Philip E. Bourne

Philip E. Bourne: The reaming of life: based on the 2010 Jim Gray eScience Award Lecture. Concurrency and Computation: Practice and Experience 25(4): 445-453 (2013)

Peter W. Rose, Chunxiao Bi, Wolfgang Bluhm, Cole H. Christie, Dimitris Dimitropoulos, Shuchismita Dutta, Rachel Kramer Green, David S. Goodsell, Andreas Prlic, Martha Quesada, Greg B. Quinn, Alexander G. Ramos, John D. Westbrook, Jasmine Young, Christine Zardecki, Helen M. Berman, Philip E. Bourne: The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Research 41(Database-Issue): 475-482 (2013)

Andreas Prlic, Andrew Yates, Spencer Bliven, Peter W. Rose, Julius Jacobsen, Peter V. Troshin, Mark Chapman, Jianjiong Gao, Chuan Hock Koh, Sylvain Foisy, Richard R. C. Holland, Gediminas Rimsa, Michael L. Heuer, Hannes Brandstätter-Müller, Philip E. Bourne, Scooter Willis: BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics 28(20): 2693-2695 (2012)

Nikolai Hecker, Jessica Ahmed, Joachim von Eichborn, Mathias Dunkel, Karel Macha, Andreas Eckert, Michael K. Gilson, Philip E. Bourne, Robert Preissner: SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Research 40(Database-Issue): 1113-1117 (2012)

Yohan Kim, Julia V. Ponomarenko, Zhanyang Zhu, Dorjee Tamang, Peng Wang, Jason Greenbaum, Claus Lundegaard, Alessandro Sette, Ole Lund, Philip E. Bourne, Morten Nielsen, Bjoern Peters: Immune epitope database analysis resource. Nucleic Acids Research 40(Web-Server-Issue): 525-530 (2012)

Rosemary Dickin, Chris James Hall, Laura K. Taylor, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne: A Review of 2011 for PLoS Computational Biology. PLoS Computational Biology 8(1) (2012)

Anthony C. Fletcher, Philip E. Bourne: Ten Simple Rules for Starting a Company. PLoS Computational Biology 8(3) (2012)

Shoshana J. Wodak, Daniel Mietchen, Andrew M. Collings, Robert B. Russell, Philip E. Bourne: Topic Pages: PLoS Computational Biology Meets Wikipedia. PLoS Computational Biology 8(3) (2012)

Anthony C. Fletcher, Philip E. Bourne: Ten Simple Rules To Commercialize Scientific Research. PLoS Computational Biology 8(9) (2012)

Philip E. Bourne: Seven Years; It's Time for a Change. PLoS Computational Biology 8(10) (2012)

Thomas Evangelidis, Philip E. Bourne, Li Xie, Lei Xie: An integrated workflow for proteome-wide off-target identification and polypharmacology drug design. BIBM Workshops 2012: 32-39

Joachim von Eichborn, Philip E. Bourne, Robert Preissner: Cobweb: a Java applet for network exploration and visualisation. Bioinformatics 27(12): 1725-1726 (2011)

Apostol Gramada, Philip E. Bourne: Coarse-graining the electrostatic potential via distributed multipole expansions. Computer Physics Communications 182(7): 1455-1462 (2011)

Peter W. Rose, Bojan Beran, Chunxiao Bi, Wolfgang Bluhm, Dimitris Dimitropoulos, David S. Goodsell, Andreas Prlic, Martha Quesada, Greg B. Quinn, John D. Westbrook, Jasmine Young, Benjamin T. Yukich, Christine Zardecki, Helen M. Berman, Philip E. Bourne: The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Research 39(Database-Issue): 392-401 (2011)

Joachim von Eichborn, Manuela S. Murgueitio, Mathias Dunkel, Soeren Koerner, Philip E. Bourne, Robert Preissner: PROMISCUOUS: a database for network-based drug-repositioning. Nucleic Acids Research 39(Database-Issue): 1060-1066 (2011)

Julia V. Ponomarenko, Nikitas Papangelopoulos, Dirk M. Zajonc, Björn Peters, Alessandro Sette, Philip E. Bourne: IEDB-3D: structural data within the immune epitope database. Nucleic Acids Research 39(Database-Issue): 1164-1170 (2011)

Philip E. Bourne: Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS Computational Biology 7(1) (2011)

Rosemary Dickin, Cecy Marden, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne: A Review of 2010 for PLoS Computational Biology. PLoS Computational Biology 7(1) (2011)

Li Xie, Thomas Evangelidis, Lei Xie, Philip E. Bourne: Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir. PLoS Computational Biology 7(4) (2011)

Philip E. Bourne, Virginia Barbour: Ten Simple Rules for Building and Maintaining a Scientific Reputation. PLoS Computational Biology 7(6) (2011)

Fran Lewitter, Philip E. Bourne: Teaching Bioinformatics at the Secondary School Level. PLoS Computational Biology 7(10) (2011)

Philip E. Bourne, Timothy W. Clark, Robert Dale, Anita de Waard, Ivan Herman, Eduard H. Hovy, David Shotton: Improving The Future of Research Communications and e-Scholarship (Dagstuhl Perspectives Workshop 11331). Dagstuhl Manifestos 1(1): 41-60 (2011)

Andreas Prlic, Spencer Bliven, Peter W. Rose, Wolfgang Bluhm, Chris Bizon, Adam Godzik, Philip E. Bourne: Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics 26(23): 2983-2985 (2010)

J. Lynn Fink, Pablo Fernicola, Rahul Chandran, Savas Parastatidis, Alex Wade, Oscar Naim, Greg B. Quinn, Philip E. Bourne: Word add-in for ontology recognition: semantic enrichment of scientific literature. BMC Bioinformatics 11: 103 (2010)

Andreas Prlic, Marco A. Martinez, Dimitris Dimitropoulos, Bojan Beran, Benjamin T. Yukich, Peter W. Rose, Philip E. Bourne, J. Lynn Fink: Integration of open access literature into the RCSB Protein Data Bank using BioLit. BMC Bioinformatics 11: 220 (2010)

Kieran Alden, Stella Veretnik, Philip E. Bourne: dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. BMC Bioinformatics 11: 310 (2010)

Jingyuan Ren, Lei Xie, Wilfred W. Li, Philip E. Bourne: SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. Nucleic Acids Research 38(Web-Server-Issue): 441-444 (2010)

Jacob D. Durrant, Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti Haapalainen, Zhijun Chen, Anne Marie Di Guilmi, Frank Wunder, Philip E. Bourne, James Andrew McCammon: A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. PLoS Computational Biology 6(1) (2010)

Philip E. Bourne, Bojan Beran, Chunxiao Bi, Wolfgang Bluhm, Roland Dunbrack, Andreas Prlic, Greg B. Quinn, Peter W. Rose, Raship Shah, Wendy Tao, Brian Weitzner, Benjamin T. Yukich: Will Widgets and Semantic Tagging Change Computational Biology? PLoS Computational Biology 6(2) (2010)

Rosemary Dickin, Cecy Marden, Catherine Nancarrow, Philip E. Bourne: A Review of 2009 for PLoS Computational Biology. PLoS Computational Biology 6(2) (2010)

Ruchira S. Datta, Matthew W. Lux, Philip E. Bourne: PLoS Computational Biology Conference Postcards from PSB 2010. PLoS Computational Biology 6(4) (2010)

Philip E. Bourne: What Do I Want from the Publisher of the Future? PLoS Computational Biology 6(5) (2010)

Roger L. Chang, Li Xie, Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson: Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model. PLoS Computational Biology 6(9) (2010)

Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Philip E. Bourne: The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications. PLoS Computational Biology 6(11) (2010)

Lei Xie, Li Xie, Philip E. Bourne: A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinformatics 25(12) (2009)

Evie Browne, Rosemary Dickin, Philip E. Bourne: A Review of 2008 for PLoS Computational Biology. PLoS Computational Biology 5(1) (2009)

Stella Veretnik, Christopher Wills, Philippe Youkharibache, Ruben E. Valas, Philip E. Bourne: Sm/Lsm Genes Provide a Glimpse into the Early Evolution of the Spliceosome. PLoS Computational Biology 5(3) (2009)

Quentin Vicens, Philip E. Bourne: Ten Simple Rules To Combine Teaching and Research. PLoS Computational Biology 5(4) (2009)

Li Xie, Jerry Li, Lei Xie, Philip E. Bourne: Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors. PLoS Computational Biology 5(5) (2009)

Sarah L. Kinnings, Nina Liu, Nancy Buchmeier, Peter J. Tonge, Lei Xie, Philip E. Bourne: Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis. PLoS Computational Biology 5(7) (2009)

Alex Bateman, Philip E. Bourne: Ten Simple Rules for Chairing a Scientific Session. PLoS Computational Biology 5(9) (2009)

Julia V. Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E. Bourne, Alessandro Sette, Björn Peters: ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics 9 (2008)

Stefan Günther, Michael Kuhn, Mathias Dunkel, Monica Campillos, Christian Senger, Evangelia Petsalaki, Jessica Ahmed, Eduardo Garcia Urdiales, Andreas Gewiess, Lars Juhl Jensen, Reinhard Schneider, Roman Skoblo, Robert B. Russell, Philip E. Bourne, Peer Bork, Robert Preissner: SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Research 36(Database-Issue): 919-922 (2008)

Raphael A. Bauer, Philip E. Bourne, Arno Formella, Cornelius Frömmel, Christoph Gille, Andrean Goede, Aysam Guerler, Andreas Hoppe, Ernst-Walter Knapp, Thorsten Pöschel, Burghardt Wittig, Valentin Ziegler, Robert Preissner: Superimposé: a 3D structural superposition server. Nucleic Acids Research 36(Web-Server-Issue): 47-54 (2008)

J. Lynn Fink, Sergey Kushch, Parker R. Williams, Philip E. Bourne: BioLit: integrating biological literature with databases. Nucleic Acids Research 36(Web-Server-Issue): 385-389 (2008)

Qing Zhang, Peng Wang, Yohan Kim, Pernille Haste-Andersen, John E. Beaver, Philip E. Bourne, Huynh-Hoa Bui, Søren Buus, Sune Frankild, Jason Greenbaum, Ole Lund, Claus Lundegaard, Morten Nielsen, Julia V. Ponomarenko, Alessandro Sette, Zhanyang Zhu, Björn Peters: Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Research 36(Web-Server-Issue): 513-518 (2008)

Philip E. Bourne, J. Lynn Fink, Mark Gerstein: Open Access: Taking Full Advantage of the Content. PLoS Computational Biology 4(3) (2008)

Manuel Corpas, Nils Gehlenborg, Sarath Chandra Janga, Philip E. Bourne: Ten Simple Rules for Organizing a Scientific Meeting. PLoS Computational Biology 4(6) (2008)

Stella Veretnik, J. Lynn Fink, Philip E. Bourne: Computational Biology Resources Lack Persistence and Usability. PLoS Computational Biology 4(7) (2008)

Philip E. Bourne, J. Lynn Fink: I Am Not a Scientist, I Am a Number. PLoS Computational Biology 4(12) (2008)

K. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman: Session Introduction. Pacific Symposium on Biocomputing 2008: 551-555

J. Gregory Caporaso, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, Lawrence Hunter: Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks. Pacific Symposium on Biocomputing 2008: 640-651

Jo-Lan Chung, John E. Beaver, Eric D. Scheeff, Philip E. Bourne: Con-Struct Map: a comparative contact map analysis tool. Bioinformatics 23(18): 2491-2492 (2007)

Jo-Lan Chung, Wei Wang, Philip E. Bourne: High-throughput identification of interacting protein-protein binding sites. BMC Bioinformatics 8 (2007)

Jenny Gu, Philip E. Bourne: Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2. BMC Bioinformatics 8 (2007)

Lei Xie, Philip E. Bourne: A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinformatics 8(S-4) (2007)

Quentin Vicens, Philip E. Bourne: Ten Simple Rules for a Successful Collaboration. PLoS Computational Biology 3(3) (2007)

Philip E. Bourne: Ten Simple Rules for Making Good Oral Presentations. PLoS Computational Biology 3(4) (2007)

Thomas C. Erren, Philip E. Bourne: Ten Simple Rules for a Good Poster Presentation. PLoS Computational Biology 3(5) (2007)

Lawrence Hunter, Russ B. Altman, Philip E. Bourne: The International Society for Computational Biology 10th Anniversary. PLoS Computational Biology 3(6) (2007)

Philip E. Bourne, Steven E. Brenner: Developing Computational Biology. PLoS Computational Biology 3(9) (2007)

Thomas C. Erren, Paul Cullen, Michael Erren, Philip E. Bourne: Ten Simple Rules for Doing Your Best Research, According to Hamming. PLoS Computational Biology 3(10) (2007)

Jenny Gu, Philip E. Bourne: Ten Simple Rules for Graduate Students. PLoS Computational Biology 3(11) (2007)

Lei Xie, Jian Wang, Philip E. Bourne: In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators. PLoS Computational Biology 3(11) (2007)

Apostol Gramada, Philip E. Bourne: Multipolar representation of protein structure. BMC Bioinformatics 7: 242 (2006)

Randi Vita, Kerrie Vaughan, Laura Zarebski, Nima Salimi, Ward Fleri, Howard Grey, Muthu Sathiamurthy, John Mokili, Huynh-Hoa Bui, Philip E. Bourne, Julia V. Ponomarenko, Romulo de Castro Jr., Russell K. Chan, John Sidney, Stephen S. Wilson, Scott Stewart, Scott Way, Björn Peters, Alessandro Sette: Curation of complex, context-dependent immunological data. BMC Bioinformatics 7: 341 (2006)

Eric D. Scheeff, Philip E. Bourne: Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics 7: 410 (2006)

Andrei Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John D. Westbrook, Philip E. Bourne, Helen M. Berman: The RCSB PDB information portal for structural genomics. Nucleic Acids Research 34(Database-Issue): 302-305 (2006)

Philip E. Bourne, Leo M. Chalupa: Ten Simple Rules for Getting Grants. PLoS Computational Biology 2(2) (2006)

Goran Neshich, Philip E. Bourne, Søren Brunak: ISMB 2006. PLoS Computational Biology 2(2) (2006)

Jenny Gu, Michael Gribskov, Philip E. Bourne: Wiggle - Predicting Functionally Flexible Regions from Primary Sequence. PLoS Computational Biology 2(7) (2006)

Philip E. Bourne: One Year of PLoS Computational Biology. PLoS Computational Biology 2(8) (2006)

Philip E. Bourne, Alon Korngreen: Ten Simple Rules for Reviewers. PLoS Computational Biology 2(9) (2006)

Philip E. Bourne, Johanna R. McEntyre: Biocurators: Contributors to the World of Science. PLoS Computational Biology 2(10) (2006)

Philip E. Bourne, Iddo Friedberg: Ten Simple Rules for Selecting a Postdoctoral Position. PLoS Computational Biology 2(11) (2006)

Philip E. Bourne, Iddo Friedberg: Correction: Ten Simple Rules for Selecting a Postdoctoral Position. PLoS Computational Biology 2(12) (2006)

Philip E. Bourne, Søren Brunak: ISMB 2006. ISMB (Supplement of Bioinformatics) 2006: 1-2

Alessandro Sette, Huynh-Hoa Bui, John Sidney, Philip E. Bourne, Søren Buus, Ward Fleri, R. Kubo, Ole Lund, D. Nemazee, Julia V. Ponomarenko, Muthu Sathiamurthy, Scott Stewart, Scott Way, Stephen S. Wilson, Björn Peters: The Immune Epitope Database and Analysis Resource. PRIB 2006: 126-132

John L. Moreland, Apostol Gramada, Oleksandr V. Buzko, Qing Zhang, Philip E. Bourne: The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. BMC Bioinformatics 6: 21 (2005)

Nita Deshpande, Kenneth J. Addess, Wolfgang Bluhm, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Qing Zhang, Charlie Knezevich, Lie Xie, Li Chen, Zukang Feng, Rachel Kramer Green, Judith L. Flippen-Anderson, John D. Westbrook, Helen M. Berman, Philip E. Bourne: The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Research 33(Database-Issue): 233-237 (2005)

Philip E. Bourne, Steven E. Brenner, Michael B. Eisen: PLoS Computational Biology: A New Community Journal. PLoS Computational Biology 1(1) (2005)

Philip E. Bourne: Will a Biological Database Be Different from a Biological Journal? PLoS Computational Biology 1(3) (2005)

Lei Xie, Philip E. Bourne: Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models. PLoS Computational Biology 1(3) (2005)

Philip E. Bourne: Ten Simple Rules for Getting Published. PLoS Computational Biology 1(5) (2005)

Eric D. Scheeff, Philip E. Bourne: Structural Evolution of the Protein Kinase-Like Superfamily. PLoS Computational Biology 1(5) (2005)

Patricia C. Babbitt, Philip E. Bourne, Sean D. Mooney: Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular STructure. Pacific Symposium on Biocomputing 2005

Philip E. Bourne, John D. Westbrook, Helen M. Berman: The Protein Data Bank and lessons in data management. Briefings in Bioinformatics 5(1): 23-30 (2004)

Werner G. Krebs, Philip E. Bourne: Statistically rigorous automated protein annotation. Bioinformatics 20(7): 1066-1073 (2004)

Dmitry Pekurovsky, Ilya N. Shindyalov, Philip E. Bourne: A case study of high-throughput biological data processing on parallel platforms. Bioinformatics 20(12): 1940-1947 (2004)

Werner G. Krebs, Philip E. Bourne: Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. J. Bioinformatics and Computational Biology 2(1): 61-76 (2004)

Yuting Jia, T. Gregory Dewey, Ilya N. Shindyalov, Philip E. Bourne: A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE. Journal of Computational Biology 11(5): 787-799 (2004)

Philip E. Bourne, Kenneth J. Addess, Wolfgang Bluhm, Li Chen, Nita Deshpande, Zukang Feng, Ward Fleri, Rachel Kramer Green, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Helge Weissig, John D. Westbrook, Helen M. Berman: The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Research 32(Database-Issue): 223-225 (2004)

Chittibabu Guda, Sifang Lu, Eric D. Scheeff, Philip E. Bourne, Ilya N. Shindyalov: CE-MC: a multiple protein structure alignment server. Nucleic Acids Research 32(Web-Server-Issue): 100-103 (2004)

Wilfred W. Li, Robert W. Byrnes, Jim Hayes, Adam Birnbaum, Vicente M. Reyes, Atif Shahab, Coleman Mosley, Dmitry Pekurovsky, Greg B. Quinn, Ilya N. Shindyalov, Henri Casanova, Larry Ang, Fran Berman, Peter W. Arzberger, Mark A. Miller, Philip E. Bourne: The Encyclopedia of Life Project: Grid Software and Deployment. New Generation Comput. 22(2): 127-136 (2004)

Philip E. Bourne: The Future of Bioinformatics. APBC 2004: 3

Atif Shahab, Danny Chuon, Toyotaro Suzumura, Wilfred W. Li, Robert W. Byrnes, Kouji Tanaka, Larry Ang, Satoshi Matsuoka, Philip E. Bourne, Mark A. Miller, Peter W. Arzberger: Grid Portal Interface for Interactive Use and Monitoring of High-Throughput Proteome Annotation. LSGRID 2004: 53-67

Adam Birnbaum, James Hayes, Wilfred W. Li, Mark A. Miller, Peter W. Arzberger, Philip E. Bourne, Henri Casanova: Grid Workflow Software for a High-Throughput Proteome Annotation Pipeline. LSGRID 2004: 68-81

Sean D. Mooney, Philip E. Bourne, Patricia C. Babbitt: Session Introduction. Pacific Symposium on Biocomputing 2004: 372-374

Philip E. Bourne, C. K. J. Allerston, Werner G. Krebs, Wilfred W. Li, Ilya N. Shindyalov, Adam Godzik, Iddo Friedberg, Tong Liu, David L. Wild, Seungwoo Hwang, Zoubin Ghahramani, Li Chen, John D. Westbrook: The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures. Pacific Symposium on Biocomputing 2004: 375-386

Philip E. Bourne, Dan Gusfield (Eds.): Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004, San Diego, California, USA, March 27-31, 2004. ACM 2004, isbn 1-58113-755-9

Peng Yang, Paul A. Craig, David S. Goodsell, Philip E. Bourne: BioEditor - Simplifying Macromolecular Structure Annotation. Bioinformatics 19(7): 897-898 (2003)

Philip E. Bourne: High Performance Computational Biology - Past Progress and Future Promise. CSB 2003: 13

Werner G. Krebs, Philip E. Bourne: Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. CSB 2003: 180-189

Dmitry Pekurovsky, Ilya N. Shindyalov, Philip E. Bourne: Parallel Processing on Large Redudant Biological Data Sets: Protein Structures Classification with CEPAR. PARCO 2003: 661-668

Douglas S. Greer, John D. Westbrook, Philip E. Bourne: An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics 18(9): 1280-1281 (2002)

John D. Westbrook, Zukang Feng, Shri Jain, T. N. Bhat, Narmada Thanki, Veerasamy Ravichandran, Gary Gilliland, Wolfgang Bluhm, Helge Weissig, Douglas S. Greer, Philip E. Bourne, Helen M. Berman: The Protein Data Bank: unifying the archive. Nucleic Acids Research 30(1): 245-248 (2002)

Wilfred W. Li, Boojala V. B. Reddy, John G. Tate, Ilya N. Shindyalov, Philip E. Bourne: CKAAPs DB: a Conserved Key Amino Acid Positions DataBase. Nucleic Acids Research 30(1): 409-411 (2002)

Julia V. Ponomarenko, Philip E. Bourne, Ilya N. Shindyalov: Building an automated classification of DNA-binding protein domains. ECCB 2002: 192-201

T. N. Bhat, Philip E. Bourne, Zukang Feng, Gary Gilliland, Shri Jain, Veerasamy Ravichandran, Bohdan Schneider, Kata Schneider, Narmada Thanki, Helge Weissig, John D. Westbrook, Helen M. Berman: The PDB data uniformity project. Nucleic Acids Research 29(1): 214-218 (2001)

Ilya N. Shindyalov, Philip E. Bourne: A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. Nucleic Acids Research 29(1): 228-229 (2001)

Wilfred W. Li, Boojala V. B. Reddy, Ilya N. Shindyalov, Philip E. Bourne: CKAAPs DB: a conserved key amino acid positions database. Nucleic Acids Research 29(1): 329-331 (2001)

Chittibabu Guda, Eric D. Scheeff, Philip E. Bourne, Ilya N. Shindyalov: A New Algorithm for the Alignment of Multiple Protein Structures Using Monte Carlo Optimization. Pacific Symposium on Biocomputing 2001: 275-286

John D. Westbrook, Philip E. Bourne: STAR/mmCIF: An ontology for macromolecular structure. Bioinformatics 16(2): 159-168 (2000)

Philip E. Bourne, Michael Gribskov: ISMB-2000: Bioinformatics enters a new millennium. Bioinformatics 16(9): 749 (2000)

Helen M. Berman, John D. Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne: The Protein Data Bank. Nucleic Acids Research 28(1): 235-242 (2000)

Philip E. Bourne, Michael Gribskov, Russ B. Altman, Nancy Jensen, Debra A. Hope, Thomas Lengauer, Julie C. Mitchell, Eric D. Scheeff, Chris Smith, Shawn Strande, Helge Weissig (Eds.): Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, August 19-23, 2000, La Jolla / San Diego, CA, USA. AAAI 2000, isbn 1-57735-115-0

Helge Weissig, Philip E. Bourne: An analysis of the Protein Data Bank in search of temporal and global trends. Bioinformatics 15(10): 807-831 (1999)

Greg B. Quinn, H.-P. Wang, D. Martinez, Philip E. Bourne: Developing Protein Documentaries and Other Multimedia Presentations for Molecular Biology. Pacific Symposium on Biocomputing 1999: 380-391

Ilya N. Shindyalov, Philip E. Bourne: Protein data representation and query using optimized data decomposition. Computer Applications in the Biosciences 13(5): 487-496 (1997)

John Biggs, Calton Pu, Philip E. Bourne: Code Generation through Annotation of Macromolecular Structure Data. ISMB 1997: 52-55

Ilya N. Shindyalov, Weider Chang, J. A. Cooper, Philip E. Bourne: Design and use of a software framework to obtain information derived from macromolecular structure data. HICSS (5) 1995: 207-216

P. Zhang, E. A. Schon, S. G. Fischer, E. Cayanis, J. Weiss, S. Kistler, Philip E. Bourne: An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA. Computer Applications in the Biosciences 10(3): 309-317 (1994)

Weider Chang, Ilya N. Shindyalov, Calton Pu, Philip E. Bourne: Design and application of PDBlib, a C++ macromolecular class library. Computer Applications in the Biosciences 10(6): 575-586 (1994)

Weider Chang, Ilya N. Shindyalov, Calton Pu, Philip E. Bourne: Design and Application of a C++ Macromolecular Class Library. ISMB 1994: 70-77