Philip E. Bourne

ORCID

Publication Activity (10 Years)

Years Active: 1994-2024
Publications (10 Years): 37

Top Venues

PLoS Comput. Biol.

CoRR

Bioinform.

J. Am. Medical Informatics Assoc.

Publications

Eli J. Draizen, John Readey, Cameron Mura, Philip E. Bourne
Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data. BMC Bioinform. 25 (1) (2024)
Hassan Masum, Philip E. Bourne
Ten simple rules for humane data science. PLoS Comput. Biol. 19 (12) (2023)
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
Ten simple rules for managing laboratory information. PLoS Comput. Biol. 19 (12) (2023)
Bruce A. Corliss, Yaotian Wang, Francis P. Driscoll, Heman Shakeri, Philip E. Bourne
MAD-FC: A Fold Change Visualization with Readability, Proportionality, and Symmetry. CoRR (2023)
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
End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins. PLoS Comput. Biol. 19 (1) (2023)
Luis Felipe R. Murillo, Caitlin D. Wylie, Philip E. Bourne
Critical data ethics pedagogies: Three (non-rival) approaches. Big Data Soc. 10 (2) (2023)
Cameron Mura, Philip E. Bourne
Ten simple rules for serving as an editor. PLoS Comput. Biol. 19 (3) (2023)
Terence R. Johnson, Philip E. Bourne
The Biological Data Sustainability Paradox. CoRR (2023)
Zheng Zhao, Niraja Bohidar, Philip E. Bourne
Analysis of KRAS-Ligand Interaction Modes and Flexibilities Reveals the Binding Characteristics. J. Chem. Inf. Model. 63 (4) (2023)
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
Playing catch-up in building an open research commons. CoRR (2022)
Davide Chicco, Philip E. Bourne
Ten simple rules for organizing a special session at a scientific conference. PLoS Comput. Biol. 18 (8) (2022)
Carla Bautista, Narjes Alfuraiji, Anna Drangowska-Way, Karishma Gangwani, Alida de Flamingh, Philip E. Bourne
Ten simple rules for improving communication among scientists. PLoS Comput. Biol. 18 (6) (2022)
Matt Bawn, David Dent, Philip E. Bourne
Ten simple rules for using entrepreneurship skills to improve research careers and culture. PLoS Comput. Biol. 18 (4) (2022)
Zheng Zhao, Lei Xie, Philip E. Bourne
Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants". J. Chem. Inf. Model. 62 (1) (2022)
Philip E. Bourne
Ten simple rules for good leadership. PLoS Comput. Biol. 18 (6) (2022)
Christine L. Borgman, Philip E. Bourne
Why it takes a village to manage and share data. CoRR (2021)
Micaela S. Parker, Arlyn E. Burgess, Philip E. Bourne
Ten simple rules for starting (and sustaining) an academic data science initiative. PLoS Comput. Biol. 17 (2) (2021)
Tian Cai, Li Xie, Muge Chen, Yang Liu, Di He, Shuo Zhang, Cameron Mura, Philip E. Bourne, Lei Xie
Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology. CoRR (2021)
Cameron Mura, Mike Chalupa, Abigail M. Newbury, Jack Chalupa, Philip E. Bourne
Ten simple rules for starting research in your late teens. PLoS Comput. Biol. 16 (11) (2020)
Anthony C. Fletcher, Georges A. Wagner, Philip E. Bourne
Ten simple rules for more objective decision-making. PLoS Comput. Biol. 16 (4) (2020)
Hoe-Han Goh, Philip E. Bourne
Ten simple rules for writing scientific op-ed articles. PLoS Comput. Biol. 16 (9) (2020)
Hoe-Han Goh, Philip E. Bourne
Ten simple rules for researchers while in isolation from a pandemic. PLoS Comput. Biol. 16 (6) (2020)
Theresa A. Koleck, Caitlin N. Dreisbach, Philip E. Bourne, Suzanne Bakken
Natural language processing of symptoms documented in free-text narratives of electronic health records: a systematic review. J. Am. Medical Informatics Assoc. 26 (4) (2019)
Spencer E. Bliven, Aleix Lafita, Peter W. Rose, Guido Capitani, Andreas Prlic, Philip E. Bourne
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm. PLoS Comput. Biol. 15 (4) (2019)
Fran Lewitter, Philip E. Bourne, Teresa K. Attwood
Ten Simple Rules for avoiding and resolving conflicts with your colleagues. PLoS Comput. Biol. 15 (1) (2019)
Caitlin N. Dreisbach, Theresa A. Koleck, Philip E. Bourne, Suzanne Bakken
A systematic review of natural language processing and text mining of symptoms from electronic patient-authored text data. Int. J. Medical Informatics 125 (2019)
Sean Mullane, Ruoyan Chen, Sri Vaishnavi Vemulapalli, Eli J. Draizen, Ke Wang, Cameron Mura, Philip E. Bourne
Machine Learning for Classification of Protein Helix Capping Motifs. CoRR (2019)
Zheng Zhao, Lei Xie, Philip E. Bourne
Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants. J. Chem. Inf. Model. 59 (1) (2019)
Philip E. Bourne
Ten simple rules to aid in achieving a vision. PLoS Comput. Biol. 15 (10) (2019)
Vivek Navale, Philip E. Bourne
Cloud computing applications for biomedical science: A perspective. PLoS Comput. Biol. 14 (6) (2018)
Philip E. Bourne
Ten simple rules when considering retirement. PLoS Comput. Biol. 14 (10) (2018)
Philip E. Bourne, Fran Lewitter, Scott Markel, Jason A. Papin
One thousand simple rules. PLoS Comput. Biol. 14 (12) (2018)
Philip E. Bourne, Jessica K. Polka, Ronald D. Vale, Robert Kiley
Ten simple rules to consider regarding preprint submission. PLoS Comput. Biol. 13 (5) (2017)
Philip E. Bourne
Ten simple rules in considering a career in academia versus government. PLoS Comput. Biol. 13 (10) (2017)
Jianjiong Gao, Andreas Prlic, Chunxiao Bi, Wolfgang Bluhm, Dimitris Dimitropoulos, Dong Xu, Philip E. Bourne, Peter W. Rose
BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. Bioinform. 33 (13) (2017)
Zheng Zhao, Che L. Martin, Raymond Fan, Philip E. Bourne, Lei Xie
Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. BMC Bioinform. 17 (2016)
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
Systems biology of the structural proteome. BMC Syst. Biol. 10 (2016)
Spencer E. Bliven, Philip E. Bourne, Andreas Prlic
Detection of circular permutations within protein structures using CE-CP. Bioinform. 31 (8) (2015)
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
: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. Bioinform. 31 (1) (2015)
Philip E. Bourne
Confronting the Ethical Challenges of Big Data in Public Health. PLoS Comput. Biol. 11 (2) (2015)
Philip E. Bourne, Jon R. Lorsch, Eric D. Green
Perspective: Sustaining the big-data ecosystem. Nat. 527 (7576) (2015)
Philip E. Bourne, Steven E. Brenner, Michael B. Eisen
A Decade of Appreciation and Innovation. PLoS Comput. Biol. 11 (6) (2015)
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
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res. 43 (Database-Issue) (2015)
Ilan Samish, Philip E. Bourne, Rafael J. Najmanovich
Editor's Choice: Achievements and challenges in structural bioinformatics and computational biophysics. Bioinform. 31 (1) (2015)
Philip E. Bourne
Big data in biomedicine - An NIH perspective. BIBM (2015)
Philip E. Bourne, Vivien Bonazzi, Michelle Dunn, Eric D. Green, Mark Guyer, George A. Komatsoulis, Jennie Larkin, Beth Russell
The NIH Big Data to Knowledge (BD2K) initiative. J. Am. Medical Informatics Assoc. 22 (6) (2015)
Thomas C. Erren, Tracy E. Slanger, J. Valérie Groß, Philip E. Bourne, Paul Cullen
Ten Simple Rules for Lifelong Learning, According to Hamming. PLoS Comput. Biol. 11 (2) (2015)
Harriet Dashnow, Andrew Lonsdale, Philip E. Bourne
Ten Simple Rules for Writing a PLOS Ten Simple Rules Article. PLoS Comput. Biol. 10 (10) (2014)
Philip E. Bourne
means to me. J. Am. Medical Informatics Assoc. 21 (2) (2014)
Philip E. Bourne
Ten Simple Rules for Approaching a New Job. PLoS Comput. Biol. 10 (6) (2014)
Nicolas P. Rougier, Michael Droettboom, Philip E. Bourne
Ten Simple Rules for Better Figures. PLoS Comput. Biol. 10 (9) (2014)
Clara Ng, Ruth Hauptman, Yinliang Zhang, Philip E. Bourne, Lei Xie
Anti-Infectious Drug Repurposing Using an Integrated Chemical Genomics and Structural Systems Biology Approach. Pacific Symposium on Biocomputing (2014)
Lei Xie, Xiaoxia Ge, Hepan Tan, Li Xie, Yinliang Zhang, Thomas Hart, Xiaowei Yang, Philip E. Bourne
Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine. PLoS Comput. Biol. 10 (5) (2014)
Philip E. Bourne
The era of open. OpenSym (2013)
Philip E. Bourne
Let's Make Those Book Chapters Open Too! PLoS Comput. Biol. 9 (2) (2013)
Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson
Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst. Biol. 7 (2013)
Theodore Alexandrov, Philip E. Bourne
Learning How to Run a Lab: Interviews with Principal Investigators. PLoS Comput. Biol. 9 (11) (2013)
Philip E. Bourne
The reaming of life: based on the 2010 Jim Gray eScience Award Lecture. Concurr. Comput. Pract. Exp. 25 (4) (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 Res. 41 (Database-Issue) (2013)
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
Ten Simple Rules for Cultivating Open Science and Collaborative R&D. PLoS Comput. Biol. 9 (9) (2013)
Anthony C. Fletcher, Philip E. Bourne
Ten Simple Rules for Starting a Company. PLoS Comput. Biol. 8 (3) (2012)
Rosemary Dickin, Chris James Hall, Laura K. Taylor, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne
. PLoS Comput. Biol. 8 (1) (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 Res. 40 (Database-Issue) (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)
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
BioJava: an open-source framework for bioinformatics in 2012. Bioinform. 28 (20) (2012)
Anthony C. Fletcher, Philip E. Bourne
Ten Simple Rules To Commercialize Scientific Research. PLoS Comput. Biol. 8 (9) (2012)
Mark Jolly, Anthony C. Fletcher, Philip E. Bourne
Ten Simple Rules to Protect Your Intellectual Property. PLoS Comput. Biol. 8 (11) (2012)
Philip E. Bourne
Seven Years; It's Time for a Change. PLoS Comput. Biol. 8 (10) (2012)
Shoshana J. Wodak, Daniel Mietchen, Andrew M. Collings, Robert B. Russell, Philip E. Bourne
Meets Wikipedia. PLoS Comput. Biol. 8 (3) (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 Res. 40 (Web-Server-Issue) (2012)
Sarah L. Kinnings, Nina Liu, Peter J. Tonge, Richard M. Jackson, Lei Xie, Philip E. Bourne
Correction to "A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing". J. Chem. Inf. Model. 51 (5) (2011)
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
Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. Database J. Biol. Databases Curation 2011 (2011)
Joachim von Eichborn, Philip E. Bourne, Robert Preissner
Cobweb: a Java applet for network exploration and visualisation. Bioinform. 27 (12) (2011)
Apostol Gramada, Philip E. Bourne
Coarse-graining the electrostatic potential via distributed multipole expansions. Comput. Phys. Commun. 182 (7) (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 Res. 39 (Database-Issue) (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 Comput. Biol. 7 (4) (2011)
Fran Lewitter, Philip E. Bourne
Teaching Bioinformatics at the Secondary School Level. PLoS Comput. Biol. 7 (10) (2011)
Philip E. Bourne
Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS Comput. Biol. 7 (1) (2011)
Rosemary Dickin, Cecy Marden, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne
. PLoS Comput. Biol. 7 (1) (2011)
Sarah L. Kinnings, Nina Liu, Peter J. Tonge, Richard M. Jackson, Lei Xie, Philip E. Bourne
A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing. J. Chem. Inf. Model. 51 (2) (2011)
Philip E. Bourne, Virginia Barbour
Ten Simple Rules for Building and Maintaining a Scientific Reputation. PLoS Comput. Biol. 7 (6) (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 Res. 39 (Database-Issue) (2011)
Philip E. Bourne, Timothy W. Clark, Robert Dale, Anita de Waard, Ivan Herman, Eduard H. Hovy, David M. Shotton
Improving The Future of Research Communications and e-Scholarship (Dagstuhl Perspectives Workshop 11331). Dagstuhl Manifestos 1 (1) (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 Res. 39 (Database-Issue) (2011)
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 Bioinform. 11 (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 Bioinform. 11 (2010)
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
Will Widgets and Semantic Tagging Change Computational Biology? PLoS Comput. Biol. 6 (2) (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 Comput. Biol. 6 (1) (2010)
Rosemary Dickin, Cecy Marden, Catherine Nancarrow, Philip E. Bourne
. PLoS Comput. Biol. 6 (2) (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 Res. 38 (Web-Server-Issue) (2010)
Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Philip E. Bourne
Drugome and Its Polypharmacological Implications. PLoS Comput. Biol. 6 (11) (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 Comput. Biol. 6 (9) (2010)
J. Lynn Fink, Pablo Fernicola, Rahul Chandran, Savas Parastatidis, Alex D. Wade, Oscar Naim, Greg B. Quinn, Philip E. Bourne
Word add-in for ontology recognition: semantic enrichment of scientific literature. BMC Bioinform. 11 (2010)
Ruchira S. Datta, Matthew W. Lux, Philip E. Bourne
Conference Postcards from PSB 2010. PLoS Comput. Biol. 6 (4) (2010)
Philip E. Bourne
What Do I Want from the Publisher of the Future? PLoS Comput. Biol. 6 (5) (2010)
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. Bioinform. 26 (23) (2010)
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 Comput. Biol. 5 (5) (2009)
Evie Browne, Rosemary Dickin, Philip E. Bourne
. PLoS Comput. Biol. 5 (1) (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 Comput. Biol. 5 (7) (2009)
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. Bioinform. 25 (12) (2009)

Philip E. Bourne.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Philip E. Bourne