: 10.1016/j.jmb.2010.11.008.
69. Ulge, Umut Y., David A. Baker and Raymond J. Monnat. Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering. Nucleic Acids Research (2011). DOI: 10.1093/nar/gkr022.
70. Sgourakis, Nikolaos G., Oliver F. Lange, Frank DiMaio et al. Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings. Journal of the American Chemical Society (2011). DOI: 10.1021/ja111318m.
71. DiMaio, Frank, Thomas C. Terwilliger, Randy J. Read et al. Improved molecular replacement by density- and energy-guided protein structure optimization. Nature (2011). DOI: 10.1038/nature09964.
72. Guenaga, Javier, Pia Dosenovic, Gilad Ofek, David Baker, William R. Schief, Peter D. Kwong, Gunilla B. Karlsson Hedestam and Richard T. Wyatt. Heterologous Epitope-Scaffold Prime∶Boosting Immuno-Focuses B Cell Responses to the HIV-1 gp41 2F5 Neutralization Determinant. PLOS ONE (2011). DOI: 10.1371/journal.pone.0016074.
73. Fleishman, Sarel J., Timothy A. Whitehead, Damian C. Ekiert, Cyrille Dreyfus, Jacob E. Corn, Eva-Maria Strauch, Ian A. Wilson and David Baker. Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin. Science (2011). DOI: 10.1126/science.1202617.
74. Sanowar, Sarah, Pragya Singh, Richard A. Pfuetzner et al. Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System. mBio (2010). DOI: 10.1128/mBio.00158-10.
75. Sheffler, William and David Baker. RosettaHoles2: A volumetric packing measure for protein structure refinement and validation: RosettaHoles2 for Protein Structure. Protein Science (2010). DOI: 10.1002/pro.458.
76. Fowler, Douglas M., Carlos L. Araya, Sarel J. Fleishman, Elizabeth H. Kellogg, Jason J. Stephany, David Baker and Stanley Fields. High-resolution mapping of protein sequence-function relationships. Nature Methods (2010). DOI: 10.1038/nmeth.1492.
77. Ofek, Gilad, F. Javier Guenaga, William R. Schief, Jeff Skinner, David Baker, Richard Wyatt and Peter D. Kwong. Elicitation of structure-specific antibodies by epitope scaffolds. Proceedings of the National Academy of Sciences (2010). DOI: 10.1073/pnas.1004728107.
78. Wang, Chu, Robert Vernon, Oliver Lange, Michael Tyka and David Baker. Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry: Structure Prediction of Zinc-Binding Proteins. Protein Science (2010). DOI: 10.1002/pro.327.
79. Tang, Yuefeng, William M. Schneider, Yang Shen, Srivatsan Raman, Masayori Inouye, David Baker, Monica J. Roth and Gaetano T. Montelione. Fully automated high-quality NMR structure determination of small 2H-enriched proteins. Journal of Structural and Functional Genomics (2010). DOI: 10.1007/s10969-010-9095-6.
80. Das, Rhiju, John Karanicolas and David Baker. Atomic accuracy in predicting and designing noncanonical RNA structure. Nature Methods (2010). DOI: 10.1038/nmeth.1433.
81. Ashworth, Justin, Gregory K. Taylor, James J. Havranek, S. Arshiya Quadri, Barry L. Stoddard and David Baker. Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Research (2010). DOI: 10.1093/nar/gkq283.
82. Blum, Ben, Michael I. Jordan and David Baker. Feature space resampling for protein conformational search. Proteins: Structure, Function, and Bioinformatics (2010). DOI: 10.1002/prot.22677.
83. Correia, Bruno E., Yih-En Andrew Ban, Margaret A. Holmes et al. Computational Design of Epitope-Scaffolds Allows Induction of Antibodies Specific for a Poorly Immunogenic HIV Vaccine Epitope. Structure (2010). DOI: 10.1016/j.str.2010.06.010.
84. Baker, David. An exciting but challenging road ahead for computational enzyme design. Protein Science (2010). DOI: 10.1002/pro.481.
85. Siegel, Justin B., Alexandre Zanghellini, Helena M. Lovick et al. Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction. Science (2010). DOI: 10.1126/science.1190239.
86. Weerapana, Eranthie, Chu Wang, Gabriel M. Simon et al. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature (2010). DOI: 10.1038/nature09472.
87. Raman, Srivatsan, Oliver F. Lange, Paolo Rossi et al. NMR Structure Determination for Larger Proteins Using Backbone-Only Data. Science (2010). DOI: 10.1126/science.1183649.
88. Cooper, Seth, David Baker, Zoran Popović et al. The challenge of designing scientific discovery games. the Fifth International Conference (2010). DOI: 10.1145/1822348.1822354.
89. Sampathkumar, Parthasarathy, Frances Lu, Xun Zhao et al. Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 Å resolution: Structure of a Putative Benzoate Specific Porin. Proteins: Structure, Function, and Bioinformatics (2010). DOI: 10.1002/prot.22829.
90. Raman, Srivatsan, Yuanpeng J. Huang, Binchen Mao, Paolo Rossi, James M. Aramini, Gaohua Liu, Gaetano T. Montelione and David Baker. Accurate Automated Protein NMR Structure Determination Using Unassigned NOESY Data. Journal of the American Chemical Society (2010). DOI: 10.1021/ja905934c.
91. Liu, Lingfeng, Paul Murphy, David Baker and Stefan Lutz. Computational design of orthogonal nucleoside kinases. Chem. Commun. (2010). DOI: 10.1039/C0CC02961K.
92. Fleishman, Sarel J., Jacob E. Corn, Eva M. Strauch et al. Rosetta in CAPRI rounds 13-19: Rosetta in CAPRI Rounds 13-19. Proteins: Structure, Function, and Bioinformatics (2010). DOI: 10.1002/prot.22784.
93. Kiss, Gert, Daniela Röthlisberger, David Baker and K. N. Houk. Evaluation and ranking of enzyme designs. Protein Science (2010). DOI: 10.1002/pro.462.
94. Kim, David E., Ben Blum, Philip Bradley and David Baker. Sampling Bottlenecks in De novo Protein Structure Prediction. Journal of Molecular Biology (2009). DOI: 10.1016/j.jmb.2009.07.063.
95. Havranek, James J. and David Baker. Motif-directed flexible backbone design of functional interactions. Protein Science (2009). DOI: 10.1002/pro.142.
96. Luo, Bing-Hao, John Karanicolas, Laura D. Harmacek, David Baker and Timothy A. Springer. Rationally Designed Integrin β3 Mutants Stabilized in the High Affinity Conformation. Journal of Biological Chemistry (2009). DOI: 10.1074/jbc.M806312200.
97. Sadreyev, R. I., S. Shi, D. Baker and N. V. Grishin. Structure similarity measure with penalty for close non-equivalent residues. Bioinformatics (2009). DOI: 10.1093/bioinformatics/btp148.
98. Raman, Srivatsan, Robert Vernon, James Thompson et al. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins: Structure, Function, and Bioinformatics (2009). DOI: 10.1002/prot.22540.
99. Krieger, Elmar, Keehyoung Joo, Jinwoo Lee et al. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins: Structure, Function, and Bioinformatics (2009). DOI: 10.1002/prot.22570.
100. Ashworth, Justin and David Baker. Assessment of the optimization of affinity and specificity at protein–DNA interfaces. Nucleic Acids Research (2009). DOI: 10.1093/nar/gkp242.
101. Zhu, Jieqing, Bing-Hao Luo, Patrick Barth, Jack Schonbrun, David Baker and Timothy A. Springer. The Structure of a Receptor with Two Associating Transmembrane Domains on the Cell Surface: Integrin αIIbβ3. Molecular Cell (2009). DOI: 10.1016/j.molcel.2009.02.022.
102. Barth, P., B. Wallner and D. Baker. Prediction of membrane protein structures with complex topologies using limited constraints. Proceedings of the National Academy of Sciences (2009). DOI: 10.1073/pnas.0808323106.
103. DiMaio, Frank, Michael D. Tyka, Matthew L. Baker, Wah Chiu and David Baker. Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta. Journal of Molecular Biology (2009). DOI: 10.1016/j.jmb.2009.07.008.
104. Shen, Yang, Robert Vernon, David Baker and Ad Bax. De novo protein structure generation from incomplete chemical shift assignments. Journal of Biomolecular NMR (2009). DOI: 10.1007/s10858-008-9288-5.
105. Kidd, Brian A., David Baker and Wendy E. Thomas. Computation of Conformational Coupling in Allosteric Proteins. PLoS Computational Biology (2009). DOI: 10.1371/journal.pcbi.1000484.
106. Thyme, Summer B., Jordan Jarjour, Ryo Takeuchi, James J. Havranek, Justin Ashworth, Andrew M. Scharenberg, Barry L. Stoddard and David Baker. Exploitation of binding energy for catalysis and design. Nature (2009). DOI: 10.1038/nature08508.
107. Das, Rhiju, Ingemar André, Yang Shen et al. Simultaneous prediction of protein folding and docking at high resolution. Proceedings of the National Academy of Sciences of the United States of America (2009). DOI: 10.1073/pnas.0904407106.
108. Das, Rhiju and David Baker. Prospects for de novo phasing with de novo protein models. Acta Crystallographica Section D: Biological Crystallography (2009). DOI: 10.1107/S0907444908020039.
109. Murphy, Paul M., Jill M. Bolduc, Jasmine L. Gallaher, Barry L. Stoddard and David Baker. Alteration of enzyme specificity by computational loop remodeling and design. Proceedings of the National Academy of Sciences (2009). DOI: 10.1073/pnas.0811070106.
110. Muratore, Kathryn E., Markus A. Seeliger, Zhihong Wang et al. Comparative Analysis of Mutant Tyrosine Kinase Chemical Rescue. Biochemistry (2009). DOI: 10.1021/bi900057g.
111. Rosato, Antonio, Anurag Bagaria, David Baker et al. CASD-NMR: critical assessment of automated structure determination by NMR. Nature Methods (2009). DOI: 10.1038/nmeth0909-625.
112. Davis, Ian W., Kaushik Raha, Martha S. Head and David Baker. Blind docking of pharmaceutically relevant compounds using RosettaLigand. Protein Science (2009). DOI: 10.1002/pro.192.
113. Ban, YA, BE Correia, M. Holmes et al. P05-09. 4e10 epitope-scaffolds mimic the antibody-bound epitope conformation and block neutralization by sera from rare HIV+ individuals. Retrovirology (2009). DOI: 10.1186/1742-4690-6-S3-P85.
114. Shen, Yang, Oliver Lange, Frank Delaglio et al. Consistent blind protein structure generation from NMR chemical shift data. Proceedings of the National Academy of Sciences of the United States of America (2008). DOI: 10.1073/pnas.0800256105.
115. Das, Rhiju and David Baker. Macromolecular Modeling with Rosetta. Annual Review of Biochemistry (2008). DOI: 10.1146/annurev.biochem.77.062906.171838.
116. McBeth, Christine, Audrey Seamons, Juan C. Pizarro, Sarel J. Fleishman, David Baker, Tanja Kortemme, Joan M. Goverman and Roland K. Strong. A New Twist in TCR Diversity Revealed by a Forbidden αβ TCR. Journal of Molecular Biology (2008). DOI: https://doi.org/10.1016/j.jmb.2007.11.020.
117. Röthlisberger, Daniela, Olga Khersonsky, Andrew M. Wollacott et al. Kemp elimination catalysts by computational enzyme design. Nature (2008). DOI: 10.1038/nature06879.
118. Sheffler, Will and David Baker. RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design and validation. Protein Science (2008). DOI: 10.1002/pro.8.
119. Keeble, Anthony H., Lukasz A. Joachimiak, María Jesus Maté, Nicola Meenan, Nadine Kirkpatrick, David Baker and Colin Kleanthous. Experimental and Computational Analyses of the Energetic Basis for Dual Recognition of Immunity Proteins by Colicin Endonucleases. Journal of Molecular Biology (2008). DOI: 10.1016/j.jmb.2008.03.055.
120. Raman, S., B. Qian, D. Baker and R. C. Walker. Advances in Rosetta protein structure prediction on massively parallel systems. IBM Journal of Research and Development (2008). DOI: 10.1147/rd.521.0007.
121. Fan, Erkang, David Baker, Stanley Fields et al. Structural Genomics of Pathogenic Protozoa: an Overview. Structural Proteomics (2008).
122. Das, Rhiju, Madhuri Kudaravalli, Magdalena Jonikas et al. Structural inference of native and partially folded RNA by high-throughput contact mapping. Proceedings of the National Academy of Sciences of the United States of America (2008). DOI: 10.1073/pnas.0709032105.
123. Alexandrova, Anastassia N., Daniela Röthlisberger, David Baker and William L. Jorgensen. Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination. Journal of the American Chemical Society (2008). DOI: 10.1021/ja804040s.
124. Jiang, Lin, Eric A. Althoff, Fernando R. Clemente et al. De Novo Computational Design of Retro-Aldol Enzymes. Science (New York, N.Y.) (2008). DOI: 10.1126/science.1152692.
125. André, Ingemar, Charlie E. M. Strauss, David B. Kaplan, Philip Bradley and David Baker. Emergence of symmetry in homooligomeric biological assemblies. Proceedings of the National Academy of Sciences (2008). DOI: 10.1073/pnas.0807576105.
126. Qiu, Jian, Will Sheffler, David Baker and William Stafford Noble. Ranking predicted protein structures with support vector regression. Proteins: Structure, Function, and Bioinformatics (2007). DOI: 10.1002/prot.21809.
127. Das, Rhiju, Bin Qian, Srivatsan Raman et al. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins (2007). DOI: 10.1002/prot.21636.
128. Das, Rhiju and David Baker. Automated de novo prediction of native-like RNA tertiary structures. Proceedings of the National Academy of Sciences (2007). DOI: 10.1073/pnas.0703836104.
129. Knight, James D. R., Bin Qian, David Baker and Rashmi Kothary. Conservation, Variability and the Modeling of Active Protein Kinases. PLOS ONE (2007). DOI: 10.1371/journal.pone.0000982.
130. Wojtowicz, Woj M., Wei Wu, Ingemar Andre, Bin Qian, David Baker and S. Lawrence Zipursky. A Vast Repertoire of Dscam Binding Specificities Arises from Modular Interactions of Variable Ig Domains. Cell (2007). DOI: 10.1016/j.cell.2007.08.026.
131. Wang, Chu, Philip Bradley and David Baker. Protein–Protein Docking with Backbone Flexibility. Journal of Molecular Biology (2007). DOI: 10.1016/j.jmb.2007.07.050.
132. Stankunas, Kryn, J. Henri Bayle, James J. Havranek, Thomas J. Wandless, David Baker, Gerald R. Crabtree and Jason E. Gestwicki. Rescue of Degradation-Prone Mutants of the FK506-Rapamycin Binding (FRB) Protein with Chemical Ligands. ChemBioChem (2007). DOI: 10.1002/cbic.200700087.
133. Qian, Bin, Srivatsan Raman, Rhiju Das, Philip Bradley, Airlie J. McCoy, Randy J. Read and David Baker. High-resolution structure prediction and the crystallographic phase problem. Nature (2007). DOI: 10.1038/nature06249.
134. Lengyel, Candice S.E., Lindsey J. Willis, Patrick Mann, David Baker, Tanja Kortemme, Roland K. Strong and Benjamin J. McFarland. Mutations Designed to Destabilize the Receptor-Bound Conformation Increase MICA-NKG2D Association Rate and Affinity. Journal of Biological Chemistry (2007). DOI: 10.1074/jbc.M704513200.
135. Watters, Alexander L., Pritilekha Deka, Colin Corrent, David Callender, Gabriele Varani, Tobin Sosnick and David Baker. The Highly Cooperative Folding of Small Naturally Occurring Proteins Is Likely the Result of Natural Selection. Cell (2007). DOI: 10.1016/j.cell.2006.12.042.
136. Goobes, Gil, Rivka Goobes, Wendy J. Shaw et al. The structure, dynamics, and energetics of protein adsorption—lessons learned from adsorption of statherin to hydroxyapatite. Magnetic Resonance in Chemistry (2007). DOI: 10.1002/mrc.2123.
137. Barth, P., J. Schonbrun and D. Baker. Toward high-resolution prediction and design of transmembrane helical protein structures. Proceedings of the National Academy of Sciences (2007). DOI: 10.1073/pnas.0702515104.
138. Ozer, Stuart, David Kim and David Baker. Reporting@Home: Delivering Dynamic Graphical Feedback to Participants and Researchers in Community Computing Projects. (2007).
139. Jauch, Ralf, Hock Chuan Yeo, Prasanna R. Kolatkar and Neil D. Clarke. Assessment of CASP7 structure predictions for template free targets. Proteins: Structure, Function, and Bioinformatics (2007). DOI: 10.1002/prot.21771.
140. André, Ingemar, Philip Bradley, Chu Wang and David Baker. Prediction of the structure of symmetrical protein assemblies. Proceedings of the National Academy of Sciences (2007). DOI: 10.1073/pnas.0702626104.
141. Tress, Michael, Jianlin Cheng, Pierre Baldi et al. Assessment of predictions submitted for the CASP7 domain prediction category. Proteins: Structure, Function, and Bioinformatics (2007). DOI: 10.1002/prot.21675.
142. Dantas, Gautam, Colin Corrent, Steve L. Reichow et al. High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design. Journal of Molecular Biology (2007). DOI: 10.1016/j.jmb.2006.11.080.
143. Shcherbata, Halyna R, Andriy S Yatsenko, Larissa Patterson, Vanita D Sood, Uri Nudel, David Yaffe, David Baker and Hannele Ruohola-Baker. Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy. The EMBO Journal (2007). DOI: 10.1038/sj.emboj.7601503.
144. Wollacott, Andrew M., Alexandre Zanghellini, Paul Murphy and David Baker. Prediction of structures of multidomain proteins from structures of the individual domains. Protein Science: A Publication of the Protein Society (2007). DOI: 10.1110/ps.062270707.
145. Windbichler, Nikolai, Philippos Aris Papathanos, Flaminia Catteruccia, Hilary Ranson, Austin Burt and Andrea Crisanti. Homing endonuclease mediated gene targeting in Anopheles gambiae cells and embryos. Nucleic Acids Research (2007). DOI: 10.1093/nar/gkm632.
146. Wang, Chu, Ora Schueler-Furman, Ingemar Andre, Nir London, Sarel J. Fleishman, Philip Bradley, Bin Qian and David Baker. RosettaDock in CAPRI rounds 6-12. Proteins: Structure, Function, and Bioinformatics (2007). DOI: 10.1002/prot.21684.
147. Tsemekhman, Kiril, Lukasz Goldschmidt, David Eisenberg and David Baker. Cooperative hydrogen bonding in amyloid formation. Protein Science (2007). DOI: 10.1110/ps.062609607.
148. Malmström, Lars, Michael Riffle, Charlie E. M. Strauss, Dylan Chivian, Trisha N. Davis, Richard Bonneau and David Baker. Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS biology (2007). DOI: 10.1371/journal.pbio.0050076.
149. Kopp, Jürgen, Lorenza Bordoli, James N.D. Battey, Florian Kiefer and Torsten Schwede. Assessment of CASP7 predictions for template-based modeling targets. Proteins: Structure, Function, and Bioinformatics (2007). DOI: 10.1002/prot.21753.
150. Morozov, Alexandre V., Kiril Tsemekhman and David Baker. Electron Density Redistribution Accounts for Half the Cooperativity of α Helix Formation. The Journal of Physical Chemistry B (2006). DOI: 10.1021/jp057161f.
151. Chivian, Dylan and David Baker. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Research (2006). DOI: 10.1093/nar/gkl480.
152. Palmer, Amy E., Marta Giacomello, Tanja Kortemme, S. Andrew Hires, Varda Lev-Ram, David Baker and Roger Y. Tsien. Ca2+ Indicators Based on Computationally Redesigned Calmodulin-Peptide Pairs. Chemistry & Biology (2006). DOI: 10.1016/j.chembiol.2006.03.007.
153. Joachimiak, Lukasz A., Tanja Kortemme, Barry L. Stoddard and David Baker. Computational Design of a New Hydrogen Bond Network and at Least a 300-fold Specificity Switch at a Protein−Protein Interface. Journal of Molecular Biology (2006). DOI: 10.1016/j.jmb.2006.05.022.
154. Bradley, Philip and David Baker. Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins: Structure, Function, and Bioinformatics (2006). DOI: 10.1002/prot.21133.
155. Thompson, Michael J., Stuart A. Sievers, John Karanicolas, Magdalena I. Ivanova, David Baker and David Eisenberg. The 3D profile method for identifying fibril-forming segments of proteins. Proceedings of the National Academy of Sciences (2006). DOI: 10.1073/pnas.0511295103.
156. Baker, Matthew L., Wen Jiang, William J. Wedemeyer, Frazer J. Rixon, David Baker and Wah Chiu. Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density. PLOS Computational Biology (2006). DOI: 10.1371/journal.pcbi.0020146.
157. Goobes, Gil, Rivka Goobes, Ora Schueler-Furman, David Baker, Patrick S. Stayton and Gary P. Drobny. Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals. Proceedings of the National Academy of Sciences (2006). DOI: 10.1073/pnas.0607193103.
158. Dobson, Neil, Gautam Dantas, David Baker and Gabriele Varani. High-Resolution Structural Validation of the Computational Redesign of Human U1A Protein. Structure (2006). DOI: 10.1016/j.str.2006.02.011.
159. Yarov-Yarovoy, Vladimir, Jack Schonbrun and David Baker. Multipass membrane protein structure prediction using Rosetta. Proteins (2006). DOI: 10.1002/prot.20817.
160. Sprague, Elizabeth R., Chu Wang, David Baker and Pamela J. Bjorkman. Crystal Structure of the HSV-1 Fc Receptor Bound to Fc Reveals a Mechanism for Antibody Bipolar Bridging. PLOS Biology (2006). DOI: 10.1371/journal.pbio.0040148.
161. Meiler, Jens and David Baker. ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility. Proteins: Structure, Function, and Bioinformatics (2006). DOI: 10.1002/prot.21086.
162. Zanghellini, Alexandre, Lin Jiang, Andrew M. Wollacott, Gong Cheng, Jens Meiler, Eric A. Althoff, Daniela Röthlisberger and David Baker. New algorithms and an in silico benchmark for computational enzyme design. Protein Science (2006). DOI: 10.1110/ps.062353106.
163. Baker, David. Prediction and design of macromolecular structures and interactions. Philosophical Transactions of the Royal Society B: Biological Sciences (2006). DOI: 10.1098/rstb.2005.1803.
164. Misura, Kira M. S., Dylan Chivian, Carol A. Rohl, David E. Kim and David Baker. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proceedings of the National Academy of Sciences of the United States of America (2006). DOI: 10.1073/pnas.0509355103.
165. Dantas, Gautam, Alexander L. Watters, Bradley M. Lunde et al. Mis-translation of a Computationally Designed Protein Yields an Exceptionally Stable Homodimer: Implications for Protein Engineering and Evolution. Journal of Molecular Biology (2006). DOI: 10.1016/j.jmb.2006.07.092.
166. Ashworth, Justin, James J. Havranek, Carlos M. Duarte, Django Sussman, Raymond J. Monnat, Barry L. Stoddard and David Baker. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature (2006). DOI: 10.1038/nature04818.
167. Yarov-Yarovoy, Vladimir, David Baker and William A. Catterall. Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels. Proceedings of the National Academy of Sciences of the United States of America (2006). DOI: 10.1073/pnas.0602350103.
168. Sood, Vanita D. and David Baker. Recapitulation and Design of Protein Binding Peptide Structures and Sequences. Journal of Molecular Biology (2006). DOI: 10.1016/j.jmb.2006.01.045.
169. Chivian, Dylan, David E. Kim, Lars Malmström, Jack Schonbrun, Carol A. Rohl and David Baker. Prediction of CASP6 structures using automated Robetta protocols. Proteins (2005). DOI: 10.1002/prot.20733.
170. Schueler-Furman, Ora, Chu Wang, Phil Bradley, Kira Misura and David Baker. Progress in Modeling of Protein Structures and Interactions. Science (2005). DOI: 10.1126/science.1112160.
171. Daily, Michael D., David Masica, Arvind Sivasubramanian, Sony Somarouthu and Jeffrey J. Gray. CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock. Proteins: Structure, Function, and Bioinformatics (2005). DOI: 10.1002/prot.20555.
172. Misura, Kira M.S. and David Baker. Progress and challenges in high-resolution refinement of protein structure models. Proteins: Structure, Function, and Bioinformatics (2005). DOI: 10.1002/prot.20376.
173. Graña, Osvaldo, David Baker, Robert M. MacCallum, Jens Meiler, Marco Punta, Burkhard Rost, Michael L. Tress and Alfonso Valencia. CASP6 assessment of contact prediction. Proteins: Structure, Function, and Bioinformatics (2005). DOI: 10.1002/prot.20739.
174. Bradley, Philip, Lars Malmström, Bin Qian et al. Free modeling with Rosetta in CASP6. Proteins (2005). DOI: 10.1002/prot.20729.
175. Korkegian, Aaron, Margaret E. Black, David Baker and Barry L. Stoddard. Computational Thermostabilization of an Enzyme. Science (2005). DOI: 10.1126/science.1107387.
176. Schueler-Furman, Ora, Chu Wang and David Baker. Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins: Structure, Function, and Bioinformatics (2005). DOI: 10.1002/prot.20556.
177. Bradley, Philip, Kira M. S. Misura and David Baker. Toward High-Resolution de Novo Structure Prediction for Small Proteins. Science (2005). DOI: 10.1126/science.1113801.
178. Wang, Chu, Ora Schueler-Furman and David Baker. Improved side-chain modeling for protein–protein docking. Protein Science (2005). DOI: 10.1110/ps.041222905.
179. Lacy, D. Borden, Henry C. Lin, Roman A. Melnyk, Ora Schueler-Furman, Laura Reither, Kristina Cunningham, David Baker and R. John Collier. A model of anthrax toxin lethal factor bound to protective antigen. Proceedings of the National Academy of Sciences of the United States of America (2005). DOI: 10.1073/pnas.0508259102.
180. Cheng, Gong, Bin Qian, Ram Samudrala and David Baker. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Research (2005). DOI: 10.1093/nar/gki894.
181. Saunders, Christopher T. and David Baker. Recapitulation of Protein Family Divergence using Flexible Backbone Protein Design. Journal of Molecular Biology (2005). DOI: 10.1016/j.jmb.2004.11.062.
182. Morozov, A. V. Protein-DNA binding specificity predictions with structural models. Nucleic Acids Research (2005). DOI: 10.1093/nar/gki875.
183. Meiler, Jens and David Baker. The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy. Journal of Magnetic Resonance (2005). DOI: 10.1016/j.jmr.2004.11.031.

SAT@home

1. Zaikin, Oleg. SAT-Based Cryptanalysis: From Parallel Computing to Volunteer Computing. (2019). DOI: 10.1007/978-3-030-36592-9_57.
2. Zaikin, Oleg, Maxim Manzyuk, Stepan Kochemazov, Igor Bychkov and Alexander Semenov. A Volunteer-Computing-Based Grid Architecture Incorporating Idle Resources of Computational Clusters. (2017). DOI: 10.1007/978-3-319-57099-0_89.
3. Semenov, Alexander and Oleg Zaikin. Algorithm for finding partitionings of hard variants of boolean satisfiability problem with application to inversion of some cryptographic functions. SpringerPlus (2016). DOI: 10.1186/s40064-016-2187-4.
4. Zaikin, Oleg, Alexey Zhuravlev, Stepan Kochemazov and Eduard Vatutin. On the Construction of Triples of Diagonal Latin Squares of Order 10. Electronic Notes in Discrete Mathematics (2016). DOI: 10.1016/j.endm.2016.09.053.
5. Institute for System Dynamics and Control Theory SB RAS, O.S. Zaikin, I. V. Otpuschennikov, Institute for System Dynamics and Control Theory SB RAS, A. A. Semenov and Institute for System Dynamics and Control Theory SB RAS. Estimations of cryptographic resistance of ciphers in the trivium family to sat-based cryptanalysis. Prikladnaya diskretnaya matematika. Prilozhenie (2016). DOI: 10.17223/2226308X/9/19.
6. Zaikin, Oleg, Stepan Kochemazov and Alexander Semenov. SAT-based search for systems of diagonal latin squares in volunteer computing project SAT@home. 2016 39th International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO) (2016). DOI: 10.1109/MIPRO.2016.7522152.
7. Oleg, Zaikin and Kochemazov Stepan. The search for systems of diagonal Latin squares using the SAT@home project. International Journal of Open Information Technologies (2015).
8. Zaikin, Oleg, Alexander Semenov and Ilya Otpuschennikov. Solving weakened cryptanalysis problems for the Bivium cipher in the volunteer computing project SAT@home. International Journal of Open Information Technologies (2015).

SETI@home

1. Zhang, Zhi-Song, Dan Werthimer, Tong-Jie Zhang et al. First SETI Observations with China’s Five-hundred-meter Aperture Spherical Radio Telescope (FAST). The Astrophysical Journal (2020). DOI: 10.3847/1538-4357/ab7376.
2. Korpela, Eric J., Andrew P. V. Siemion, Dan Werthimer, Matt Lebofsky, Jeff Cobb, Steve Croft and David Anderson. The next phases of SETI@home. SPIE Optical Engineering + Applications (2015). DOI: 10.1117/12.2188619.
3. Korpela, Eric J. SETI@home, BOINC, and Volunteer Distributed Computing. Annual Review of Earth and Planetary Sciences (2012). DOI: 10.1146/annurev-earth-040809-152348.
4. Korpela, Eric. Distributed Processing of SETI Data. Searching for Extraterrestrial Intelligence (2011).
5. Korpela, Eric J., David P. Anderson, Robert Bankay et al. Status of the UC-Berkeley SETI Efforts. (2011). DOI: 10.48550/ARXIV.1108.3134.
6. Korpela, Eric J., Jeff Cobb, Matt Lebofsky, Andrew Siemion, Joshua von Korff, Robert C. Bankay, Dan Werthimer and David Anderson. Candidate Identification and Interference Removal in SETI@home. (2011). DOI: 10.48550/ARXIV.1109.1595.
7. Korpela, E. J., D. P. Anderson, R. Bankay et al. SETI with Help from Five Million Volunteers: The Berkeley SETI Efforts. (2009).
8. Korpela, Eric J., Jeff Cobb, Steve Fulton et al. Three Years of SETI@home: A Status Report. Symposium - International Astronomical Union (2004). DOI: 10.1017/S0074180900193635.
9. Demorest, Paul, Aaron Golden, Eric Korpela, Dan Werthimer and Ron Ekers. Serendipitous Detection of Radio Pulses from Evaporating Black Holes, GRBs and Extragalactic Supernova Using SETI@home. Astronomy, Cosmology and Fundamental Physics (2003).
10. Anderson, David P., Jeff Cobb, Eric Korpela, Matt Lebofsky and Dan Werthimer. SETI@home: an experiment in public-resource computing. Communications of the ACM (2002). DOI: 10.1145/581571.581573.
11. Werthimer, Dan, David Anderson, C. Stuart Bowyer et al. Berkeley radio and optical SETI programs: SETI@home, SERENDIP, and SEVENDIP. Photonics West 2001 - LASE (2001). DOI: 10.1117/12.435384.
12. Sullivan, Woodruff T., III, Dan Werthimer, Stuart Bowyer, Jeff Cobb, David Gedye and David Anderson. A new major SETI project based on project SERENDIP data and 100,000 personal computers. Proceedings of the 5th international conference on bioastronomy; IAU Colloquium No. 161 (1997).

SIMAP

1. Arnold, Roland, Florian Goldenberg, Hans-Werner Mewes and Thomas Rattei. SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. Nucleic Acids Research (2014). DOI: 10.1093/nar/gkt970.
2. Taylor, Simon J. E., Mohammadmersad Ghorbani, Navonil Mustafee, Stephen J. Turner, Tamas Kiss, Daniel Farkas, Shane Kite and Steffen Strassburger. Distributed computing and modeling & simulation: Speeding up simulations and creating large models. 2011 Winter Simulation Conference - (WSC 2011) (2011). DOI: 10.1109/WSC.2011.6147748.
3. Rattei, Thomas, Patrick Tischler, Stefan Götz, Marc-André Jehl, Jonathan Hoser, Roland Arnold, Ana Conesa and Hans-Werner Mewes. SIMAP—a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic Acids Research (2010). DOI: 10.1093/nar/gkp949.
4. Rattei, T., P. Tischler, R. Arnold et al. SIMAP structuring the network of protein similarities. Nucleic Acids Research (2007). DOI: 10.1093/nar/gkm963.
5. Rattei, T. SIMAP: the similarity matrix of proteins. Nucleic Acids Research (2006). DOI: 10.1093/nar/gkj106.

SZTAKI Desktop Grid

1. Ódor, Géza, Bartosz Liedke and Karl-Heinz Heinig. Surface pattern formation and scaling described by conserved lattice gases. Physical Review E (2010). DOI: 10.1103/PhysRevE.81.051114.
2. Marosi, Attila. Exploring University Classes in Nonequilibrium Systems on SZTAKI Desktop Grid. Third AlmereGrid Desktop Grid Experience workshop (2010).
3. Ódor, Géza, Bartosz Liedke and Karl-Heinz Heinig. Mapping of ( 2 + 1 ) -dimensional Kardar-Parisi-Zhang growth onto a driven lattice gas model of dimers. Physical Review E (2009). DOI: 10.1103/PhysRevE.79.021125.
4. Kacsuk, Peter, Jozsef Kovacs, Zoltan Farkas, Attila Csaba Marosi, Gabor Gombas and Zoltan Balaton. SZTAKI Desktop Grid (SZDG): A Flexible and Scalable Desktop Grid System. Journal of Grid Computing (2009). DOI: 10.1007/s10723-009-9139-y.
5. Burcsi, Péter and Attila Kovács. Exhaustive search methods for CNS polynomials. Monatshefte für Mathematik (2008). DOI: 10.1007/s00605-008-0005-y.

SiDock@home

1. Nikitina, Natalia and Evgeny Ivashko. Optimization of the Workflow in a BOINC-Based Desktop Grid for Virtual Drug Screening. (2022). DOI: 10.1007/978-3-031-22941-1_50.
2. Jukić, Marko, Sebastjan Kralj, Natalia Nikitina and Urban Bren. Bioinformatic and MD Analysis of N501Y SARS-CoV-2 (UK) Variant. (2021). DOI: 10.1007/978-3-030-86582-5_1.
3. Nikitina, Natalia, Maxim Manzyuk, Črtomir Podlipnik and Marko Jukić. Volunteer Computing Project SiDock@home for Virtual Drug Screening Against SARS-CoV-2. (2021). DOI: 10.1007/978-3-030-86582-5_3.
4. Nikitina, Natalia, Maxim Manzyuk, Črtomir Podlipnik and Marko Jukić. Performance Estimation of a BOINC-Based Desktop Grid for Large-Scale Molecular Docking. (2021). DOI: 10.1007/978-3-030-86359-3_26.
5. Nikitina, Natalia, Maxim Manzyuk, Marko Jukić, Črtomir Podlipnik, Ilya Kurochkin and Alexander Albertian. Toward Crowdsourced Drug Discovery: Start-Up of the Volunteer Computing Project SiDock@home. (2021). DOI: 10.1007/978-3-030-92864-3_39.
6. Nikitina, Natalia, Evgeny Ivashko and Andrei Tchernykh. Congestion Game Scheduling Implementation for High-Throughput Virtual Drug Screening Using BOINC-Based Desktop Grid. Parallel Computing Technologies (2017).

SimOne@home

1. Pieraccini, Stefano, Simone Conti, Shilpi Chaurasia and Maurizio Sironi. Modelling the effect of osmolytes on peptide mechanical unfolding. Chemical Physics Letters (2013). DOI: 10.1016/j.cplett.2013.06.008.

Spinhenge@home

1. Powell, George, Larry Engelhardt, Thomas Hilbig and Christian Schroder. How to use 100,000 PCs for studying magnetism. (2009).
2. Schröder, Christian, Ruslan Prozorov, Paul Kögerler et al. Multiple nearest-neighbor exchange model for the frustrated magnetic molecules Mo72Fe30 and Mo72Cr30. (2008). DOI: 10.48550/ARXIV.0801.2065.
3. Rainey, Cameron, Larry Engelhardt, Christian Schröder and Thomas Hilbig. QMC Goes BOINC: Using Public Resource Computing to Perform Quantum Monte Carlo Calculations. (2008).

SubsetSum@Home

1. O'Neil, T. E. and T. Desell. Empirical support for the high-density subset sum decision threshold. 2015 IEEE 14th Canadian Workshop on Information Theory (CWIT) (2015). DOI: 10.1109/CWIT.2015.7255176.

Superlink@Technion

1. Silberstein, Mark. Building an Online Domain-Specific Computing Service over Non-dedicated Grid and Cloud Resources: The Superlink-Online Experience. 2011 11th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (2011). DOI: 10.1109/CCGrid.2011.46.
2. Silberstein, Mark. Building an Online Computing Service over Volunteer Grid Resources. 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (2011). DOI: 10.1109/IPDPS.2011.352.
3. Silberstein, Mark, Artyom Sharov, Dan Geiger and Assaf Schuster. GridBot: execution of bags of tasks in multiple grids. the Conference (2009). DOI: 10.1145/1654059.1654071.
4. Silberstein, Mark, Dan Geiger and Assaf Schuster. A Distributed System for Genetic Linkage Analysis. Distributed, High-Performance and Grid Computing in Computational Biology (2007).

TANPAKU

1. Ando, Tadashi and Ichiro Yamato. Brownian Dynamics Approach to Protein Folding. Frontiers of Computational Science (2007).
2. Ando, T. and I. Yamato. Free energy landscapes of two model peptides: α-helical and β-hairpin peptides explored with Brownian dynamics simulation. Molecular Simulation (2005). DOI: 10.1080/08927020500183257.

TN-Grid gene@home

1. Pilati, Stefania, Giulia Malacarne, David Navarro-Payá et al. Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families. Biomolecules (2021). DOI: 10.3390/biom11121744.
2. Blanzieri, Enrico, Toma Tebaldi, Valter Cavecchia et al. A Computing System for Discovering Causal Relationships Among Human Genes to Improve Drug Repositioning. IEEE Transactions on Emerging Topics in Computing (2021). DOI: 10.1109/TETC.2020.3031024.
3. Asnicar, Francesco, Luca Masera, Davide Pistore, Samuel Valentini, Valter Cavecchia and Enrico Blanzieri. OneGenE: Regulatory Gene Network Expansion via Distributed Volunteer Computing on BOINC. 2019 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP) (2019). DOI: 10.1109/EMPDP.2019.8671629.
4. Malacarne, Giulia, Stefania Pilati, Samuel Valentini et al. Discovering Causal Relationships in Grapevine Expression Data to Expand Gene Networks. A Case Study: Four Networks Related to Climate Change. Frontiers in Plant Science (2018). DOI: 10.3389/fpls.2018.01385.
5. Asnicar, Francesco, Luca Masera, Emanuela Coller et al. NES ² RA: Network expansion by stratified variable subsetting and ranking aggregation. The International Journal of High Performance Computing Applications (2018). DOI: 10.1177/1094342016662508.
6. Asnicar, Francesco, Luca Erculiani, Francesca Galante et al. Discovering Candidates for Gene Network Expansion by Distributed Volunteer Computing. 2015 IEEE Trustcom/BigDataSE/ISPA (2015). DOI: 10.1109/Trustcom.2015.640.
7. Erculiani, Luca, Francesca Galante, Caterina Gallo et al. Discovering candidates for gene network expansion by variable subsetting and ranking aggregation. (2015). DOI: 10.7490/F1000RESEARCH.1110311.1.
8. Asnicar, F., Nadir Sella, L. Masera et al. TN-Grid and gene@home project: volunteer computing for bioinformatics. International Conference on High Performance Computing (2015).

Templet Project

1. Vostokin, S. V. Study of the Event Log Method to Organize Fault Tolerant and Self-Balancing Calculations in a Hybrid Environment. Physics of Particles and Nuclei (2024). DOI: 10.1134/S1063779624030900.

The Lattice Project

1. Bazinet, Adam L. and Michael P. Cummings. Subdividing Long-Running, Variable-Length Analyses Into Short, Fixed-Length BOINC Workunits. Journal of Grid Computing (2016). DOI: 10.1007/s10723-015-9348-5.
2. Bazinet, Adam L., Derrick J. Zwickl and Michael P. Cummings. A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0. Systematic Biology (2014). DOI: 10.1093/sysbio/syu031.
3. Bazinet, Adam L., Michael P. Cummings, Kim T. Mitter and Charles W. Mitter. Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study. PLoS ONE (2013). DOI: 10.1371/journal.pone.0082615.
4. Lloyd, Michael W., Lesley Campbell and Maile C. Neel. The Power to Detect Recent Fragmentation Events Using Genetic Differentiation Methods. PLoS ONE (2013). DOI: 10.1371/journal.pone.0063981.
5. Regier, Jerome C. and Andreas Zwick. Sources of Signal in 62 Protein-Coding Nuclear Genes for Higher-Level Phylogenetics of Arthropods. PLoS ONE (2011). DOI: 10.1371/journal.pone.0023408.
6. Zwick, Andreas, Jerome C. Regier, Charles Mitter and Michael P. Cummings. Increased gene sampling yields robust support for higher-level clades within Bombycoidea (Lepidoptera). Systematic Entomology (2011). DOI: 10.1111/j.1365-3113.2010.00543.x.
7. Cho, Soowon, Andreas Zwick, Jerome C. Regier et al. Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?. Systematic Biology (2011). DOI: 10.1093/sysbio/syr079.
8. Kawahara, Akito Y, Issei Ohshima, Atsushi Kawakita et al. Increased gene sampling strengthens support for higher-level groups within leaf-mining moths and relatives (Lepidoptera: Gracillariidae). BMC Evolutionary Biology (2011). DOI: 10.1186/1471-2148-11-182.
9. Reyna-Fabián, Miriam E., Juan Pedro Laclette, Michael P. Cummings and Martín García-Varela. Validating the systematic position of Plationus Segers, Murugan & Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase. Hydrobiologia (2010). DOI: 10.1007/s10750-010-0203-1.
10. Regier, Jerome C., Jeffrey W. Shultz, Andreas Zwick, April Hussey, Bernard Ball, Regina Wetzer, Joel W. Martin and Clifford W. Cunningham. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature (2010). DOI: 10.1038/nature08742.
11. Regier, Jerome C, Andreas Zwick, Michael P Cummings et al. Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evolutionary Biology (2009). DOI: 10.1186/1471-2148-9-280.
12. Pettengill, James B and Maile C Neel. Phylogenetic patterns and conservation among North American members of the genus Agalinis (Orobanchaceae). BMC Evolutionary Biology (2008). DOI: 10.1186/1471-2148-8-264.
13. Bazinet, Adam L., Daniel S. Myers, John Fuetsch and Michael P. Cummings. Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services. Future Generation Computer Systems (2007). DOI: 10.1016/j.future.2006.07.009.
14. Tishkoff, S. A., M. K. Gonder, B. M. Henn et al. History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation. Molecular Biology and Evolution (2007). DOI: 10.1093/molbev/msm155.
15. Myers, Daniel S., Adam L. Bazinet and Michael P. Cummings. Expanding the Reach of Grid Computing: Combining Globus- and BOINC-Based Systems. Grid Computing for Bioinformatics and Computational Biology (2007).
16. Lee, Sung, Taowei David Wang, Nada Hashmi and Michael P. Cummings. Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences. Future Generation Computer Systems (2007). DOI: 10.1016/j.future.2006.07.011.

The Ramanujan Machine

1. Elimelech, Rotem, Ofir David, Carlos De la Cruz Mengual et al. Algorithm-assisted discovery of an intrinsic order among mathematical constants. (2023). DOI: 10.48550/ARXIV.2308.11829.

TheSkyNet

1. Chambers, K. C., E. A. Magnier, N. Metcalfe et al. The Pan-STARRS1 Surveys. (2016). DOI: 10.48550/ARXIV.1612.05560.
2. Thilker, David A., K. Vinsen and PS1 Galaxy Properties Key Project. Early science from the Pan-STARRS1 Optical Galaxy Survey (POGS): Maps of stellar mass and star formation rate surface density obtained from distributed-computing pixel-SED fitting. (2014).
3. Vinsen, Kevin and David Thilker. A BOINC based, citizen-science project for pixel spectral energy distribution fitting of resolved galaxies in multi-wavelength surveys. Astronomy and Computing (2013). DOI: 10.1016/j.ascom.2013.10.001.

USPEX@HOME

1. Khrapov, Nikolay P., Valery V. Rozen, Artem I. Samtsevich, Mikhail A. Posypkin, Vladimir A. Sukhomlin and Artem R. Oganov. Using virtualization to protect the proprietary material science applications in volunteer computing. Open Engineering (2018). DOI: 10.1515/eng-2018-0009.
2. Khrapov, N., V. Roizen, M. Posypkin, A. Samtsevich and A. R. Oganov. Volunteer computing for computational materials design. Lobachevskii Journal of Mathematics (2017). DOI: 10.1134/S1995080217050195.

Universe@home

1. Banerjee, Sambaran, Aleksandra Olejak and Krzysztof Belczynski. Symmetry breaking in merging binary black holes from young massive clusters and isolated binaries. (2023).
2. Wiktorowicz, Grzegorz, Jean-Pierre Lasota, Krzysztof Belczynski, Youjun Lu, Jifeng Liu and Krystian Iłkiewicz. Wind-powered Ultraluminous X-ray Sources. The Astrophysical Journal (2021). DOI: 10.3847/1538-4357/ac0cf7.
3. Wiktorowicz, Grzegorz, Matthew Middleton, Norman Khan, Adam Ingram, Poshak Gandhi and Hugh Dickinson. Predicting the self-lensing population in optical surveys. Monthly Notices of the Royal Astronomical Society (2021). DOI: 10.1093/mnras/stab2135.
4. Wiktorowicz, Grzegorz, Youjun Lu, Łukasz Wyrzykowski, Haotong Zhang, Jifeng Liu, Stephen Justham and Krzysztof Belczynski. Noninteracting Black Hole Binaries with Gaia and LAMOST. The Astrophysical Journal (2020). DOI: 10.3847/1538-4357/abc699.
5. Wiktorowicz, Grzegorz, Jean-Pierre Lasota, Matthew Middleton and Krzysztof Belczynski. The Observed versus Total Population of ULXs. The Astrophysical Journal (2019). DOI: 10.3847/1538-4357/ab0f27.
6. Wiktorowicz, Grzegorz, Łukasz Wyrzykowski, Martyna Chruslinska, Jakub Klencki, Krzysztof A. Rybicki and Krzysztof Belczynski. Populations of Stellar-mass Black Holes from Binary Systems. The Astrophysical Journal (2019). DOI: 10.3847/1538-4357/ab45e6.
7. Belczynski, K., T. Bulik, A. Olejak et al. Binary neutron star formation and the origin of GW170817. (2018). DOI: 10.48550/ARXIV.1812.10065.
8. Belczynski, K., A. Askar, M. Arca-Sedda et al. The origin of the first neutron star – neutron star merger. Astronomy & Astrophysics (2018). DOI: 10.1051/0004-6361/201732428.
9. Wiktorowicz, G., A. Drago, G. Pagliara and S. B. Popov. Strange Quark Stars in Binaries: Formation Rates, Mergers, and Explosive Phenomena. The Astrophysical Journal (2017). DOI: 10.3847/1538-4357/aa8629.
10. Klencki, Jakub, Grzegorz Wiktorowicz, Wojciech Gładysz and Krzysztof Belczynski. Dynamical formation of black hole low-mass X-ray binaries in the field: an alternative to the common envelope. Monthly Notices of the Royal Astronomical Society (2017). DOI: 10.1093/mnras/stx842.
11. Wiktorowicz, Grzegorz, Małgorzata Sobolewska, Jean-Pierre Lasota and Krzysztof Belczynski. The Origin of the Ultraluminous X-Ray Sources. The Astrophysical Journal (2017). DOI: 10.3847/1538-4357/aa821d.
12. Belczynski, Krzysztof, Daniel E. Holz, Tomasz Bulik and Richard O'Shaughnessy. The first gravitational-wave source from the isolated evolution of two 40-100 Msun stars. (2016). DOI: 10.48550/ARXIV.1602.04531.
13. Wiktorowicz, Grzegorz, Małgorzata Sobolewska, Aleksander Sa˛dowski and Krzysztof Belczynski. NATURE OF THE EXTREME ULTRALUMINOUS X-RAY SOURCES. The Astrophysical Journal (2015). DOI: 10.1088/0004-637X/810/1/20.
14. Merritt, David. GRAVITATIONAL ENCOUNTERS AND THE EVOLUTION OF GALACTIC NUCLEI. III. ANOMALOUS RELAXATION. The Astrophysical Journal (2015). DOI: 10.1088/0004-637X/810/1/2.

Unknown projects

1. Pellicer, S., N. Ahmed, Yi Pan and Yao Zheng. Gene Sequence Alignment on a Public Computing Platform. 2005 International Conference on Parallel Processing Workshops (ICPPW'05) (2005). DOI: 10.1109/ICPPW.2005.35.
2. Pellicer, Stephen, Yi Pan and Minyi Guo. Distributed MD4 Password Hashing with Grid Computing Package BOINC. Grid and Cooperative Computing - GCC 2004 (2004).

VGTU@home

1. Ramanauskas, Mikalojus, Dmitrij Šešok, Julius Žilinskas, Vadimas Starikovičius, Arnas Kačeniauskas and Rimantas Belevičius. Global optimization of grillage-type foundations using a distributed genetic algorithm. Journal of Global Optimization (2020). DOI: 10.1007/s10898-019-00838-2.
2. Čiegis, Raimondas, Vadimas Starikovičius, Natalija Tumanova and Minvydas Ragulskis. Application of distributed parallel computing for dynamic visual cryptography. The Journal of Supercomputing (2016). DOI: 10.1007/s11227-016-1733-8.

Van Der Waerden Numbers

1. Monroe, Daniel. New Lower Bounds for van der Waerden Numbers Using Distributed Computing. (2016). DOI: 10.48550/ARXIV.1603.03301.

Virtual Prairie

1. Mony, C., M. Garbey, M. Smaoui and M.-L. Benot. Large scale parameter study of an individual-based model of clonal plant with volunteer computing. Ecological Modelling (2011). DOI: 10.1016/j.ecolmodel.2010.10.014.

Virus Respiratorio Sincitial (VRS)

1. Acedo, L., J.-A. Moraño, R.-J. Villanueva, J. Villanueva-Oller and J. Díez-Domingo. Using random networks to study the dynamics of respiratory syncytial virus (RSV) in the Spanish region of Valencia. Mathematical and Computer Modelling (2011). DOI: 10.1016/j.mcm.2010.11.068.

Volpex@Home

1. Subhlok, Jaspal, Hien Nguyen, Edgar Gabriel and Mohammad Tanvir Rahman. Resilient parallel computing on volunteer PC grids. Concurrency and Computation: Practice and Experience (2018). DOI: 10.1002/cpe.4478.
2. Rahman, Mohammad Tanvir, Hien Nguyen, Jaspal Subhlok and Gopal Pandurangan. Checkpointing to Minimize Completion Time for Inter-Dependent Parallel Processes on Volunteer Grids. 2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid) (2016). DOI: 10.1109/CCGrid.2016.78.
3. Islam, Md Tarikul, Hien Nguyen, Jaspal Subhlok and Edgar Gabriel. Efficient Message Logging to Support Process Replicas in a Volunteer Computing Environment. 2015 IEEE International Parallel and Distributed Processing Symposium Workshop (2015). DOI: 10.1109/IPDPSW.2015.91.
4. Nguyen, Hien, Eshwar Pedamallu, Jaspal Subhlok, Edgar Gabriel, Qian Wang, Margaret S. Cheung and David Anderson. An Execution Environment for Robust Parallel Computing on Volunteer PC Grids. 2012 41st International Conference on Parallel Processing (ICPP) (2012). DOI: 10.1109/ICPP.2012.18.
5. Rohit, Eshwar, Hien Nguyen, Nagarajan Kanna, Jaspal Subhlok, Edgar Gabriel, Qian Wang, Margaret S. Cheung and David Anderson. A Robust Communication Framework for Parallel Execution on Volunteer PC Grids. 2011 11th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (2011). DOI: 10.1109/CCGrid.2011.72.
6. Anand, Rakhi, Edgar Gabriel and Jaspal Subhlok. Communication Target Selection for Replicated MPI Processes. Recent Advances in the Message Passing Interface (2010).
7. LeBlanc, Troy P., Jaspal Subhlok and Edgar Gabriel. A High-Level Interpreted MPI Library for Parallel Computing in Volunteer Environments. 2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing (2010). DOI: 10.1109/CCGRID.2010.85.
8. Kanna, Nagarajan, Jaspal Subhlok, Edgar Gabriel, Eshwar Rohit and David Anderson. A Communication Framework for Fault-Tolerant Parallel Execution. Languages and Compilers for Parallel Computing (2010).
9. LeBlanc, Troy, Rakhi Anand, Edgar Gabriel and Jaspal Subhlok. VolpexMPI: An MPI Library for Execution of Parallel Applications on Volatile Nodes. Recent Advances in Parallel Virtual Machine and Message Passing Interface (2009).

World Community Grid (Computing for Clean Water)

1. Cao, Wei, Jin Wang and Ming Ma. Carbon nanostructure based mechano-nanofluidics. Journal of Micromechanics and Microengineering (2018). DOI: 10.1088/1361-6439/aaa782.
2. Ma, Ming, François Grey, Luming Shen, Michael Urbakh, Shuai Wu, Jefferson Zhe Liu, Yilun Liu and Quanshui Zheng. Water transport inside carbon nanotubes mediated by phonon-induced oscillating friction. Nature Nanotechnology (2015). DOI: 10.1038/nnano.2015.134.
3. Ma, Ming D., Luming Shen, John Sheridan, Jefferson Zhe Liu, Chao Chen and Quanshui Zheng. Friction of water slipping in carbon nanotubes. Physical Review E (2011). DOI: 10.1103/PhysRevE.83.036316.

World Community Grid (Discovering Dengue Drugs)

1. Viswanathan, Usha, Suzanne M. Tomlinson, John M. Fonner, Stephen A. Mock and Stanley J. Watowich. Identification of a novel inhibitor of dengue virus protease through use of a virtual screening drug discovery Web portal. Journal of Chemical Information and Modeling (2014). DOI: 10.1021/ci500531r.
2. Tomlinson, S. M., R. D. Malmstrom and S. J. Watowich. New Approaches to Structure-Based Discovery of Dengue Protease Inhibitors. Infectious Disorders - Drug Targets (2009). DOI: 10.2174/1871526510909030327.

World Community Grid (Drug Search for Leishmaniasis)

1. Ochoa, Rodrigo, Stanley J. Watowich, Andrés Flórez, Carol V. Mesa, Sara M. Robledo and Carlos Muskus. Drug search for leishmaniasis: a virtual screening approach by grid computing. Journal of Computer-Aided Molecular Design (2016). DOI: 10.1007/s10822-016-9921-4.
2. Flórez, Andrés F., Stanley Watowich, Carlos Muskus, Andrés F. Flórez, Stanley Watowich and Carlos Muskus. Current Advances in Computational Strategies for Drug Discovery in Leishmaniasis. (2012).

World Community Grid (FightAIDS@Home)

1. Goodsell, David S., Michel F. Sanner, Arthur J. Olson and Stefano Forli. The AutoDock suite at 30. Protein Science (2021). DOI: 10.1002/pro.3934.
2. Craveur, Pierrick, Anna T. Gres, Karen A. Kirby et al. Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket. mBio (2019). DOI: 10.1128/mBio.02858-18.
3. Xia, Junchao, William Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson and Ronald M. Levy. Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. Journal of Chemical Information and Modeling (2019). DOI: 10.1021/acs.jcim.8b00817.
4. Forli, Stefano and Arthur J. Olson. Computational Challenges of Structure-Based Approaches Applied to HIV. The Future of HIV-1 Therapeutics (2015).
5. Xia, Junchao, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan and Ronald M. Levy. Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. Journal of Computational Chemistry (2015). DOI: 10.1002/jcc.23996.
6. Gallicchio, Emilio, Junchao Xia, William F. Flynn, Baofeng Zhang, Sade Samlalsingh, Ahmet Mentes and Ronald M. Levy. Asynchronous replica exchange software for grid and heterogeneous computing. Computer Physics Communications (2015). DOI: 10.1016/j.cpc.2015.06.010.
7. Perryman, Alexander L., Daniel N. Santiago, Stefano Forli, Diogo Santos-Martins and Arthur J. Olson. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein–ligand binding challenge. Journal of Computer-Aided Molecular Design (2014). DOI: 10.1007/s10822-014-9709-3.
8. Perryman, Alexander L., Qing Zhang, Holly H. Soutter, Robin Rosenfeld, Duncan E. McRee, Arthur J. Olson, John E. Elder and C. David Stout. Fragment-Based Screen against HIV Protease. Chemical Biology & Drug Design (2010). DOI: 10.1111/j.1747-0285.2009.00943.x.
9. Perryman, Alex L., Stefano Forli, Garrett M. Morris et al. A Dynamic Model of HIV Integrase Inhibition and Drug Resistance. Journal of Molecular Biology (2010). DOI: 10.1016/j.jmb.2010.01.033.
10. Cosconati, Sandro, Stefano Forli, Alex L Perryman, Rodney Harris, David S Goodsell and Arthur J Olson. Virtual Screening with AutoDock: Theory and Practice. Expert Opinion on Drug Discovery (2010). DOI: 10.1517/17460441.2010.484460.
11. Morris, Garrett M., Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell and Arthur J. Olson. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry (2009). DOI: 10.1002/jcc.21256.
12. Chang, Max W., William Lindstrom, Arthur J. Olson and Richard K. Belew. Analysis of HIV Wild-Type and Mutant Structures via in Silico Docking against Diverse Ligand Libraries. Journal of Chemical Information and Modeling (2007). DOI: 10.1021/ci700044s.

World Community Grid (GO Fight Against Malaria)

1. Perryman, Alexander L., Weixuan Yu, Xin Wang et al. A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of Mycobacterium tuberculosis InhA. Journal of Chemical Information and Modeling (2015). DOI: 10.1021/ci500672v.

World Community Grid (Genome Comparison)

1. Lifschitz, Sérgio, Carlos Juliano M. Viana, Cristian Tristão, Marcos Catanho, Wim M. Degrave, Antonio Basílio de Miranda, Márcia Bezerra and Thomas D. Otto. Design and Implementation of ProteinWorldDB. Advances in Bioinformatics and Computational Biology (2012).
2. Otto, Thomas Dan, Marcos Catanho, Cristian Tristão et al. ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes. Bioinformatics (2010). DOI: 10.1093/bioinformatics/btq011.

World Community Grid (Help Conquer Cancer)

1. Kotseruba, Yulia, Christian A. Cumbaa and Igor Jurisica. High-throughput protein crystallization on the World Community Grid and the GPU. Journal of Physics: Conference Series (2012). DOI: 10.1088/1742-6596/341/1/012027.
2. Cumbaa, Christian A. and Igor Jurisica. Protein crystallization analysis on the World Community Grid. Journal of Structural and Functional Genomics (2010). DOI: 10.1007/s10969-009-9076-9.
3. Snell, Edward H., Angela M. Lauricella, Stephen A. Potter et al. Establishing a training set through the visual analysis of crystallization trials. Part II: crystal examples. Acta Crystallographica Section D: Biological Crystallography (2008). DOI: 10.1107/S0907444908028059.
4. Snell, Edward H., Joseph R. Luft, Stephen A. Potter et al. Establishing a training set through the visual analysis of crystallization trials. Part I: ∼150 000 images. Acta Crystallographica Section D: Biological Crystallography (2008). DOI: 10.1107/S0907444908028047.

World Community Grid (Help Cure Muscular Dystrophy)

1. Dequeker, Chloé, Elodie Laine and Alessandra Carbone. Decrypting protein surfaces by combining evolution, geometry, and molecular docking. Proteins: Structure, Function, and Bioinformatics (2019). DOI: 10.1002/prot.25757.
2. Lagarde, Nathalie, Alessandra Carbone and Sophie Sacquin-Mora. Hidden partners: Using cross-docking calculations to predict binding sites for proteins with multiple interactions. Proteins: Structure, Function, and Bioinformatics (2018). DOI: 10.1002/prot.25506.
3. Laine, Elodie and Alessandra Carbone. Protein social behavior makes a stronger signal for partner identification than surface geometry. Proteins: Structure, Function, and Bioinformatics (2017). DOI: 10.1002/prot.25206.
4. Vamparys, Lydie, Benoist Laurent, Alessandra Carbone and Sophie Sacquin-Mora. Great interactions: How binding incorrect partners can teach us about protein recognition and function. Proteins: Structure, Function, and Bioinformatics (2016). DOI: 10.1002/prot.25086.
5. Lopes, Anne, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty and Alessandra Carbone. Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information. PLOS Computational Biology (2013). DOI: 10.1371/journal.pcbi.1003369.
6. Bertis, Viktors, Raphaël Bolze, Frédéric Desprez and Kevin Reed. From Dedicated Grid to Volunteer Grid: Large Scale Execution of a Bioinformatics Application. Journal of Grid Computing (2009). DOI: 10.1007/s10723-009-9130-7.
7. Engelen, Stefan, Ladislas A. Trojan, Sophie Sacquin-Mora, Richard Lavery and Alessandra Carbone. Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling. PLOS Computational Biology (2009). DOI: 10.1371/journal.pcbi.1000267.
8. Sacquin-Mora, Sophie, Alessandra Carbone and Richard Lavery. Identification of Protein Interaction Partners and Protein–Protein Interaction Sites. Journal of Molecular Biology (2008). DOI: 10.1016/j.jmb.2008.08.002.

World Community Grid (Help Defeat Cancer)

1. Foran, David J, Lin Yang, Wenjin Chen et al. ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology. Journal of the American Medical Informatics Association (2011). DOI: 10.1136/amiajnl-2011-000170.
2. Wang, Fusheng. Grid-Enabled, High-performance Microscopy Image Analysis. (2010).
3. Lin Yang, Wenjin Chen, P. Meer, G. Salaru, L.A. Goodell, V. Berstis and D.J. Foran. Virtual Microscopy and Grid-Enabled Decision Support for Large-Scale Analysis of Imaged Pathology Specimens. IEEE Transactions on Information Technology in Biomedicine (2009). DOI: 10.1109/TITB.2009.2020159.
4. Lin Yang, O. Tuzel, Wenjin Chen, P. Meer, G. Salaru, L.A. Goodell and D.J. Foran. PathMiner: A Web-Based Tool for Computer-Assisted Diagnostics in Pathology. IEEE Transactions on Information Technology in Biomedicine (2009). DOI: 10.1109/TITB.2008.2008801.
5. DiPaola, Robert S., Dmitri Dvorzhinski, Anu Thalasila et al. Therapeutic starvation and autophagy in prostate cancer: A new paradigm for targeting metabolism in cancer therapy. The Prostate (2008). DOI: 10.1002/pros.20837.

World Community Grid (Help Fight Childhood Cancer)

1. Fukuda, Mayu, Atsushi Takatori, Yohko Nakamura, Akiko Suganami, Tyuji Hoshino, Yutaka Tamura and Akira Nakagawara. Effects of novel small compounds targeting TrkB on neuronal cell survival and depression-like behavior. Neurochemistry International (2016). DOI: 10.1016/j.neuint.2016.04.017.
2. Nakamura, Yohko, Akiko Suganami, Mayu Fukuda et al. Identification of novel candidate compounds targeting TrkB to induce apoptosis in neuroblastoma. Cancer Medicine (2014). DOI: 10.1002/cam4.175.

World Community Grid (Help Stop TB)

1. Groenewald, Wilma, Ricardo A. Parra-Cruz, Christof M. Jäger and Anna K. Croft. Revealing solvent-dependent folding behavior of mycolic acids from Mycobacterium tuberculosis by advanced simulation analysis. Journal of Molecular Modeling (2019). DOI: 10.1007/s00894-019-3943-5.

World Community Grid (Human Proteome Folding)

1. Baltz, Alexander G., Mathias Munschauer, Björn Schwanhäusser et al. The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts. Molecular Cell (2012). DOI: 10.1016/j.molcel.2012.05.021.
2. Pentony, M. M., P. Winters, D. Penfold-Brown, K. Drew, A. Narechania, R. DeSalle, R. Bonneau and M. D. Purugganan. The Plant Proteome Folding Project: Structure and Positive Selection in Plant Protein Families. Genome Biology and Evolution (2012). DOI: 10.1093/gbe/evs015.
3. Drew, Kevin, Patrick Winters, Glenn L. Butterfoss et al. The Proteome Folding Project: Proteome-scale prediction of structure and function. Genome Research (2011). DOI: 10.1101/gr.121475.111.
4. Boxem, Mike, Zoltan Maliga, Niels Klitgord et al. A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis. Cell (2008). DOI: 10.1016/j.cell.2008.07.009.
5. Bonneau, Richard, Marc T. Facciotti, David J. Reiss et al. A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell. Cell (2007). DOI: 10.1016/j.cell.2007.10.053.
6. Malmström, Lars, Michael Riffle, Charlie E. M. Strauss, Dylan Chivian, Trisha N. Davis, Richard Bonneau and David Baker. Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS biology (2007). DOI: 10.1371/journal.pbio.0050076.
7. Andersen-Nissen, Erica, Kelly D. Smith, Richard Bonneau, Roland K. Strong and Alan Aderem. A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin. Journal of Experimental Medicine (2007). DOI: 10.1084/jem.20061400.
8. Avila-Campillo, Iliana, Kevin Drew, John Lin, David J. Reiss and Richard Bonneau. BioNetBuilder: automatic integration of biological networks. Bioinformatics (2007). DOI: 10.1093/bioinformatics/btl604.
9. Malmström, Lars. Genome-wide structural and functional protein characterization by ab initio protein structure prediction. Report / Department of Electrical Measurements. Lund Institute of Technology (2005).

World Community Grid (Mapping Cancer Markers)

1. Hauschild, Anne-Christin, Chiara Pastrello, Andrea E.M. Rossos and Igor Jurisica. Visualization of Biomedical Networks. Encyclopedia of Bioinformatics and Computational Biology (2019).
2. Paulitti, Alice, Eva Andreuzzi, Dario Bizzotto et al. The ablation of the matricellular protein EMILIN2 causes defective vascularization due to impaired EGFR-dependent IL-8 production affecting tumor growth. Oncogene (2018). DOI: 10.1038/s41388-017-0107-x.
3. Wong, Serene W.H., Chiara Pastrello, Max Kotlyar, Christos Faloutsos and Igor Jurisica. SDREGION: Fast Spotting of Changing Communities in Biological Networks. KDD '18: The 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (2018). DOI: 10.1145/3219819.3219854.
4. Anne-Christin Hauschild, Christian A Cumbaa, Mike Tsay and Igor Jurisica. Network Motif Families for Lung Cancer Diagnostics: A World Community Grid Approach. (2017). DOI: 10.13140/RG.2.2.34687.51363.
5. Fortney, Kristen, Joshua Griesman, Max Kotlyar, Chiara Pastrello, Marc Angeli, Ming Sound-Tsao and Igor Jurisica. Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data. PLOS Computational Biology (2015). DOI: 10.1371/journal.pcbi.1004068.
6. Kotlyar, Max, Chiara Pastrello, Flavia Pivetta et al. In silico prediction of physical protein interactions and characterization of interactome orphans. Nature Methods (2015). DOI: 10.1038/nmeth.3178.

World Community Grid (Microbiome Immunity Project)

1. Koehler Leman, Julia, Pawel Szczerbiak, P. Douglas Renfrew et al. Sequence-structure-function relationships in the microbial protein universe. Nature Communications (2023). DOI: 10.1038/s41467-023-37896-w.

World Community Grid (Nutritious Rice for the World)

1. Hung, Ling-Hong and Ram Samudrala. Rice protein models from the Nutritious Rice for the World Project. (2016). DOI: 10.1101/091975.
2. Hung, Ling-Hong and Ram Samudrala. fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data. Bioinformatics (2014). DOI: 10.1093/bioinformatics/btu098.
3. Hung, Ling-Hong and Ram Samudrala. Accelerated protein structure comparison using TM-score-GPU. Bioinformatics (2012). DOI: 10.1093/bioinformatics/bts345.
4. Hung, Ling-Hong, Michal Guerquin and Ram Samudrala. GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition. BMC Research Notes (2011). DOI: 10.1186/1756-0500-4-97.

World Community Grid (OpenZika)

1. Mottin, Melina, Bruna Katiele de Paula Sousa, Nathalya Cristina de Moraes Roso Mesquita et al. Discovery of New Zika Protease and Polymerase Inhibitors through the Open Science Collaboration Project OpenZika. Journal of Chemical Information and Modeling (2022). DOI: 10.1021/acs.jcim.2c00596.
2. Silva, Suely, Jacqueline Farinha Shimizu, Débora Moraes de Oliveira et al. A diarylamine derived from anthranilic acid inhibits ZIKV replication. Scientific Reports (2019). DOI: 10.1038/s41598-019-54169-z.
3. Hernandez, Helen W., Melinda Soeung, Kimberley M. Zorn et al. High Throughput and Computational Repurposing for Neglected Diseases. Pharmaceutical Research (2019). DOI: 10.1007/s11095-018-2558-3.
4. Mottin, Melina, Joyce Villa Verde Bastos Borba, Cleber Camilo Melo-Filho et al. Computational drug discovery for the Zika virus. Brazilian Journal of Pharmaceutical Sciences (2018). DOI: 10.1590/s2175-97902018000001002.
5. Mottin, Melina, Joyce V.V.B. Borba, Rodolpho C. Braga et al. The A–Z of Zika drug discovery. Drug Discovery Today (2018). DOI: 10.1016/j.drudis.2018.06.014.
6. Mottin, Melina, Rodolpho C. Braga, Roosevelt A. da Silva, Joao H. Martins da Silva, Alexander L. Perryman, Sean Ekins and Carolina Horta Andrade. Molecular dynamics simulations of Zika virus NS3 helicase: Insights into RNA binding site activity. Biochemical and Biophysical Research Communications (2017). DOI: 10.1016/j.bbrc.2017.03.070.
7. Ekins, Sean, Alexander L. Perryman and Carolina Horta Andrade. OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery. PLOS Neglected Tropical Diseases (2016). DOI: 10.1371/journal.pntd.0005023.
8. Ekins, Sean, John Liebler, Bruno J. Neves, Warren G. Lewis, Megan Coffee, Rachelle Bienstock, Christopher Southan and Carolina H. Andrade. Illustrating and homology modeling the proteins of the Zika virus. F1000Research (2016). DOI: 10.12688/f1000research.8213.2.

World Community Grid (The Clean Energy Project)

1. Lopez, Steven A., Benjamin Sanchez-Lengeling, Julio De Goes Soares and Alán Aspuru-Guzik. Design Principles and Top Non-Fullerene Acceptor Candidates for Organic Photovoltaics. Joule (2017). DOI: 10.1016/j.joule.2017.10.006.
2. Pyzer-Knapp, Edward O., Changwon Suh, Rafael Gómez-Bombarelli, Jorge Aguilera-Iparraguirre and Alán Aspuru-Guzik. What Is High-Throughput Virtual Screening? A Perspective from Organic Materials Discovery. Annual Review of Materials Research (2015). DOI: 10.1146/annurev-matsci-070214-020823.
3. Pyzer-Knapp, Edward O., Kewei Li and Alan Aspuru-Guzik. Learning from the Harvard Clean Energy Project: The Use of Neural Networks to Accelerate Materials Discovery. Advanced Functional Materials (2015). DOI: 10.1002/adfm.201501919.
4. Hachmann, Johannes, Roberto Olivares-Amaya, Adrian Jinich et al. Lead candidates for high-performance organic photovoltaics from high-throughput quantum chemistry – the Harvard Clean Energy Project. Energy Environ. Sci. (2014). DOI: 10.1039/C3EE42756K.
5. Olivares-Amaya, Roberto, Carlos Amador-Bedolla, Johannes Hachmann, Sule Atahan-Evrenk, Roel S. Sánchez-Carrera, Leslie Vogt and Alán Aspuru-Guzik. Accelerated computational discovery of high-performance materials for organic photovoltaics by means of cheminformatics. Energy & Environmental Science (2011). DOI: 10.1039/c1ee02056k.
6. Hachmann, Johannes, Roberto Olivares-Amaya, Sule Atahan-Evrenk et al. The Harvard Clean Energy Project: Large-Scale Computational Screening and Design of Organic Photovoltaics on the World Community Grid. The Journal of Physical Chemistry Letters (2011). DOI: 10.1021/jz200866s.
7. Sokolov, Anatoliy N., Sule Atahan-Evrenk, Rajib Mondal et al. From computational discovery to experimental characterization of a high hole mobility organic crystal. Nature Communications (2011). DOI: 10.1038/ncomms1451.

XANSONS for COD

1. Neverov, Vladislav S. and Nikolay P. Khrapov. “XANSONS for COD”: a new small BOINC project in crystallography. Open Engineering (2018). DOI: 10.1515/eng-2018-0014.
2. Neverov, V. S. XaNSoNS: GPU-accelerated simulator of diffraction patterns of nanoparticles. SoftwareX (2017). DOI: 10.1016/j.softx.2017.01.004.

Yoyo@home (Evolution@home)

1. Waxman, D. and L. Loewe. A stochastic model for a single click of Muller's ratchet. Journal of Theoretical Biology (2010). DOI: 10.1016/j.jtbi.2010.03.014.
2. Loewe, Laurence and Asher D Cutter. On the potential for extinction by Muller's Ratchet in Caenorhabditis elegans. BMC Evolutionary Biology (2008). DOI: 10.1186/1471-2148-8-125.
3. Loewe, Laurence and Dunja K Lamatsch. Quantifying the threat of extinction from Muller's ratchet in the diploid Amazon molly (Poecilia formosa). BMC Evolutionary Biology (2008). DOI: 10.1186/1471-2148-8-88.
4. Loewe, Laurence. Evolution@home: observations on participant choice, work unit variation and low-effort global computing. Software: Practice and Experience (2007). DOI: 10.1002/spe.806.
5. Loewe, Laurence. Quantifying the genomic decay paradox due to Muller's ratchet in human mitochondrial DNA. Genetical Research (2006). DOI: 10.1017/S0016672306008123.
6. Loewe, Laurence. Evolution@home: Global computing quantifies evolution due to Muller's ratchet. BMC Bioinformatics (2005). DOI: 10.1186/1471-2105-6-S3-P18.

Yoyo@home (Harmonious Trees)

1. Fang, Wenjie and Uwe Beckert. Parallel Tree Search in Volunteer Computing: a Case Study. Journal of Grid Computing (2018). DOI: 10.1007/s10723-017-9411-5.

Yoyo@home (Muon)

1. Brooks, S. Muon capture schemes for the neutrino factory. (2010).

Yoyo@home (ORG)

1. Gerbicz, Robert, Jean-Charles Meyrignac and Uwe Beckert. All solutions of the Diophantine equation a^6+b^6=c^6+d^6+e^6+f^6+g^6 for a,b,c,d,e,f,g < 250000 found with a distributed Boinc project. (2011). DOI: 10.48550/ARXIV.1108.0462.

boinc@duq

1. General, Ignacio J., Eliana K. Asciutto and Jeffry D. Madura. Structure of Aqueous Sodium Perchlorate Solutions. The Journal of Physical Chemistry B (2008). DOI: 10.1021/jp806269w.

µFluids

1. Manning, Robert and Steven Collicott. Liquid Plugs in Rectangular Channels Under a Transverse Gravity Field. 48th AIAA Aerospace Sciences Meeting Including the New Horizons Forum and Aerospace Exposition (2010). DOI: 10.2514/6.2010-1476.
2. Braun, Jonathan and Steven Collicott. Zero-Gravity Stability of Droplets in a Bent Circular Cylinder. 44th AIAA Aerospace Sciences Meeting and Exhibit (2006). DOI: 10.2514/6.2006-732.
3. Manning, Robert and Steven Collicott. Bubble Penetration Through a Single Layer Sphere Bed. 44th AIAA Aerospace Sciences Meeting and Exhibit (2006). DOI: 10.2514/6.2006-736.