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Table of Contents

• This page is no longer active.
• Scientific publications of BOINC-based projects
• Climateprediction.net
• Einstein@Home
• Lattice
• QMC@Home
• Rosetta@home
• SETI@home
• SIMAP
• Spinhenge@home
• uFluids
• World Community Grid

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Please see this page: Publications_by_BOINC_projects

Scientific publications of BOINC-based projects

Science research projects typically publish their results in scientific journals. Preliminary results are often published in conferences. In the academic world, the scientific contribution of a project is measured largely by the number of its publications, and the prestige of the journals and conferences in which they appear (high-prestige journals include Nature, Science, and PNAS).

We encourage BOINC volunteers to support projects that make a major scientific contribution. Keep in mind that doing research and publishing papers may take several years, so newer projects will naturally have few or no publications.

The following scientific papers have resulted from BOINC-based projects (this list does not include papers about volunteer computing or about BOINC itself; those are here).

Climateprediction.net

1. James Murphy, David Sexton, David Barnett, Gareth Jones, Mark Webb, Matthew Collins & David Stainforth, Quantification of modelling uncertainties in a large ensemble of climate change simulations, Nature, 430, pp. 768-772, August 2004.
2. D. A. Stainforth, T. Aina, C. Christensen, M. Collins, N. Faull, D. J. Frame, J. A. Kettleborough, S. Knight, A. Martin, J. M. Murphy, C. Piani, D. Sexton, L. A. Smith, R. A. Spicer, A. J. Thorpe & M. R. Allen, Uncertainty in predictions of the climate response to rising levels of greenhouse gases, Nature, 433, pp. 403-406, January 2005.
3. D. J. Frame, 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 Review Letters, 32, May 2005.
4. C. Piani, D. J. Frame, D. A. Stainforth, and M. R. Allen, Constraints on climate change from a multi-thousand member ensemble of simulations, Geophysical Review Letters, 32, December 2005.
5. P. Pall, M.R. Allen, D.A. Stone, Testing the Clausius-Clapeyron constraint on changes in extreme precipitation under CO2 warming. Climate Dynamics, 23:4, pp. 351-363, August 2006.
6. M. Collins and S. Knight (Eds.), Ensembles and probabilities: a new era in the prediction of climate change, Phil. Trans. R. Soc. A, Print: 1364-503X, Online: 1471-2962, 2007.
7. C.G. Knight, S.H.E. Knight, N. Massey, T. Aina, C. Christensen, D.J. Frame, J.A. Kettleborough, A. Martin, S. Pascoe, B. Sanderson, D.A. Stainforth, M.R. Allen, Association of parameter, software and hardware variation with large scale behavior across 57,000 climate models, PNAS, July 2007.
8. B. M. Sanderson, R. Knutti, T. Aina, C. M. Christensen, N. E. Faull, D. J. Frame, W. J. Ingram, C. Piani, D. A. Stainforth, D. A. Stone and M. R. Allen. Constraints on model response to greenhouse gas forcing and the role of sub-grid scale processes, Journal of Climate, in press, 2007.
9. C. Piani, T. Aina, C. Christensen, D. Frame, N. Faull and M. Allen. Regional probabilistic climate forecasts from a multi-thousand, multi-model ensemble of simulations, Journal of Geophysical Research, accepted, 2007.
10. D. J. Frame, N. E. Faull, M. M. Joshi & M. R. Allen, Probabilistic climate forecasts and inductive problems, Philosophical Transactions of the Royal Society A, 2007.

Einstein@Home

1. First Report on the S3 Analysis
2. Final Report on the S3 Analysis

Lattice

1. Grand, J., M. P. Cummings, A. G. Rebelo, T. H. Ricketts, and M. C. Neel. Biased data reduce efficiency and effectiveness of conservation reserve networks. Ecology Letters 10:364-374, 2007.
2. Tishkoff, S. A., Gonder, M. K., Henn, B. M., Mortensen, H., Knight, A., Gignoux, C., Fernandopulle, N., Lema, G., Nyambo, T. B., Ramakrishnan, U., Floyd A. Reed, F. A. & Mountain, J. L. History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation. Molecular Biology and Evolution 24(10), 2180-2195 (2007).
3. N.J. Edwards and F. Pineda. Poster at ASMS (2006). Rapid Microorganism Identification Database (www.RMIDb.org), 2006.
4. Varadan, R., Assfalg, M., Raasi, S., Pickart, C. & Fushman, D. Structural Determinants for Selective Recognition of a Lys48-Linked Polyubiquitin Chain by a UBA Domain. Mol Cell 18, 687-98 (2005).

QMC@Home

1. Korth, M., Lüchow, A., and Grimme, S. Toward the Exact Solution of the Electronic Schrödinger Equation for Noncovalent Molecular Interactions: Worldwide Distributed Quantum Monte Carlo Calculations, J. Phys. Chem. A, 112 (10), 2104 -2109.

Rosetta@home

1. Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. High-resolution structure prediction and the crystallographic phase problem, Nature 450, 259-64 (2007).
2. Wang C, Bradley P, Baker D. Protein-protein docking with backbone flexibility. J. Mol. Biol. 373, 503-19 (2007).
3. Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc. Natl. Acad. Sci. U.S.A. 103, 5361-6 (2006).
4. Rhiju Das, Madhuri Kudaravalli, Magdalena Jonikas, Alain Laederach, Robert Fong, Jason P. Schwans, David Baker, Joseph A. Piccirilli, Russ B. Altman, and Daniel Herschlag, Structural inference of native and partially folded RNA by high throughput contact mapping, PNAS, in press (2008).
5. Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, Andre I, Baker D. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 69 Suppl 8, 118-28 (2007).
6. Das R, Baker D. Automated de novo prediction of native-like RNA tertiary structures. Proc. Natl. Acad. Sci. U.S.A. 104, 14664-9 (2007).

SETI@home

1. David P. Anderson, Jeff Cobb, Eric Korpela, Matt Lebofsky, Dan Werthimer. SETI@home: An Experiment in Public-Resource Computing. Communications of the ACM, Vol. 45 No. 11, November 2002, pp. 56-61.

SIMAP

1. Rattei T, Tischler P, Arnold R, Hamberger F, Krebs J, Krumsiek J, Wachinger B, Stümpflen V, Mewes W. SIMAP--structuring the network of protein similarities. Nucleic Acids Res. 2008 Jan;36(Database issue):D289-92. Epub 2007 Nov 23.
2. Rattei T, Arnold R, Tischler P, Lindner D, Stümpflen V, Mewes HW. SIMAP: the similarity matrix of proteins. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D252-6.
3. Arnold R, Rattei T, Tischler P, Truong MD, Stümpflen V, Mewes W. SIMAP--the similarity matrix of proteins. Bioinformatics. 2005 Sep 1;21 Suppl 2:ii42-6.

Spinhenge@home

1. Christian Schröder, Ruslan Prozorov, Paul Kögerler, Matthew D. Vannette, Xikui Fang, Marshall Luban, Akira Matsuo, Koichi Kindo, Achim Müller, Ana Maria Todea, Multiple nearest-neighbor exchange model for the frustrated Keplerate magnetic molecules {Mo72Fe30} and {Mo72Cr30}. submitted to PHYSICAL REVIEW B 77, 224409 (2008), arXiv.org e-Print archiv, Jan 2008

uFluids

1. Robert E Manning & Steven H. Collicott. Bubble Penetration Through a Single Layer Sphere Bed. 45th AIAA Aerospace Sciences Meeting and Exhibit, January 2006.

World Community Grid

FightAIDS@Home

1. Max W. Chang, 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. J. Chem. Inf. Model., 47 (3), 1258 -1262, 2007. Help Conquer Cancer
2. C.A. Cumbaa & I. Jurisica, Scale Changes Everything – Crystallography Image Analysis on the World Community Grid. 22nd High Performance Computing Symposium - Québec City, CA. June, 2008 Help Defeat Cancer
3. Lin Yang, Wenjin Chen, Peter Meer1, Gratian Salaru, Michael D. Feldman, and David J. Foran High Throughput Analysis of Breast Cancer Specimens on the Grid. Proceedings on Medical Image Computing and Computer-Assisted Intervention. (MICCAI) Brisbane, Australia. October, 2007. Human Proteome Folding - Phase I
4. Lars Malmström, Michael Riffle, Charlie E. M. Strauss, Dylan Chivian, Trisha N. Davis, Richard Bonneau, David Baker. Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology. PLoS Biol 5(4).

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