Philip E. Bourne

188 papers A 3B 2C 2Misc 8Journal 163Unranked 10

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13. J. Chem. Inf. Model. 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, Vincent Blay, Albina Bolotokova, Philip E. Bourne, Marko Breznik, Peter J. Brown, Aaron D. G. Campbell, Emanuele Carosati, Irene Chau, Daniel J. Cole, Ben Cree, Wim Dehaen, Katrin Denzinger, Karina dos Santos Machado, Ian Dunn, Prasannavenkatesh Durai, Kristina Edfeldt, Aled M. Edwards, Darren Fayne, Daniel Felfoldi, Kallie Friston, Pegah Ghiabi, Elisa Gibson, Judith Guenther, Anders Gunnarsson, Alexander Hillisch, Douglas R. Houston, Jan Halborg Jensen, Rachel J. Harding, Kate S. Harris, Laurent Hoffer, Anders Hogner, Joshua T. Horton, Scott Houliston, Judd F. Hultquist, Ashley Hutchinson, John J. Irwin, Marko Jukic, Shubhangi Kandwal, Andrea Karlova, Vittorio L. Katis, Ryan P. Kich, Dmitri Kireev, David Koes, Nicole L. Inniss, Uta F. Lessel, Sijie Liu, Peter Loppnau, Wei Lu, Sam Alexander Martino, Miles McGibbon, Jens Meiler, Akhila Mettu, Sam Money-Kyrle, Rocco Moretti, Yurii S. Moroz, Charuvaka Muvva, Joseph A. Newman, Leon Obendorf, Brooks Paige, Amit Pandit, Keunwan Park, Sumera Perveen, Rachael Pirie, Gennady Poda, Mykola V. Protopopov, Vera Pütter, Federico Ricci, Natalie J. Roper, Edina Rosta, Margarita Rzhetskaya, Yogesh Sabnis, Karla J. F. Satchell, Frederico Schmitt Kremer, Thomas Scott, Almagul Seitova, Casper Steinmann, Valerij Talagayev, Olga O. Tarkhanova, Natalie J. Tatum, Dakota Treleaven, Adriano Velasque Werhli, W. Patrick Walters, Xiaowen Wang, Jude Wells, Geoffrey Wells, Yvonne Westermaier, Gerhard Wolber, Lars Wortmann, Jixian Zhang, Zheng Zhao, Shuangjia Zheng, Matthieu Schapira
2025	J	`jnl`	Programmable Virtual Humans Toward Human Physiologically-Based Drug Discovery. CoRR You Wu, Philip E. Bourne, Lei Xie
2024	J	`jnl`	Exploring Extended Warheads toward Developing Cysteine-Targeted Covalent Kinase Inhibitors. J. Chem. Inf. Model. Zheng Zhao, Philip E. Bourne
2024	J	`jnl`	Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data. BMC Bioinform. Eli J. Draizen, John Readey, Cameron Mura, Philip E. Bourne
2023	J	`jnl`	Analysis of KRAS-Ligand Interaction Modes and Flexibilities Reveals the Binding Characteristics. J. Chem. Inf. Model. Zheng Zhao, Niraja Bohidar, Philip E. Bourne
2023	J	`jnl`	Critical data ethics pedagogies: Three (non-rival) approaches. Big Data Soc. Luis Felipe R. Murillo, Caitlin D. Wylie, Philip E. Bourne
2023	J	`jnl`	End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins. PLoS Comput. Biol. Tian Cai, Li Xie, Shuo Zhang, Muge Chen, Di He, Amitesh Badkul, Yang Liu, Hari Krishna Namballa, Michael Dorogan, Wayne W. Harding, Cameron Mura, Philip E. Bourne, Lei Xie
2023	J	`jnl`	MAD-FC: A Fold Change Visualization with Readability, Proportionality, and Symmetry. CoRR Bruce A. Corliss, Yaotian Wang, Francis P. Driscoll, Heman Shakeri, Philip E. Bourne
2023	J	`jnl`	Ten simple rules for humane data science. PLoS Comput. Biol. Hassan Masum, Philip E. Bourne
2023	J	`jnl`	Ten simple rules for managing laboratory information. PLoS Comput. Biol. 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, Katie M. Miller, Tae Seok Moon, Jason H. Moore, Brian Munsky, Chris J. Myers, Dequina A. Nicholas, Samuel J. Peccoud, Wen Zhou, Jean Peccoud
2023	J	`jnl`	Ten simple rules for serving as an editor. PLoS Comput. Biol. Cameron Mura, Philip E. Bourne
2023	J	`jnl`	The Biological Data Sustainability Paradox. CoRR Terence R. Johnson, Philip E. Bourne
2022	J	`jnl`	Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants". J. Chem. Inf. Model. Zheng Zhao, Lei Xie, Philip E. Bourne
2022	J	`jnl`	Playing catch-up in building an open research commons. CoRR 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, Michael Stebbins, George O. Strawn, Alex Szalay
2022	J	`jnl`	Ten simple rules for good leadership. PLoS Comput. Biol. Philip E. Bourne
2022	J	`jnl`	Ten simple rules for improving communication among scientists. PLoS Comput. Biol. Carla Bautista, Narjes Alfuraiji, Anna Drangowska-Way, Karishma Gangwani, Alida de Flamingh, Philip E. Bourne
2022	J	`jnl`	Ten simple rules for organizing a special session at a scientific conference. PLoS Comput. Biol. Davide Chicco, Philip E. Bourne
2022	J	`jnl`	Ten simple rules for using entrepreneurship skills to improve research careers and culture. PLoS Comput. Biol. Matt Bawn, David Dent, Philip E. Bourne
2021	J	`jnl`	Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology. CoRR Tian Cai, Li Xie, Muge Chen, Yang Liu, Di He, Shuo Zhang, Cameron Mura, Philip E. Bourne, Lei Xie
2021	J	`jnl`	Informatics-enabled citizen science to advance health equity. J. Am. Medical Informatics Assoc. Rupa S. Valdez, Don E. Detmer, Philip E. Bourne, Katherine K. Kim, Robin Austin, Anna McCollister-Slipp, Courtney C. Rogers, Karen C. Waters-Wicks
2021	J	`jnl`	Ten simple rules for starting (and sustaining) an academic data science initiative. PLoS Comput. Biol. Micaela S. Parker, Arlyn E. Burgess, Philip E. Bourne
2021	J	`jnl`	Why it takes a village to manage and share data. CoRR Christine L. Borgman, Philip E. Bourne
2020	J	`jnl`	Ten simple rules for more objective decision-making. PLoS Comput. Biol. Anthony C. Fletcher, Georges A. Wagner, Philip E. Bourne
2020	J	`jnl`	Ten simple rules for researchers while in isolation from a pandemic. PLoS Comput. Biol. Hoe-Han Goh, Philip E. Bourne
2020	J	`jnl`	Ten simple rules for starting research in your late teens. PLoS Comput. Biol. Cameron Mura, Mike Chalupa, Abigail M. Newbury, Jack Chalupa, Philip E. Bourne
2020	J	`jnl`	Ten simple rules for writing scientific op-ed articles. PLoS Comput. Biol. Hoe-Han Goh, Philip E. Bourne
2019	J	`jnl`	A systematic review of natural language processing and text mining of symptoms from electronic patient-authored text data. Int. J. Medical Informatics Caitlin N. Dreisbach, Theresa A. Koleck, Philip E. Bourne, Suzanne Bakken
2019	J	`jnl`	Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm. PLoS Comput. Biol. Spencer E. Bliven, Aleix Lafita, Peter W. Rose, Guido Capitani, Andreas Prlic, Philip E. Bourne
2019	J	`jnl`	Machine Learning for Classification of Protein Helix Capping Motifs. CoRR Sean Mullane, Ruoyan Chen, Sri Vaishnavi Vemulapalli, Eli J. Draizen, Ke Wang, Cameron Mura, Philip E. Bourne
2019	J	`jnl`	Natural language processing of symptoms documented in free-text narratives of electronic health records: a systematic review. J. Am. Medical Informatics Assoc. Theresa A. Koleck, Caitlin N. Dreisbach, Philip E. Bourne, Suzanne Bakken
2019	J	`jnl`	Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants. J. Chem. Inf. Model. Zheng Zhao, Lei Xie, Philip E. Bourne
2019	J	`jnl`	Ten Simple Rules for avoiding and resolving conflicts with your colleagues. PLoS Comput. Biol. Fran Lewitter, Philip E. Bourne, Teresa K. Attwood
2019	J	`jnl`	Ten simple rules to aid in achieving a vision. PLoS Comput. Biol. Philip E. Bourne
2018	J	`jnl`	Cloud computing applications for biomedical science: A perspective. PLoS Comput. Biol. Vivek Navale, Philip E. Bourne
2018	J	`jnl`	One thousand simple rules. PLoS Comput. Biol. Philip E. Bourne, Fran Lewitter, Scott Markel, Jason A. Papin
2018	J	`jnl`	Ten simple rules when considering retirement. PLoS Comput. Biol. Philip E. Bourne
2017	J	`jnl`	BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. Bioinform. Jianjiong Gao, Andreas Prlic, Chunxiao Bi, Wolfgang Bluhm, Dimitris Dimitropoulos, Dong Xu, Philip E. Bourne, Peter W. Rose
2017	J	`jnl`	Ten simple rules in considering a career in academia versus government. PLoS Comput. Biol. Philip E. Bourne
2017	J	`jnl`	Ten simple rules to consider regarding preprint submission. PLoS Comput. Biol. Philip E. Bourne, Jessica K. Polka, Ronald D. Vale, Robert Kiley
2016	J	`jnl`	Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. BMC Bioinform. Zheng Zhao, Che L. Martin, Raymond Fan, Philip E. Bourne, Lei Xie
2016	J	`jnl`	Systems biology of the structural proteome. BMC Syst. Biol. 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
2015	—	`conf`	Big data in biomedicine - An NIH perspective. BIBM Philip E. Bourne
2015	J	`jnl`	Confronting the Ethical Challenges of Big Data in Public Health. PLoS Comput. Biol. Philip E. Bourne
2015	J	`jnl`	Detection of circular permutations within protein structures using CE-CP. Bioinform. Spencer E. Bliven, Philip E. Bourne, Andreas Prlic
2015	J	`jnl`	Editor's Choice: Achievements and challenges in structural bioinformatics and computational biophysics. Bioinform. Ilan Samish, Philip E. Bourne, Rafael J. Najmanovich
2015	J	`jnl`	Perspective: Sustaining the big-data ecosystem. Nat. Philip E. Bourne, Jon R. Lorsch, Eric D. Green
2015	J	`jnl`	RCSB PDB Bioinform. 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
2015	J	`jnl`	Ten Simple Rules for Lifelong Learning, According to Hamming. PLoS Comput. Biol. Thomas C. Erren, Tracy E. Slanger, J. Valérie Groß, Philip E. Bourne, Paul Cullen
2015	J	`jnl`	Ten Years of PLoS Comput. Biol. Philip E. Bourne, Steven E. Brenner, Michael B. Eisen
2015	J	`jnl`	The NIH Big Data to Knowledge (BD2K) initiative. J. Am. Medical Informatics Assoc. Philip E. Bourne, Vivien Bonazzi, Michelle Dunn, Eric D. Green, Mark Guyer, George A. Komatsoulis, Jennie Larkin, Beth Russell
2015	J	`jnl`	The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res. 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, Helen M. Berman, Philip E. Bourne, Stephen K. Burley
2014	Misc	`conf`	Anti-Infectious Drug Repurposing Using an Integrated Chemical Genomics and Structural Systems Biology Approach. Pacific Symposium on Biocomputing Clara Ng, Ruth Hauptman, Yinliang Zhang, Philip E. Bourne, Lei Xie
2014	J	`jnl`	Ten Simple Rules for Approaching a New Job. PLoS Comput. Biol. Philip E. Bourne
2014	J	`jnl`	Ten Simple Rules for Better Figures. PLoS Comput. Biol. Nicolas P. Rougier, Michael Droettboom, Philip E. Bourne
2014	J	`jnl`	Ten Simple Rules for Writing a PLOS Ten Simple Rules Article. PLoS Comput. Biol. Harriet Dashnow, Andrew Lonsdale, Philip E. Bourne
2014	J	`jnl`	Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine. PLoS Comput. Biol. Lei Xie, Xiaoxia Ge, Hepan Tan, Li Xie, Yinliang Zhang, Thomas Hart, Xiaowei Yang, Philip E. Bourne
2014	J	`jnl`	What J. Am. Medical Informatics Assoc. Philip E. Bourne
2013	J	`jnl`	Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst. Biol. Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson
2013	J	`jnl`	Learning How to Run a Lab: Interviews with Principal Investigators. PLoS Comput. Biol. Theodore Alexandrov, Philip E. Bourne
2013	J	`jnl`	Let's Make Those Book Chapters Open Too! PLoS Comput. Biol. Philip E. Bourne
2013	J	`jnl`	Ten Simple Rules for Cultivating Open Science and Collaborative R&D. PLoS Comput. Biol. 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
2013	J	`jnl`	The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res. 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
2013	C	`conf`	The era of open. OpenSym Philip E. Bourne
2013	J	`jnl`	The reaming of life: based on the 2010 Jim Gray eScience Award Lecture. Concurr. Comput. Pract. Exp. Philip E. Bourne
2012	J	`jnl`	A Review of 2011 for PLoS Comput. Biol. Rosemary Dickin, Chris James Hall, Laura K. Taylor, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne
2012	—	`conf`	An integrated workflow for proteome-wide off-target identification and polypharmacology drug design. BIBM Workshops Thomas Evangelidis, Philip E. Bourne, Li Xie, Lei Xie
2012	J	`jnl`	BioJava: an open-source framework for bioinformatics in 2012. Bioinform. 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, Michael L. Heuer, Hannes Brandstätter-Müller, Philip E. Bourne, Scooter Willis
2012	J	`jnl`	Immune epitope database analysis resource. Nucleic Acids Res. 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
2012	J	`jnl`	Seven Years; It's Time for a Change. PLoS Comput. Biol. Philip E. Bourne
2012	J	`jnl`	SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res. Nikolai Hecker, Jessica Ahmed, Joachim von Eichborn, Mathias Dunkel, Karel Macha, Andreas Eckert, Michael K. Gilson, Philip E. Bourne, Robert Preissner
2012	J	`jnl`	Ten Simple Rules To Commercialize Scientific Research. PLoS Comput. Biol. Anthony C. Fletcher, Philip E. Bourne
2012	J	`jnl`	Ten Simple Rules for Starting a Company. PLoS Comput. Biol. Anthony C. Fletcher, Philip E. Bourne
2012	J	`jnl`	Ten Simple Rules to Protect Your Intellectual Property. PLoS Comput. Biol. Mark Jolly, Anthony C. Fletcher, Philip E. Bourne
2012	J	`jnl`	Topic Pages: PLoS Comput. Biol. Shoshana J. Wodak, Daniel Mietchen, Andrew M. Collings, Robert B. Russell, Philip E. Bourne
2011	J	`jnl`	A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing. J. Chem. Inf. Model. Sarah L. Kinnings, Nina Liu, Peter J. Tonge, Richard M. Jackson, Lei Xie, Philip E. Bourne
2011	J	`jnl`	A Review of 2010 for PLoS Comput. Biol. Rosemary Dickin, Cecy Marden, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne
2011	J	`jnl`	Coarse-graining the electrostatic potential via distributed multipole expansions. Comput. Phys. Commun. Apostol Gramada, Philip E. Bourne
2011	J	`jnl`	Cobweb: a Java applet for network exploration and visualisation. Bioinform. Joachim von Eichborn, Philip E. Bourne, Robert Preissner
2011	J	`jnl`	Correction to "A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing". J. Chem. Inf. Model. Sarah L. Kinnings, Nina Liu, Peter J. Tonge, Richard M. Jackson, Lei Xie, Philip E. Bourne
2011	J	`jnl`	Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir. PLoS Comput. Biol. Li Xie, Thomas Evangelidis, Lei Xie, Philip E. Bourne
2011	J	`jnl`	IEDB-3D: structural data within the immune epitope database. Nucleic Acids Res. Julia V. Ponomarenko, Nikitas Papangelopoulos, Dirk M. Zajonc, Björn Peters, Alessandro Sette, Philip E. Bourne
2011	J	`jnl`	Improving The Future of Research Communications and e-Scholarship (Dagstuhl Perspectives Workshop 11331). Dagstuhl Manifestos Philip E. Bourne, Timothy W. Clark, Robert Dale, Anita de Waard, Ivan Herman, Eduard H. Hovy, David M. Shotton
2011	J	`jnl`	PROMISCUOUS: a database for network-based drug-repositioning. Nucleic Acids Res. Joachim von Eichborn, Manuela S. Murgueitio, Mathias Dunkel, Soeren Koerner, Philip E. Bourne, Robert Preissner
2011	J	`jnl`	Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. Database J. Biol. Databases Curation 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
2011	J	`jnl`	Teaching Bioinformatics at the Secondary School Level. PLoS Comput. Biol. Fran Lewitter, Philip E. Bourne
2011	J	`jnl`	Ten Simple Rules for Building and Maintaining a Scientific Reputation. PLoS Comput. Biol. Philip E. Bourne, Virginia Barbour
2011	J	`jnl`	Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS Comput. Biol. Philip E. Bourne
2011	J	`jnl`	The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 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
2010	J	`jnl`	A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. PLoS Comput. Biol. 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
2010	J	`jnl`	A Review of 2009 for PLoS Comput. Biol. Rosemary Dickin, Cecy Marden, Catherine Nancarrow, Philip E. Bourne
2010	J	`jnl`	Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model. PLoS Comput. Biol. Roger L. Chang, Li Xie, Lei Xie, Philip E. Bourne, Bernhard Ø. Palsson
2010	J	`jnl`	Integration of open access literature into the RCSB Protein Data Bank using BioLit. BMC Bioinform. Andreas Prlic, Marco A. Martinez, Dimitris Dimitropoulos, Bojan Beran, Benjamin T. Yukich, Peter W. Rose, Philip E. Bourne, J. Lynn Fink
2010	J	`jnl`	Pre-calculated protein structure alignments at the RCSB PDB website. Bioinform. Andreas Prlic, Spencer Bliven, Peter W. Rose, Wolfgang Bluhm, Chris Bizon, Adam Godzik, Philip E. Bourne
2010	J	`jnl`	SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. Nucleic Acids Res. Jingyuan Ren, Lei Xie, Wilfred W. Li, Philip E. Bourne
2010	J	`jnl`	The PLoS Comput. Biol. Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Philip E. Bourne
2010	J	`jnl`	What Do I Want from the Publisher of the Future? PLoS Comput. Biol. Philip E. Bourne
2010	J	`jnl`	Will Widgets and Semantic Tagging Change Computational Biology? PLoS Comput. Biol. 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
2010	J	`jnl`	Word add-in for ontology recognition: semantic enrichment of scientific literature. BMC Bioinform. J. Lynn Fink, Pablo Fernicola, Rahul Chandran, Savas Parastatidis, Alex D. Wade, Oscar Naim, Greg B. Quinn, Philip E. Bourne
2010	J	`jnl`	dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. BMC Bioinform. Kieran Alden, Stella Veretnik, Philip E. Bourne
2009	J	`jnl`	A Review of 2008 for PLoS Comput. Biol. Evie Browne, Rosemary Dickin, Philip E. Bourne
2009	J	`jnl`	A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinform. Lei Xie, Li Xie, Philip E. Bourne
2009	J	`jnl`	Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors. PLoS Comput. Biol. Li Xie, Jerry Li, Lei Xie, Philip E. Bourne
2009	J	`jnl`	Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis. PLoS Comput. Biol. Sarah L. Kinnings, Nina Liu, Nancy Buchmeier, Peter J. Tonge, Lei Xie, Philip E. Bourne
2009	J	`jnl`	Sm/Lsm Genes Provide a Glimpse into the Early Evolution of the Spliceosome. PLoS Comput. Biol. Stella Veretnik, Christopher Wills, Philippe Youkharibache, Ruben E. Valas, Philip E. Bourne
2009	J	`jnl`	Ten Simple Rules To Combine Teaching and Research. PLoS Comput. Biol. Quentin Vicens, Philip E. Bourne
2009	J	`jnl`	Ten Simple Rules for Chairing a Scientific Session. PLoS Comput. Biol. Alex Bateman, Philip E. Bourne
2008	J	`jnl`	BioLit: integrating biological literature with databases. Nucleic Acids Res. J. Lynn Fink, Sergey Kushch, Parker R. Williams, Philip E. Bourne
2008	J	`jnl`	Computational Biology Resources Lack Persistence and Usability. PLoS Comput. Biol. Stella Veretnik, J. Lynn Fink, Philip E. Bourne
2008	J	`jnl`	ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinform. Julia V. Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E. Bourne, Alessandro Sette, Björn Peters
2008	J	`jnl`	I Am Not a Scientist, I Am a Number. PLoS Comput. Biol. Philip E. Bourne, J. Lynn Fink
2008	J	`jnl`	Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res. 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
2008	Misc	`conf`	Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks. Pacific Symposium on Biocomputing J. Gregory Caporaso, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, Lawrence Hunter
2008	J	`jnl`	Open Access: Taking Full Advantage of the Content. PLoS Comput. Biol. Philip E. Bourne, J. Lynn Fink, Mark Gerstein
2008	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing K. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman
2008	J	`jnl`	SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res. 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
2008	J	`jnl`	Superimposé: a 3D structural superposition server. Nucleic Acids Res. 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
2008	J	`jnl`	Ten Simple Rules for Organizing a Scientific Meeting. PLoS Comput. Biol. Manuel Corpas, Nils Gehlenborg, Sarath Chandra Janga, Philip E. Bourne
2007	J	`jnl`	A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinform. Lei Xie, Philip E. Bourne
2007	J	`jnl`	Con-Struct Map: a comparative contact map analysis tool. Bioinform. Jo-Lan Chung, John E. Beaver, Eric D. Scheeff, Philip E. Bourne
2007	J	`jnl`	Developing Computational Biology. PLoS Comput. Biol. Philip E. Bourne, Steven E. Brenner
2007	J	`jnl`	High-throughput identification of interacting protein-protein binding sites. BMC Bioinform. Jo-Lan Chung, Wei Wang, Philip E. Bourne
2007	J	`jnl`	Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2. BMC Bioinform. Jenny Gu, Philip E. Bourne
2007	J	`jnl`	In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators. PLoS Comput. Biol. Lei Xie, Jian Wang, Philip E. Bourne
2007	J	`jnl`	Ten Simple Rules for Doing Your Best Research, According to Hamming. PLoS Comput. Biol. Thomas C. Erren, Paul Cullen, Michael Erren, Philip E. Bourne
2007	J	`jnl`	Ten Simple Rules for Graduate Students. PLoS Comput. Biol. Jenny Gu, Philip E. Bourne
2007	J	`jnl`	Ten Simple Rules for Making Good Oral Presentations. PLoS Comput. Biol. Philip E. Bourne
2007	J	`jnl`	Ten Simple Rules for a Good Poster Presentation. PLoS Comput. Biol. Thomas C. Erren, Philip E. Bourne
2007	J	`jnl`	Ten Simple Rules for a Successful Collaboration. PLoS Comput. Biol. Quentin Vicens, Philip E. Bourne
2007	J	`jnl`	The International Society for Computational Biology 10th Anniversary. PLoS Comput. Biol. Lawrence Hunter, Russ B. Altman, Philip E. Bourne
2006	J	`jnl`	Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinform. Eric D. Scheeff, Philip E. Bourne
2006	J	`jnl`	Biocurators: Contributors to the World of Science. PLoS Comput. Biol. Philip E. Bourne, Johanna R. McEntyre
2006	J	`jnl`	Correction: Ten Simple Rules for Selecting a Postdoctoral Position. PLoS Comput. Biol. Philip E. Bourne, Iddo Friedberg
2006	J	`jnl`	Curation of complex, context-dependent immunological data. BMC Bioinform. 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
2006	—	`conf`	ISMB 2006. ISMB (Supplement of Bioinformatics) Philip E. Bourne, Søren Brunak
2006	J	`jnl`	ISMB 2006. PLoS Comput. Biol. Goran Neshich, Philip E. Bourne, Søren Brunak
2006	J	`jnl`	Multipolar representation of protein structure. BMC Bioinform. Apostol Gramada, Philip E. Bourne
2006	J	`jnl`	One Year of PLoS Comput. Biol. Philip E. Bourne
2006	J	`jnl`	Ten Simple Rules for Getting Grants. PLoS Comput. Biol. Philip E. Bourne, Leo M. Chalupa
2006	J	`jnl`	Ten Simple Rules for Reviewers. PLoS Comput. Biol. Philip E. Bourne, Alon Korngreen
2006	J	`jnl`	Ten Simple Rules for Selecting a Postdoctoral Position. PLoS Comput. Biol. Philip E. Bourne, Iddo Friedberg
2006	—	`conf`	The Immune Epitope Database and Analysis Resource. PRIB 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
2006	J	`jnl`	The RCSB PDB information portal for structural genomics. Nucleic Acids Res. Andrei Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John D. Westbrook, Philip E. Bourne, Helen M. Berman
2006	J	`jnl`	Wiggle - Predicting Functionally Flexible Regions from Primary Sequence. PLoS Comput. Biol. Jenny Gu, Michael Gribskov, Philip E. Bourne
2005	J	`jnl`	Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models. PLoS Comput. Biol. Lei Xie, Philip E. Bourne
2005	Misc	`conf`	Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular STructure. Pacific Symposium on Biocomputing Patricia C. Babbitt, Philip E. Bourne, Sean D. Mooney
2005	J	`jnl`	Structural Evolution of the Protein Kinase-Like Superfamily. PLoS Comput. Biol. Eric D. Scheeff, Philip E. Bourne
2005	J	`jnl`	Ten Simple Rules for Getting Published. PLoS Comput. Biol. Philip E. Bourne
2005	J	`jnl`	The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. BMC Bioinform. John L. Moreland, Apostol Gramada, Oleksandr V. Buzko, Qing Zhang, Philip E. Bourne
2005	J	`jnl`	The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res. 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
2005	J	`jnl`	Will a Biological Database Be Different from a Biological Journal? PLoS Comput. Biol. Philip E. Bourne
2004	J	`jnl`	A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE. J. Comput. Biol. Yuting Jia, T. Gregory Dewey, Ilya N. Shindyalov, Philip E. Bourne
2004	J	`jnl`	A case study of high-throughput biological data processing on parallel platforms. Bioinform. Dmitry Pekurovsky, Ilya N. Shindyalov, Philip E. Bourne
2004	J	`jnl`	CE-MC: a multiple protein structure alignment server. Nucleic Acids Res. Chittibabu Guda, Sifang Lu, Eric D. Scheeff, Philip E. Bourne, Ilya N. Shindyalov
2004	—	`conf`	Grid Portal Interface for Interactive Use and Monitoring of High-Throughput Proteome Annotation. LSGRID 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
2004	—	`conf`	Grid Workflow Software for a High-Throughput Proteome Annotation Pipeline. LSGRID Adam Birnbaum, James Hayes, Wilfred W. Li, Mark A. Miller, Peter W. Arzberger, Philip E. Bourne, Henri Casanova
2004	B	`ed.`	Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004, San Diego, California, USA, March 27-31, 2004 RECOMB Philip E. Bourne, Dan Gusfield
2004	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Sean D. Mooney, Philip E. Bourne, Patricia C. Babbitt
2004	J	`jnl`	Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. J. Bioinform. Comput. Biol. Werner G. Krebs, Philip E. Bourne
2004	J	`jnl`	Statistically rigorous automated protein annotation. Bioinform. Werner G. Krebs, Philip E. Bourne
2004	J	`jnl`	The Encyclopedia of Life Project: Grid Software and Deployment. New Gener. Comput. 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
2004	B	`conf`	The Future of Bioinformatics. APBC Philip E. Bourne
2004	J	`jnl`	The Protein Data Bank and lessons in data management. Briefings Bioinform. Philip E. Bourne, John D. Westbrook, Helen M. Berman
2004	Misc	`conf`	The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures. Pacific Symposium on Biocomputing 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
2004	J	`jnl`	The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res. 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
2003	J	`jnl`	BioEditor - Simplifying Macromolecular Structure Annotation. Bioinform. Peng Yang, Paul A. Craig, David S. Goodsell, Philip E. Bourne
2003	—	`conf`	High Performance Computational Biology - Past Progress and Future Promise. CSB Philip E. Bourne
2003	—	`conf`	Parallel Processing on Large Redudant Biological Data Sets: Protein Structures Classification with CEPAR. PARCO Dmitry Pekurovsky, Ilya N. Shindyalov, Philip E. Bourne
2003	—	`conf`	Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. CSB Werner G. Krebs, Philip E. Bourne
2002	J	`jnl`	An ontology driven architecture for derived representations of macromolecular structure. Bioinform. Douglas S. Greer, John D. Westbrook, Philip E. Bourne
2002	C	`conf`	Building an automated classification of DNA-binding protein domains. ECCB Julia V. Ponomarenko, Philip E. Bourne, Ilya N. Shindyalov
2002	J	`jnl`	CKAAPs DB: a Conserved Key Amino Acid Positions DataBase. Nucleic Acids Res. Wilfred W. Li, Boojala V. B. Reddy, John G. Tate, Ilya N. Shindyalov, Philip E. Bourne
2002	J	`jnl`	The Protein Data Bank: unifying the archive. Nucleic Acids Res. 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
2001	Misc	`conf`	A New Algorithm for the Alignment of Multiple Protein Structures Using Monte Carlo Optimization. Pacific Symposium on Biocomputing Chittibabu Guda, Eric D. Scheeff, Philip E. Bourne, Ilya N. Shindyalov
2001	J	`jnl`	A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. Nucleic Acids Res. Ilya N. Shindyalov, Philip E. Bourne
2001	J	`jnl`	CKAAPs DB: a conserved key amino acid positions database. Nucleic Acids Res. Wilfred W. Li, Boojala V. B. Reddy, Ilya N. Shindyalov, Philip E. Bourne
2001	J	`jnl`	The PDB data uniformity project. Nucleic Acids Res. 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
2000	J	`jnl`	ISMB-2000: Bioinformatics enters a new millennium. Bioinform. Philip E. Bourne, Michael Gribskov
2000	A	`ed.`	Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, August 19-23, 2000, La Jolla / San Diego, CA, USA ISMB 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
2000	J	`jnl`	STAR/mmCIF: An ontology for macromolecular structure. Bioinform. John D. Westbrook, Philip E. Bourne
2000	J	`jnl`	The Protein Data Bank. Nucleic Acids Res. Helen M. Berman, John D. Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne
1999	J	`jnl`	An analysis of the Protein Data Bank in search of temporal and global trends. Bioinform. Helge Weissig, Philip E. Bourne
1999	Misc	`conf`	Developing Protein Documentaries and Other Multimedia Presentations for Molecular Biology. Pacific Symposium on Biocomputing Greg B. Quinn, H.-P. Wang, David Martínez, Philip E. Bourne
1997	A	`conf`	Code Generation through Annotation of Macromolecular Structure Data. ISMB John Biggs, Calton Pu, Philip E. Bourne
1997	J	`jnl`	Protein data representation and query using optimized data decomposition. Comput. Appl. Biosci. Ilya N. Shindyalov, Philip E. Bourne
1995	—	`conf`	Design and use of a software framework to obtain information derived from macromolecular structure data. HICSS (5) Ilya N. Shindyalov, Weider Chang, J. A. Cooper, Philip E. Bourne
1994	J	`jnl`	An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA. Comput. Appl. Biosci. Peisen Zhang, Eric A. Schon, Stuart G. Fischer, Eftihia Cayanis, Janie Weiss, Susan Kistler, Philip E. Bourne
1994	A	`conf`	Design and Application of a C++ Macromolecular Class Library. ISMB Weider Chang, Ilya N. Shindyalov, Calton Pu, Philip E. Bourne
1994	J	`jnl`	Design and application of PDBlib, a C++ macromolecular class library. Comput. Appl. Biosci. Weider Chang, Ilya N. Shindyalov, Calton Pu, Philip E. Bourne