== '''This page is no longer active.''' == Please see this page: http://boinc.berkeley.edu/wiki/Publications_by_BOINC_projects = Scientific publications of BOINC-based projects = Science research projects typically publish their results in [WikiPedia:Scientific_journals scientific journals]. Preliminary results are often published in [WikiPedia:Scientific_conference 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 [BoincPapers here]). == [http://climateprediction.net/ Climateprediction.net] == #cpdn 1. James Murphy, David Sexton, David Barnett, Gareth Jones, Mark Webb, Matthew Collins & David Stainforth, [http://www.climateprediction.net/science/pubs/nature_murphy_02771.pdf Quantification of modelling uncertainties in a large ensemble of climate change simulations], Nature, 430, pp. 768-772, August 2004. 1. 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, [http://www.climateprediction.net/science/pubs/nature_first_results.pdf Uncertainty in predictions of the climate response to rising levels of greenhouse gases], Nature, 433, pp. 403-406, January 2005. 1. D. J. Frame, B. B. B. Booth, J. A. Kettleborough, D. A. Stainforth, J. M. Gregory, M. Collins, and M. R. Allen, [http://www.climateprediction.net/science/pubs/2004GL022241.pdf Constraining climate forecasts: The role of prior assumptions], Geophysical Review Letters, 32, May 2005. 1. C. Piani, D. J. Frame, D. A. Stainforth, and M. R. Allen, [http://www.agu.org/pubs/crossref/2005/2005GL024452.shtml Constraints on climate change from a multi-thousand member ensemble of simulations], Geophysical Review Letters, 32, December 2005. 1. P. Pall, M.R. Allen, D.A. Stone, [http://www.springerlink.com/content/7qu6714203652815/ Testing the Clausius-Clapeyron constraint on changes in extreme precipitation under CO2 warming]. Climate Dynamics, 23:4, pp. 351-363, August 2006. 1. M. Collins and S. Knight (Eds.), [http://publishing.royalsoc.ac.uk/index.cfm?page=1302 Ensembles and probabilities: a new era in the prediction of climate change], Phil. Trans. R. Soc. A, Print: 1364-503X, Online: 1471-2962, 2007. 1. 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, [http://www.pnas.org/cgi/content/abstract/104/30/12259 Association of parameter, software and hardware variation with large scale behavior across 57,000 climate models], PNAS, July 2007. 1. 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. 1. C. Piani, T. Aina, C. Christensen, D. Frame, N. Faull and M. Allen. [http://www.agu.org/pubs/crossref/2007/2007JD008712.shtml Regional probabilistic climate forecasts from a multi-thousand, multi-model ensemble of simulations], Journal of Geophysical Research, accepted, 2007. 1. D. J. Frame, N. E. Faull, M. M. Joshi & M. R. Allen, [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&uid=17580293&cmd=showdetailview&indexed=google Probabilistic climate forecasts and inductive problems], Philosophical Transactions of the Royal Society A, 2007. == [http://einstein.phys.uwm.edu/ Einstein@Home] == #einstein 1. [http://einstein.phys.uwm.edu/PartialS3Results First Report on the S3 Analysis] 1. [http://einstein.phys.uwm.edu/FinalS3Results Final Report on the S3 Analysis] == [http://boinc.umiacs.umd.edu/ Lattice] == #lattice 1. Grand, J., M. P. Cummings, A. G. Rebelo, T. H. Ricketts, and M. C. Neel. [http://lattice.umiacs.umd.edu/files/grand_et_al_2007.pdf Biased data reduce efficiency and effectiveness of conservation reserve networks]. Ecology Letters 10:364-374, 2007. 1. 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. [http://mbe.oxfordjournals.org/cgi/content/full/24/10/2180 History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation]. Molecular Biology and Evolution 24(10), 2180-2195 (2007). 1. N.J. Edwards and F. Pineda. [http://lattice.umiacs.umd.edu/files/ASMS2006.pdf Poster at ASMS] (2006). Rapid Microorganism Identification Database (www.RMIDb.org), 2006. 1. Varadan, R., Assfalg, M., Raasi, S., Pickart, C. & Fushman, D. [http://lattice.umiacs.umd.edu/files/MolCell_w_cover.pdf Structural Determinants for Selective Recognition of a Lys48-Linked Polyubiquitin Chain by a UBA Domain]. Mol Cell 18, 687-98 (2005). == [http://qah.uni-muenster.de/index.php QMC@Home] == #qmc 1. Korth, M., Lüchow, A., and Grimme, S. [http://pubs.acs.org/cgi-bin/abstract.cgi/jpcafh/2008/112/i10/abs/jp077592t.html 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. == [http://boinc.bakerlab.org/rosetta/ Rosetta@home] == #rosetta 1. Qian B, Raman S, Das R, Bradley P, !McCoy AJ, Read RJ, Baker D. [http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html High-resolution structure prediction and the crystallographic phase problem], Nature 450, 259-64 (2007). 1. Wang C, Bradley P, Baker D. [http://www.iscb.org/ismb2004/posters/maxATmolsoft.com_647.html Protein-protein docking with backbone flexibility]. J. Mol. Biol. 373, 503-19 (2007). 1. Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1459360 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). 1. 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). 1. 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. [http://www3.interscience.wiley.com/cgi-bin/abstract/116323415/ABSTRACT?CRETRY=1&SRETRY=0 Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home]. Proteins 69 Suppl 8, 118-28 (2007). 1. Das R, Baker D. [http://www.pnas.org/cgi/content/abstract/0703836104v1?etoc Automated de novo prediction of native-like RNA tertiary structures]. Proc. Natl. Acad. Sci. U.S.A. 104, 14664-9 (2007). == [http://setiathome.berkeley.edu SETI@home] == #seti 1. David P. Anderson, Jeff Cobb, Eric Korpela, Matt Lebofsky, Dan Werthimer. [http://delivery.acm.org/10.1145/590000/581573/p56-anderson.pdf?key1=581573&key2=8347574021&coll=GUIDE&dl=GUIDE&CFID=18978395&CFTOKEN=69072094 SETI@home: An Experiment in Public-Resource Computing]. Communications of the ACM, Vol. 45 No. 11, November 2002, pp. 56-61. == [http://boinc.bio.wzw.tum.de/boincsimap/ SIMAP] == #simap 1. Rattei T, Tischler P, Arnold R, Hamberger F, Krebs J, Krumsiek J, Wachinger B, Stümpflen V, Mewes W. [http://www.ncbi.nlm.nih.gov/pubmed/18037617 SIMAP--structuring the network of protein similarities.] Nucleic Acids Res. 2008 Jan;36(Database issue):D289-92. Epub 2007 Nov 23. 1. Rattei T, Arnold R, Tischler P, Lindner D, Stümpflen V, Mewes HW. [http://www.ncbi.nlm.nih.gov/pubmed/16381858 SIMAP: the similarity matrix of proteins]. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D252-6. 1. Arnold R, Rattei T, Tischler P, Truong MD, Stümpflen V, Mewes W. [http://www.ncbi.nlm.nih.gov/pubmed/16204123 SIMAP--the similarity matrix of proteins]. Bioinformatics. 2005 Sep 1;21 Suppl 2:ii42-6. == [http://spin.fh-bielfeld.de Spinhenge@home] == #spinhenge 1. Christian Schröder, Ruslan Prozorov, Paul Kögerler, Matthew D. Vannette, Xikui Fang, Marshall Luban, Akira Matsuo, Koichi Kindo, Achim Müller, Ana Maria Todea, [http://arxiv.org/abs/0801.2065 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 == [http://www.ufluids.net uFluids] == #ufluids 1. Robert E Manning & Steven H. Collicott. [http://www.ufluids.net/files/AIAApaper05.pdf Bubble Penetration Through a Single Layer Sphere Bed]. 45th AIAA Aerospace Sciences Meeting and Exhibit, January 2006. == [http://www.worldcommunitygrid.org/ World Community Grid] == #wcg '''FightAIDS@Home''' 1. Max W. Chang, William Lindstrom, Arthur J. Olson, and Richard K. Belew . [http://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/2007/47/i03/abs/ci700044s.html 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''' 1. 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''' 1. Lin Yang, Wenjin Chen, Peter Meer1, Gratian Salaru, Michael D. Feldman, and David J. Foran [http://pleiad.umdnj.edu/IBM/pdfs/Yang_et_al_miccai07.pdf 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''' 1. Lars Malmström, Michael Riffle, Charlie E. M. Strauss, Dylan Chivian, Trisha N. Davis, Richard Bonneau, David Baker. [http://www.ncbi.nlm.nih.gov/pubmed/17373854 Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology]. PLoS Biol 5(4).