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

Design and application of PDBlib, a C++ macromolecular class library. - Weider Chang; Ilya N. Shindyalov; Calton Pu; Philip E. Bourne (Comput. Appl. Biosci., 1994)

An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA. - Peisen Zhang; Eric A. Schon; Stuart G. Fischer; Eftihia Cayanis; Janie Weiss; Susan Kistler; Philip E. Bourne (Comput. Appl. Biosci., 1994)

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

Code Generation through Annotation of Macromolecular Structure Data. - John Biggs; Calton Pu; Philip E. Bourne (ISMB, 1997)

Protein data representation and query using optimized data decomposition. - Ilya N. Shindyalov; Philip E. Bourne (Comput. Appl. Biosci., 1997)

Developing Protein Documentaries and Other Multimedia Presentations for Molecular Biology. - Greg B. Quinn; H.-P. Wang; David Martínez 003; Philip E. Bourne (Pacific Symposium on Biocomputing, 1999)

An analysis of the Protein Data Bank in search of temporal and global trends. - Helge Weissig; Philip E. Bourne (Bioinform., 1999)

ISMB-2000: Bioinformatics enters a new millennium. - Philip E. Bourne; Michael Gribskov (Bioinform., 2000)

STAR/mmCIF: An ontology for macromolecular structure. - John D. Westbrook; Philip E. Bourne (Bioinform., 2000)

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

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

The PDB data uniformity project. - 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 (Nucleic Acids Res., 2001)

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

A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. - Ilya N. Shindyalov; Philip E. Bourne (Nucleic Acids Res., 2001)

Building an automated classification of DNA-binding protein domains. - Julia V. Ponomarenko; Philip E. Bourne; Ilya N. Shindyalov (ECCB, 2002)

An ontology driven architecture for derived representations of macromolecular structure. - Douglas S. Greer; John D. Westbrook; Philip E. Bourne (Bioinform., 2002)

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

The Protein Data Bank: unifying the archive. - 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 (Nucleic Acids Res., 2002)

High Performance Computational Biology - Past Progress and Future Promise. - Philip E. Bourne (CSB, 2003)

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

BioEditor - Simplifying Macromolecular Structure Annotation. - Peng Yang; Paul A. Craig; David S. Goodsell; Philip E. Bourne (Bioinform., 2003)

The Future of Bioinformatics. - Philip E. Bourne (APBC, 2004)

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

Grid Portal Interface for Interactive Use and Monitoring of High-Throughput Proteome Annotation. - 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 (LSGRID, 2004)

The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures. - 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 022; et al. (Pacific Symposium on Biocomputing, 2004)

Session Introduction. - Sean D. Mooney; Philip E. Bourne; Patricia C. Babbitt (Pacific Symposium on Biocomputing, 2004)

The Protein Data Bank and lessons in data management. - Philip E. Bourne; John D. Westbrook; Helen M. Berman (Briefings Bioinform., 2004)

Statistically rigorous automated protein annotation. - Werner G. Krebs; Philip E. Bourne (Bioinform., 2004)

A case study of high-throughput biological data processing on parallel platforms. - Dmitry Pekurovsky; Ilya N. Shindyalov; Philip E. Bourne (Bioinform., 2004)

Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. - Werner G. Krebs; Philip E. Bourne (J. Bioinform. Comput. Biol., 2004)

A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE. - Yuting Jia; T. Gregory Dewey; Ilya N. Shindyalov; Philip E. Bourne (J. Comput. Biol., 2004)

The distribution and query systems of the RCSB Protein Data Bank. - Philip E. Bourne; Kenneth J. Addess; Wolfgang Bluhm; Li Chen 022; Nita Deshpande; Zukang Feng; Ward Fleri; Rachel Kramer Green; Jeffrey C. Merino-Ott; Wayne Townsend-Merino; Helge Weissig; John D. Westbrook; et al. (Nucleic Acids Res., 2004)

CE-MC: a multiple protein structure alignment server. - Chittibabu Guda; Sifang Lu; Eric D. Scheeff; Philip E. Bourne; Ilya N. Shindyalov (Nucleic Acids Res., 2004)

The Encyclopedia of Life Project: Grid Software and Deployment. - 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; et al. (New Gener. Comput., 2004)

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

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

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. - Nita Deshpande; Kenneth J. Addess; Wolfgang Bluhm; Jeffrey C. Merino-Ott; Wayne Townsend-Merino; Qing Zhang; Charlie Knezevich; Lie Xie; Li Chen 022; Zukang Feng; Rachel Kramer Green; Judith L. Flippen-Anderson; et al. (Nucleic Acids Res., 2005)

Will a Biological Database Be Different from a Biological Journal? - Philip E. Bourne (PLoS Comput. Biol., 2005)

Ten Simple Rules for Getting Published. - Philip E. Bourne (PLoS Comput. Biol., 2005)

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

Structural Evolution of the Protein Kinase-Like Superfamily. - Eric D. Scheeff; Philip E. Bourne (PLoS Comput. Biol., 2005)

Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models. - Lei Xie 006; Philip E. Bourne (PLoS Comput. Biol., 2005)

ISMB 2006. - Philip E. Bourne; Søren Brunak (ISMB (Supplement of Bioinformatics), 2006)

The Immune Epitope Database and Analysis Resource. - 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; et al. (PRIB, 2006)

Multipolar representation of protein structure. - Apostol Gramada; Philip E. Bourne (BMC Bioinform., 2006)

Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. - Eric D. Scheeff; Philip E. Bourne (BMC Bioinform., 2006)

Curation of complex, context-dependent immunological data. - 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.; et al. (BMC Bioinform., 2006)

The RCSB PDB information portal for structural genomics. - Andrei Kouranov; Lei Xie 006; Joanna de la Cruz; Li Chen 022; John D. Westbrook; Philip E. Bourne; Helen M. Berman (Nucleic Acids Res., 2006)

One Year of PLoS Computational Biology. - Philip E. Bourne (PLoS Comput. Biol., 2006)

Ten Simple Rules for Getting Grants. - Philip E. Bourne; Leo M. Chalupa (PLoS Comput. Biol., 2006)

Ten Simple Rules for Selecting a Postdoctoral Position. - Philip E. Bourne; Iddo Friedberg (PLoS Comput. Biol., 2006)

Correction: Ten Simple Rules for Selecting a Postdoctoral Position. - Philip E. Bourne; Iddo Friedberg (PLoS Comput. Biol., 2006)

Ten Simple Rules for Reviewers. - Philip E. Bourne; Alon Korngreen (PLoS Comput. Biol., 2006)

Biocurators: Contributors to the World of Science. - Philip E. Bourne; Johanna R. McEntyre (PLoS Comput. Biol., 2006)

Wiggle - Predicting Functionally Flexible Regions from Primary Sequence. - Jenny Gu; Michael Gribskov; Philip E. Bourne (PLoS Comput. Biol., 2006)

ISMB 2006. - Goran Neshich; Philip E. Bourne; Søren Brunak (PLoS Comput. Biol., 2006)

Con-Struct Map: a comparative contact map analysis tool. - Jo-Lan Chung; John E. Beaver; Eric D. Scheeff; Philip E. Bourne (Bioinform., 2007)

High-throughput identification of interacting protein-protein binding sites. - Jo-Lan Chung; Wei Wang 051; Philip E. Bourne (BMC Bioinform., 2007)

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

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. - Lei Xie 006; Philip E. Bourne (BMC Bioinform., 2007)

Ten Simple Rules for Making Good Oral Presentations. - Philip E. Bourne (PLoS Comput. Biol., 2007)

Developing Computational Biology. - Philip E. Bourne; Steven E. Brenner (PLoS Comput. Biol., 2007)

Ten Simple Rules for a Good Poster Presentation. - Thomas C. Erren; Philip E. Bourne (PLoS Comput. Biol., 2007)

Ten Simple Rules for Doing Your Best Research, According to Hamming. - Thomas C. Erren; Paul Cullen; Michael Erren; Philip E. Bourne (PLoS Comput. Biol., 2007)

Ten Simple Rules for Graduate Students. - Jenny Gu; Philip E. Bourne (PLoS Comput. Biol., 2007)

The International Society for Computational Biology 10th Anniversary. - Lawrence Hunter; Russ B. Altman; Philip E. Bourne (PLoS Comput. Biol., 2007)

Ten Simple Rules for a Successful Collaboration. - Quentin Vicens; Philip E. Bourne (PLoS Comput. Biol., 2007)

In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators. - Lei Xie 006; Jian Wang; Philip E. Bourne (PLoS Comput. Biol., 2007)

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

Session Introduction. - K. Bretonnel Cohen; Hong Yu 001; Philip E. Bourne; Lynette Hirschman (Pacific Symposium on Biocomputing, 2008)

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

Superimposé: a 3D structural superposition server. - 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; et al. (Nucleic Acids Res., 2008)

BioLit: integrating biological literature with databases. - J. Lynn Fink; Sergey Kushch; Parker R. Williams; Philip E. Bourne (Nucleic Acids Res., 2008)

SuperTarget and Matador: resources for exploring drug-target relationships. - Stefan Günther; Michael Kuhn 004; Mathias Dunkel; Monica Campillos; Christian Senger; Evangelia Petsalaki; Jessica Ahmed; Eduardo Garcia Urdiales; Andreas Gewiess; Lars Juhl Jensen; Reinhard Schneider 002; Roman Skoblo; et al. (Nucleic Acids Res., 2008)

Immune epitope database analysis resource (IEDB-AR). - Qing Zhang; Peng Wang 014; Yohan Kim; Pernille Haste-Andersen; John E. Beaver; Philip E. Bourne; Huynh-Hoa Bui; Søren Buus; Sune Frankild; Jason Greenbaum; Ole Lund; Claus Lundegaard; et al. (Nucleic Acids Res., 2008)

I Am Not a Scientist, I Am a Number. - Philip E. Bourne; J. Lynn Fink (PLoS Comput. Biol., 2008)

Open Access: Taking Full Advantage of the Content. - Philip E. Bourne; J. Lynn Fink; Mark Gerstein (PLoS Comput. Biol., 2008)

Ten Simple Rules for Organizing a Scientific Meeting. - Manuel Corpas; Nils Gehlenborg; Sarath Chandra Janga; Philip E. Bourne (PLoS Comput. Biol., 2008)

Computational Biology Resources Lack Persistence and Usability. - Stella Veretnik; J. Lynn Fink; Philip E. Bourne (PLoS Comput. Biol., 2008)

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. - Lei Xie 006; Li Xie 002; Philip E. Bourne (Bioinform., 2009)

Ten Simple Rules for Chairing a Scientific Session. - Alex Bateman; Philip E. Bourne (PLoS Comput. Biol., 2009)

A Review of 2008 for PLoS Computational Biology. - Evie Browne; Rosemary Dickin; Philip E. Bourne (PLoS Comput. Biol., 2009)

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis. - Sarah L. Kinnings; Nina Liu; Nancy Buchmeier; Peter J. Tonge; Lei Xie 006; Philip E. Bourne (PLoS Comput. Biol., 2009)

Sm/Lsm Genes Provide a Glimpse into the Early Evolution of the Spliceosome. - Stella Veretnik; Christopher Wills; Philippe Youkharibache; Ruben E. Valas; Philip E. Bourne (PLoS Comput. Biol., 2009)

Ten Simple Rules To Combine Teaching and Research. - Quentin Vicens; Philip E. Bourne (PLoS Comput. Biol., 2009)

Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors. - Li Xie 002; Jerry Li 004; Lei Xie 006; Philip E. Bourne (PLoS Comput. Biol., 2009)

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

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

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

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

SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. - Jingyuan Ren; Lei Xie 006; Wilfred W. Li; Philip E. Bourne (Nucleic Acids Res., 2010)

What Do I Want from the Publisher of the Future? - Philip E. Bourne (PLoS Comput. Biol., 2010)

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

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model. - Roger L. Chang; Li Xie 002; Lei Xie 006; Philip E. Bourne; Bernhard Ø. Palsson (PLoS Comput. Biol., 2010)

PLoS Computational Biology Conference Postcards from PSB 2010. - Ruchira S. Datta; Matthew W. Lux; Philip E. Bourne (PLoS Comput. Biol., 2010)

A Review of 2009 for PLoS Computational Biology. - Rosemary Dickin; Cecy Marden; Catherine Nancarrow; Philip E. Bourne (PLoS Comput. Biol., 2010)

A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. - Jacob D. Durrant; Rommie E. Amaro; Lei Xie 006; Michael D. Urbaniak; Michael A. J. Ferguson; Antti Haapalainen; Zhijun Chen; Anne Marie Di Guilmi; Frank Wunder; Philip E. Bourne; James Andrew McCammon (PLoS Comput. Biol., 2010)

The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications. - Sarah L. Kinnings; Li Xie 002; Kingston H. Fung; Richard M. Jackson; Lei Xie 006; Philip E. Bourne (PLoS Comput. Biol., 2010)

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. - Wolfgang Bluhm; Bojan Beran; Chunxiao Bi; Dimitris Dimitropoulos; Andreas Prlic; Greg B. Quinn; Peter W. Rose; Chaitali Shah; Jasmine Young; Benjamin T. Yukich; Helen M. Berman; Philip E. Bourne (Database J. Biol. Databases Curation, 2011)

Cobweb: a Java applet for network exploration and visualisation. - Joachim von Eichborn; Philip E. Bourne; Robert Preissner (Bioinform., 2011)

Coarse-graining the electrostatic potential via distributed multipole expansions. - Apostol Gramada; Philip E. Bourne (Comput. Phys. Commun., 2011)

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

A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing. - Sarah L. Kinnings; Nina Liu; Peter J. Tonge; Richard M. Jackson; Lei Xie 006; Philip E. Bourne (J. Chem. Inf. Model., 2011)

Correction to "A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing". - Sarah L. Kinnings; Nina Liu; Peter J. Tonge; Richard M. Jackson; Lei Xie 006; Philip E. Bourne (J. Chem. Inf. Model., 2011)

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

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

The RCSB Protein Data Bank: redesigned web site and web services. - 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; et al. (Nucleic Acids Res., 2011)

Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. - Philip E. Bourne (PLoS Comput. Biol., 2011)

Ten Simple Rules for Building and Maintaining a Scientific Reputation. - Philip E. Bourne; Virginia Barbour (PLoS Comput. Biol., 2011)

A Review of 2010 for PLoS Computational Biology. - Rosemary Dickin; Cecy Marden; Andrew M. Collings; Ruth Nussinov; Philip E. Bourne (PLoS Comput. Biol., 2011)

Teaching Bioinformatics at the Secondary School Level. - Fran Lewitter; Philip E. Bourne (PLoS Comput. Biol., 2011)

Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir. - Li Xie 002; Thomas Evangelidis; Lei Xie 006; Philip E. Bourne (PLoS Comput. Biol., 2011)

An integrated workflow for proteome-wide off-target identification and polypharmacology drug design. - Thomas Evangelidis; Philip E. Bourne; Li Xie 002; Lei Xie 006 (BIBM Workshops, 2012)

BioJava: an open-source framework for bioinformatics in 2012. - Andreas Prlic; Andrew D. Yates; Spencer Bliven; Peter W. Rose; Julius O. B. Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard C. G. Holland; Gediminas Rimsa; et al. (Bioinform., 2012)

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

Immune epitope database analysis resource. - Yohan Kim; Julia V. Ponomarenko; Zhanyang Zhu; Dorjee Tamang; Peng Wang 014; Jason Greenbaum; Claus Lundegaard; Alessandro Sette; Ole Lund; Philip E. Bourne; Morten Nielsen 001; Bjoern Peters (Nucleic Acids Res., 2012)

Seven Years; It's Time for a Change. - Philip E. Bourne (PLoS Comput. Biol., 2012)

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

Ten Simple Rules for Starting a Company. - Anthony C. Fletcher; Philip E. Bourne (PLoS Comput. Biol., 2012)

Ten Simple Rules To Commercialize Scientific Research. - Anthony C. Fletcher; Philip E. Bourne (PLoS Comput. Biol., 2012)

Ten Simple Rules to Protect Your Intellectual Property. - Mark Jolly; Anthony C. Fletcher; Philip E. Bourne (PLoS Comput. Biol., 2012)

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

The era of open. - Philip E. Bourne (OpenSym, 2013)

Antibacterial mechanisms identified through structural systems pharmacology. - Roger L. Chang; Lei Xie 006; Philip E. Bourne; Bernhard O. Palsson (BMC Syst. Biol., 2013)

The reaming of life: based on the 2010 Jim Gray eScience Award Lecture. - Philip E. Bourne (Concurr. Comput. Pract. Exp., 2013)

The RCSB Protein Data Bank: new resources for research and education. - 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; et al. (Nucleic Acids Res., 2013)

Learning How to Run a Lab: Interviews with Principal Investigators. - Theodore Alexandrov; Philip E. Bourne (PLoS Comput. Biol., 2013)

Let's Make Those Book Chapters Open Too! - Philip E. Bourne (PLoS Comput. Biol., 2013)

Ten Simple Rules for Cultivating Open Science and Collaborative R&D. - Hassan Masum; Aarthi Rao; Benjamin M. Good; Matthew H. Todd; Aled M. Edwards; Leslie Chan; Barry A. Bunin; Andrew I. Su; Zakir Thomas; Philip E. Bourne (PLoS Comput. Biol., 2013)

Anti-Infectious Drug Repurposing Using an Integrated Chemical Genomics and Structural Systems Biology Approach. - Clara Ng; Ruth Hauptman; Yinliang Zhang; Philip E. Bourne; Lei Xie 006 (Pacific Symposium on Biocomputing, 2014)

What Big Data means to me. - Philip E. Bourne (J. Am. Medical Informatics Assoc., 2014)

Ten Simple Rules for Approaching a New Job. - Philip E. Bourne (PLoS Comput. Biol., 2014)

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article. - Harriet Dashnow; Andrew Lonsdale; Philip E. Bourne (PLoS Comput. Biol., 2014)

Ten Simple Rules for Better Figures. - Nicolas P. Rougier; Michael Droettboom; Philip E. Bourne (PLoS Comput. Biol., 2014)

Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine. - Lei Xie 006; Xiaoxia Ge; Hepan Tan; Li Xie 002; Yinliang Zhang; Thomas Hart; Xiaowei Yang; Philip E. Bourne (PLoS Comput. Biol., 2014)

Big data in biomedicine - An NIH perspective. - Philip E. Bourne (BIBM, 2015)

Detection of circular permutations within protein structures using CE-CP. - Spencer E. Bliven; Philip E. Bourne; Andreas Prlic (Bioinform., 2015)

RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. - Gregory B. Quinn; Chunxiao Bi; Cole H. Christie; Kyle Pang; Andreas Prlic; Takanori Nakane; Christine Zardecki; Maria Voigt; Helen M. Berman; Philip E. Bourne; Peter W. Rose (Bioinform., 2015)

Editor's Choice: Achievements and challenges in structural bioinformatics and computational biophysics. - Ilan Samish; Philip E. Bourne; Rafael J. Najmanovich (Bioinform., 2015)

The NIH Big Data to Knowledge (BD2K) initiative. - Philip E. Bourne; Vivien Bonazzi; Michelle Dunn; Eric D. Green; Mark Guyer; George A. Komatsoulis; Jennie Larkin; Beth Russell (J. Am. Medical Informatics Assoc., 2015)

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. - Peter W. Rose; Andreas Prlic; Chunxiao Bi; Wolfgang Bluhm; Cole H. Christie; Shuchismita Dutta; Rachel Kramer Green; David S. Goodsell; John D. Westbrook; Jesse Woo; Jasmine Young; Christine Zardecki; et al. (Nucleic Acids Res., 2015)

Perspective: Sustaining the big-data ecosystem. - Philip E. Bourne; Jon R. Lorsch; Eric D. Green (Nat., 2015)

Confronting the Ethical Challenges of Big Data in Public Health. - Philip E. Bourne (PLoS Comput. Biol., 2015)

Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation and Innovation. - Philip E. Bourne; Steven E. Brenner; Michael B. Eisen (PLoS Comput. Biol., 2015)

Ten Simple Rules for Lifelong Learning, According to Hamming. - Thomas C. Erren; Tracy E. Slanger; J. Valérie Groß; Philip E. Bourne; Paul Cullen (PLoS Comput. Biol., 2015)

Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. - Zheng Zhao; Che L. Martin; Raymond Fan; Philip E. Bourne; Lei Xie 006 (BMC Bioinform., 2016)

Systems biology of the structural proteome. - Elizabeth Brunk; Nathan Mih; Jonathan Monk; Zhen Zhang; Edward J. O'Brien; Spencer E. Bliven; Ke Chen; Roger L. Chang; Philip E. Bourne; Bernhard O. Palsson (BMC Syst. Biol., 2016)

BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. - Jianjiong Gao; Andreas Prlic; Chunxiao Bi; Wolfgang Bluhm; Dimitris Dimitropoulos; Dong Xu 002; Philip E. Bourne; Peter W. Rose (Bioinform., 2017)

Ten simple rules in considering a career in academia versus government. - Philip E. Bourne (PLoS Comput. Biol., 2017)

Ten simple rules to consider regarding preprint submission. - Philip E. Bourne; Jessica K. Polka; Ronald D. Vale; Robert Kiley (PLoS Comput. Biol., 2017)

Ten simple rules when considering retirement. - Philip E. Bourne (PLoS Comput. Biol., 2018)

One thousand simple rules. - Philip E. Bourne; Fran Lewitter; Scott Markel; Jason A. Papin (PLoS Comput. Biol., 2018)

Cloud computing applications for biomedical science: A perspective. - Vivek Navale; Philip E. Bourne (PLoS Comput. Biol., 2018)

Machine Learning for Classification of Protein Helix Capping Motifs. - Sean Mullane; Ruoyan Chen; Sri Vaishnavi Vemulapalli; Eli J. Draizen; Ke Wang; Cameron Mura; Philip E. Bourne (CoRR, 2019)

A systematic review of natural language processing and text mining of symptoms from electronic patient-authored text data. - Caitlin N. Dreisbach; Theresa A. Koleck; Philip E. Bourne; Suzanne Bakken (Int. J. Medical Informatics, 2019)

Natural language processing of symptoms documented in free-text narratives of electronic health records: a systematic review. - Theresa A. Koleck; Caitlin N. Dreisbach; Philip E. Bourne; Suzanne Bakken (J. Am. Medical Informatics Assoc., 2019)

Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants. - Zheng Zhao; Lei Xie 006; Philip E. Bourne (J. Chem. Inf. Model., 2019)

Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm. - Spencer E. Bliven; Aleix Lafita; Peter W. Rose; Guido Capitani; Andreas Prlic; Philip E. Bourne (PLoS Comput. Biol., 2019)

Ten simple rules to aid in achieving a vision. - Philip E. Bourne (PLoS Comput. Biol., 2019)

Ten Simple Rules for avoiding and resolving conflicts with your colleagues. - Fran Lewitter; Philip E. Bourne; Teresa K. Attwood (PLoS Comput. Biol., 2019)

Ten simple rules for more objective decision-making. - Anthony C. Fletcher; Georges A. Wagner; Philip E. Bourne (PLoS Comput. Biol., 2020)

Ten simple rules for researchers while in isolation from a pandemic. - Hoe-Han Goh; Philip E. Bourne (PLoS Comput. Biol., 2020)

Ten simple rules for writing scientific op-ed articles. - Hoe-Han Goh; Philip E. Bourne (PLoS Comput. Biol., 2020)

Ten simple rules for starting research in your late teens. - Cameron Mura; Mike Chalupa; Abigail M. Newbury; Jack Chalupa; Philip E. Bourne (PLoS Comput. Biol., 2020)

Why it takes a village to manage and share data. - Christine L. Borgman; Philip E. Bourne (CoRR, 2021)

Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology. - Tian Cai; Li Xie 002; Muge Chen; Yang Liu; Di He 003; Shuo Zhang 010; Cameron Mura; Philip E. Bourne; Lei Xie 006 (CoRR, 2021)

Informatics-enabled citizen science to advance health equity. - Rupa S. Valdez; Don E. Detmer; Philip E. Bourne; Katherine K. Kim; Robin Austin; Anna McCollister-Slipp; Courtney C. Rogers; Karen C. Waters-Wicks (J. Am. Medical Informatics Assoc., 2021)

Ten simple rules for starting (and sustaining) an academic data science initiative. - Micaela S. Parker; Arlyn E. Burgess; Philip E. Bourne (PLoS Comput. Biol., 2021)

Playing catch-up in building an open research commons. - Philip E. Bourne; Vivien Bonazzi; Amy Brand; Bonnie Carroll; Ian T. Foster; Ramanathan V. Guha; Robert J. Hanisch; Sallie Ann Keller; Mary Lee Kennedy; Christine R. Kirkpatrick; Barend Mons; Sarah M. Nusser; et al. (CoRR, 2022)

Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants". - Zheng Zhao; Lei Xie 006; Philip E. Bourne (J. Chem. Inf. Model., 2022)

Ten simple rules for improving communication among scientists. - Carla Bautista; Narjes Alfuraiji; Anna Drangowska-Way; Karishma Gangwani; Alida de Flamingh; Philip E. Bourne (PLoS Comput. Biol., 2022)

Ten simple rules for using entrepreneurship skills to improve research careers and culture. - Matt Bawn; David Dent; Philip E. Bourne (PLoS Comput. Biol., 2022)

Ten simple rules for good leadership. - Philip E. Bourne (PLoS Comput. Biol., 2022)

Ten simple rules for organizing a special session at a scientific conference. - Davide Chicco; Philip E. Bourne (PLoS Comput. Biol., 2022)

Prop3D-20. - Eli J. Draizen; Cameron Mura; Philip E. Bourne (Zenodo, 2022)

DeepUrfold Supplemental Material. - Eli J. Draizen; Stella Veretnik; Cameron Mura; Philip E. Bourne (Zenodo, 2022)

MAD-FC: A Fold Change Visualization with Readability, Proportionality, and Symmetry. - Bruce A. Corliss; Yaotian Wang; Francis P. Driscoll; Heman Shakeri; Philip E. Bourne (CoRR, 2023)

The Biological Data Sustainability Paradox. - Terence R. Johnson; Philip E. Bourne (CoRR, 2023)

End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins. - Tian Cai; Li Xie 002; Shuo Zhang 010; Muge Chen; Di He 003; Amitesh Badkul; Yang Liu; Hari Krishna Namballa; Michael Dorogan; Wayne W. Harding; Cameron Mura; Philip E. Bourne; et al. (PLoS Comput. Biol., 2023)

Analysis of KRAS-Ligand Interaction Modes and Flexibilities Reveals the Binding Characteristics. - Zheng Zhao; Niraja Bohidar; Philip E. Bourne (J. Chem. Inf. Model., 2023)

Ten simple rules for serving as an editor. - Cameron Mura; Philip E. Bourne (PLoS Comput. Biol., 2023)

Critical data ethics pedagogies: Three (non-rival) approaches. - Luis Felipe R. Murillo; Caitlin D. Wylie; Philip E. Bourne (Big Data Soc., 2023)

Ten simple rules for managing laboratory information. - Casey-Tyler Berezin; Luis U. Aguilera; Sonja Billerbeck; Philip E. Bourne; Douglas Densmore; Paul S. Freemont; Thomas E. Gorochowski; Sarah I. Hernandez; Nathan J. Hillson; Connor R. King; Michael Köpke; Shuyi Ma; et al. (PLoS Comput. Biol., 2023)

Ten simple rules for humane data science. - Hassan Masum; Philip E. Bourne (PLoS Comput. Biol., 2023)

Exploring Extended Warheads toward Developing Cysteine-Targeted Covalent Kinase Inhibitors. - Zheng Zhao; Philip E. Bourne (J. Chem. Inf. Model., 2024)

Supplemental Material for 'Deep Generative Models of Protein Structure Uncover Distant Relationships Across a Continuous Fold Space' and DeepUrfold. - Eli J. Draizen; Stella Veretnik; Cameron Mura; Philip E. Bourne (Zenodo, 2024)

Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data. - Eli J. Draizen; John Readey; Cameron Mura; Philip E. Bourne (BMC Bioinform., 2024)

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13. - Oleksandra Herasymenko; Madhushika Silva; Abd Al-Aziz A. Abu-Saleh; Ayaz Ahmad; Jesus Alvarado-Huayhuaz; Oscar Emilio Arrúa Arce; Roly J. Armstrong; Cheryl H. Arrowsmith; Kelly E. Bachta; Hartmut Beck; Dénes Berta; Mateusz K. Bieniek; et al. (J. Chem. Inf. Model., 2025)

Programmable Virtual Humans Toward Human Physiologically-Based Drug Discovery. - You Wu; Philip E. Bourne; Lei Xie 006 (CoRR, 2025)