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ORCIDPhilip E. Bourne
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- affiliation: San Diego Supercomputer Center, USA
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2020 – today
- 2024
[j157]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): 11 (2024)- [j156]Zheng Zhao
, Philip E. Bourne:
Exploring Extended Warheads toward Developing Cysteine-Targeted Covalent Kinase Inhibitors. J. Chem. Inf. Model. 64(24): 9517-9527 (2024) - [d3]Eli J. Draizen, Stella Veretnik, Cameron Mura, Philip E. Bourne:
Supplemental Material for 'Deep Generative Models of Protein Structure Uncover Distant Relationships Across a Continuous Fold Space' and DeepUrfold. Zenodo, 2024
- 2023
- [j155]Luis Felipe R. Murillo, Caitlin D. Wylie, Philip E. Bourne:
Critical data ethics pedagogies: Three (non-rival) approaches. Big Data Soc. 10(2) (2023) - [j154]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): 1362-1370 (2023) - [j153]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) - [j152]Cameron Mura, Philip E. Bourne:
Ten simple rules for serving as an editor. PLoS Comput. Biol. 19(3) (2023) - [j151]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) - [j150]Hassan Masum, Philip E. Bourne:
Ten simple rules for humane data science. PLoS Comput. Biol. 19(12) (2023) - [i6]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 abs/2303.10829 (2023) - [i5]Terence R. Johnson, Philip E. Bourne:
The Biological Data Sustainability Paradox. CoRR abs/2311.05668 (2023) - 2022
- [j149]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): 223-224 (2022) - [j148]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) - [j147]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) - [j146]Philip E. Bourne:
Ten simple rules for good leadership. PLoS Comput. Biol. 18(6) (2022) - [j145]Davide Chicco, Philip E. Bourne:
Ten simple rules for organizing a special session at a scientific conference. PLoS Comput. Biol. 18(8) (2022) - [d2]Eli J. Draizen, Cameron Mura, Philip E. Bourne:
Prop3D-20. Zenodo, 2022 - [d1]Eli J. Draizen, Stella Veretnik, Cameron Mura, Philip E. Bourne:
DeepUrfold Supplemental Material. Zenodo, 2022 - [i4]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 abs/2208.04682 (2022) - 2021
- [j144]Rupa S. Valdez, Don E. Detmer, Philip E. Bourne, Katherine K. Kim, Robin Austin, Anna McCollister-Slipp, Courtney C. Rogers, Karen C. Waters-Wicks:
Informatics-enabled citizen science to advance health equity. J. Am. Medical Informatics Assoc. 28(9): 2009-2012 (2021) - [j143]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) - [i3]Christine L. Borgman, Philip E. Bourne:
Why it takes a village to manage and share data. CoRR abs/2109.01694 (2021) - [i2]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 abs/2111.14283 (2021) - 2020
- [j142]Anthony C. Fletcher, Georges A. Wagner, Philip E. Bourne:
Ten simple rules for more objective decision-making. PLoS Comput. Biol. 16(4) (2020) - [j141]Hoe-Han Goh, Philip E. Bourne:
Ten simple rules for researchers while in isolation from a pandemic. PLoS Comput. Biol. 16(6) (2020) - [j140]Hoe-Han Goh, Philip E. Bourne:
Ten simple rules for writing scientific op-ed articles. PLoS Comput. Biol. 16(9) (2020) - [j139]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)
2010 – 2019
- 2019
- [j138]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: 37-46 (2019) - [j137]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): 364-379 (2019) - [j136]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): 453-462 (2019) - [j135]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) - [j134]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) - [j133]Philip E. Bourne:
Ten simple rules to aid in achieving a vision. PLoS Comput. Biol. 15(10) (2019) - [i1]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 abs/1905.00455 (2019) - 2018
- [j132]Vivek Navale, Philip E. Bourne:
Cloud computing applications for biomedical science: A perspective. PLoS Comput. Biol. 14(6) (2018) - [j131]Philip E. Bourne:
Ten simple rules when considering retirement. PLoS Comput. Biol. 14(10) (2018) - [j130]Philip E. Bourne, Fran Lewitter, Scott Markel, Jason A. Papin:
One thousand simple rules. PLoS Comput. Biol. 14(12) (2018) - 2017
- [j129]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): 2047-2049 (2017) - [j128]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) - [j127]Philip E. Bourne:
Ten simple rules in considering a career in academia versus government. PLoS Comput. Biol. 13(10) (2017) - 2016
- [j126]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: 90 (2016) - [j125]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: 26 (2016) - 2015
- [j124]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:
RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. Bioinform. 31(1): 126-127 (2015) - [j123]Ilan Samish, Philip E. Bourne, Rafael J. Najmanovich:
Editor's Choice: Achievements and challenges in structural bioinformatics and computational biophysics. Bioinform. 31(1): 146-150 (2015) - [j122]Spencer E. Bliven, Philip E. Bourne, Andreas Prlic:
Detection of circular permutations within protein structures using CE-CP. Bioinform. 31(8): 1316-1318 (2015) - [j121]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): 1114 (2015) - [j120]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): 345-356 (2015) - [j119]Philip E. Bourne, Jon R. Lorsch, Eric D. Green:
Perspective: Sustaining the big-data ecosystem. Nat. 527(7576): S16-S17 (2015) - [j118]Philip E. Bourne:
Confronting the Ethical Challenges of Big Data in Public Health. PLoS Comput. Biol. 11(2) (2015) - [j117]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) - [j116]Philip E. Bourne, Steven E. Brenner, Michael B. Eisen:
Ten Years of PLoS‡ Computational Biology: A Decade of Appreciation and Innovation. PLoS Comput. Biol. 11(6) (2015) - [c23]Philip E. Bourne:
Big data in biomedicine - An NIH perspective. BIBM 2015: 1 - 2014
- [j115]Philip E. Bourne:
What Big Data means to me. J. Am. Medical Informatics Assoc. 21(2): 194 (2014) - [j114]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) - [j113]Philip E. Bourne:
Ten Simple Rules for Approaching a New Job. PLoS Comput. Biol. 10(6) (2014) - [j112]Nicolas P. Rougier, Michael Droettboom, Philip E. Bourne:
Ten Simple Rules for Better Figures. PLoS Comput. Biol. 10(9) (2014) - [j111]Harriet Dashnow, Andrew Lonsdale, Philip E. Bourne:
Ten Simple Rules for Writing a PLOS Ten Simple Rules Article. PLoS Comput. Biol. 10(10) (2014) - [c22]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: 136-147 - 2013
- [j110]Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson:
Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst. Biol. 7: 102 (2013) - [j109]Philip E. Bourne:
The reaming of life: based on the 2010 Jim Gray eScience Award Lecture. Concurr. Comput. Pract. Exp. 25(4): 445-453 (2013) - [j108]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): 475-482 (2013) - [j107]Philip E. Bourne:
Let's Make Those Book Chapters Open Too! PLoS Comput. Biol. 9(2) (2013) - [j106]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) - [j105]Theodore Alexandrov, Philip E. Bourne:
Learning How to Run a Lab: Interviews with Principal Investigators. PLoS Comput. Biol. 9(11) (2013) - [c21]Philip E. Bourne:
The era of open. OpenSym 2013: 36:1 - 2012
- [j104]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): 2693-2695 (2012) - [j103]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): 1113-1117 (2012) - [j102]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): 525-530 (2012) - [j101]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 Comput. Biol. 8(1) (2012) - [j100]Anthony C. Fletcher, Philip E. Bourne:
Ten Simple Rules for Starting a Company. PLoS Comput. Biol. 8(3) (2012) - [j99]Shoshana J. Wodak, Daniel Mietchen, Andrew M. Collings, Robert B. Russell, Philip E. Bourne:
Topic Pages: PLoS Computational Biology Meets Wikipedia. PLoS Comput. Biol. 8(3) (2012) - [j98]Anthony C. Fletcher, Philip E. Bourne:
Ten Simple Rules To Commercialize Scientific Research. PLoS Comput. Biol. 8(9) (2012) - [j97]Philip E. Bourne:
Seven Years; It's Time for a Change. PLoS Comput. Biol. 8(10) (2012) - [j96]Mark Jolly, Anthony C. Fletcher, Philip E. Bourne:
Ten Simple Rules to Protect Your Intellectual Property. PLoS Comput. Biol. 8(11) (2012) - [c20]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 - 2011
- [j95]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) - [j94]Joachim von Eichborn, Philip E. Bourne, Robert Preissner:
Cobweb: a Java applet for network exploration and visualisation. Bioinform. 27(12): 1725-1726 (2011) - [j93]Apostol Gramada, Philip E. Bourne:
Coarse-graining the electrostatic potential via distributed multipole expansions. Comput. Phys. Commun. 182(7): 1455-1462 (2011) - [j92]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): 41-60 (2011) - [j91]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): 408-419 (2011) - [j90]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): 1195-1197 (2011) - [j89]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): 392-401 (2011) - [j88]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): 1060-1066 (2011) - [j87]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): 1164-1170 (2011) - [j86]Philip E. Bourne:
Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS Comput. Biol. 7(1) (2011) - [j85]Rosemary Dickin, Cecy Marden, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne:
A Review of 2010 for PLoS Computational Biology. PLoS Comput. Biol. 7(1) (2011) - [j84]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) - [j83]Philip E. Bourne, Virginia Barbour:
Ten Simple Rules for Building and Maintaining a Scientific Reputation. PLoS Comput. Biol. 7(6) (2011) - [j82]Fran Lewitter, Philip E. Bourne:
Teaching Bioinformatics at the Secondary School Level. PLoS Comput. Biol. 7(10) (2011) - 2010
- [j81]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): 2983-2985 (2010) - [j80]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: 103 (2010) - [j79]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: 220 (2010) - [j78]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: 310 (2010) - [j77]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): 441-444 (2010) - [j76]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) - [j75]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) - [j74]Rosemary Dickin, Cecy Marden, Catherine Nancarrow, Philip E. Bourne:
A Review of 2009 for PLoS Computational Biology. PLoS Comput. Biol. 6(2) (2010) - [j73]Ruchira S. Datta, Matthew W. Lux, Philip E. Bourne:
PLoS Computational Biology Conference Postcards from PSB 2010. PLoS Comput. Biol. 6(4) (2010) - [j72]Philip E. Bourne:
What Do I Want from the Publisher of the Future? PLoS Comput. Biol. 6(5) (2010) - [j71]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) - [j70]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 Comput. Biol. 6(11) (2010)
2000 – 2009
- 2009
- [j69]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) - [j68]Evie Browne, Rosemary Dickin, Philip E. Bourne:
A Review of 2008 for PLoS Computational Biology. PLoS Comput. Biol. 5(1) (2009) - [j67]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 Comput. Biol. 5(3) (2009) - [j66]Quentin Vicens, Philip E. Bourne:
Ten Simple Rules To Combine Teaching and Research. PLoS Comput. Biol. 5(4) (2009) - [j65]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) - [j64]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) - [j63]Alex Bateman, Philip E. Bourne:
Ten Simple Rules for Chairing a Scientific Session. PLoS Comput. Biol. 5(9) (2009) - 2008
- [j62]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 Bioinform. 9 (2008) - [j61]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 Res. 36(Database-Issue): 919-922 (2008) - [j60]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 Res. 36(Web-Server-Issue): 47-54 (2008) - [j59]J. Lynn Fink, Sergey Kushch, Parker R. Williams, Philip E. Bourne:
BioLit: integrating biological literature with databases. Nucleic Acids Res. 36(Web-Server-Issue): 385-389 (2008) - [j58]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 Res. 36(Web-Server-Issue): 513-518 (2008) - [j57]Philip E. Bourne, J. Lynn Fink, Mark Gerstein:
Open Access: Taking Full Advantage of the Content. PLoS Comput. Biol. 4(3) (2008) - [j56]Manuel Corpas, Nils Gehlenborg, Sarath Chandra Janga, Philip E. Bourne:
Ten Simple Rules for Organizing a Scientific Meeting. PLoS Comput. Biol. 4(6) (2008) - [j55]Stella Veretnik, J. Lynn Fink, Philip E. Bourne:
Computational Biology Resources Lack Persistence and Usability. PLoS Comput. Biol. 4(7) (2008) - [j54]Philip E. Bourne, J. Lynn Fink:
I Am Not a Scientist, I Am a Number. PLoS Comput. Biol. 4(12) (2008) - [c19]K. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman:
Session Introduction. Pacific Symposium on Biocomputing 2008: 551-555 - [c18]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 - 2007
- [j53]Jo-Lan Chung, John E. Beaver, Eric D. Scheeff, Philip E. Bourne:
Con-Struct Map: a comparative contact map analysis tool. Bioinform. 23(18): 2491-2492 (2007) - [j52]Jo-Lan Chung, Wei Wang, Philip E. Bourne:
High-throughput identification of interacting protein-protein binding sites. BMC Bioinform. 8 (2007) - [j51]Jenny Gu, Philip E. Bourne:
Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2. BMC Bioinform. 8 (2007) - [j50]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 Bioinform. 8(S-4) (2007) - [j49]Quentin Vicens, Philip E. Bourne:
Ten Simple Rules for a Successful Collaboration. PLoS Comput. Biol. 3(3) (2007) - [j48]Philip E. Bourne:
Ten Simple Rules for Making Good Oral Presentations. PLoS Comput. Biol. 3(4) (2007) - [j47]Thomas C. Erren, Philip E. Bourne:
Ten Simple Rules for a Good Poster Presentation. PLoS Comput. Biol. 3(5) (2007) - [j46]Lawrence Hunter, Russ B. Altman, Philip E. Bourne:
The International Society for Computational Biology 10th Anniversary. PLoS Comput. Biol. 3(6) (2007) - [j45]Philip E. Bourne, Steven E. Brenner:
Developing Computational Biology. PLoS Comput. Biol. 3(9) (2007) - [j44]Thomas C. Erren, Paul Cullen, Michael Erren, Philip E. Bourne:
Ten Simple Rules for Doing Your Best Research, According to Hamming. PLoS Comput. Biol. 3(10) (2007) - [j43]Jenny Gu, Philip E. Bourne:
Ten Simple Rules for Graduate Students. PLoS Comput. Biol. 3(11) (2007) - [j42]Lei Xie, Jian Wang, Philip E. Bourne:
In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators. PLoS Comput. Biol. 3(11) (2007) - 2006
- [j41]Apostol Gramada, Philip E. Bourne:
Multipolar representation of protein structure. BMC Bioinform. 7: 242 (2006) - [j40]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 Bioinform. 7: 341 (2006) - [j39]Eric D. Scheeff, Philip E. Bourne:
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinform. 7: 410 (2006) - [j38]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 Res. 34(Database-Issue): 302-305 (2006) - [j37]Philip E. Bourne, Leo M. Chalupa:
Ten Simple Rules for Getting Grants. PLoS Comput. Biol. 2(2) (2006) - [j36]Goran Neshich, Philip E. Bourne, Søren Brunak:
ISMB 2006. PLoS Comput. Biol. 2(2) (2006) - [j35]Jenny Gu, Michael Gribskov, Philip E. Bourne:
Wiggle - Predicting Functionally Flexible Regions from Primary Sequence. PLoS Comput. Biol. 2(7) (2006) - [j34]Philip E. Bourne:
One Year of PLoS Computational Biology. PLoS Comput. Biol. 2(8) (2006) - [j33]Philip E. Bourne, Alon Korngreen:
Ten Simple Rules for Reviewers. PLoS Comput. Biol. 2(9) (2006) - [j32]Philip E. Bourne, Johanna R. McEntyre:
Biocurators: Contributors to the World of Science. PLoS Comput. Biol. 2(10) (2006) - [j31]Philip E. Bourne, Iddo Friedberg:
Ten Simple Rules for Selecting a Postdoctoral Position. PLoS Comput. Biol. 2(11) (2006) - [j30]Philip E. Bourne, Iddo Friedberg:
Correction: Ten Simple Rules for Selecting a Postdoctoral Position. PLoS Comput. Biol. 2(12) (2006) - [c17]Philip E. Bourne, Søren Brunak:
ISMB 2006. ISMB (Supplement of Bioinformatics) 2006: 1-2 - [c16]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 - 2005
- [j29]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 Bioinform. 6: 21 (2005) - [j28]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 Res. 33(Database-Issue): 233-237 (2005) - [j27]Philip E. Bourne, Steven E. Brenner, Michael B. Eisen:
PLoS Computational Biology: A New Community Journal. PLoS Comput. Biol. 1(1) (2005) - [j26]Philip E. Bourne:
Will a Biological Database Be Different from a Biological Journal? PLoS Comput. Biol. 1(3) (2005) - [j25]Lei Xie, Philip E. Bourne:
Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models. PLoS Comput. Biol. 1(3) (2005) - [j24]Philip E. Bourne:
Ten Simple Rules for Getting Published. PLoS Comput. Biol. 1(5) (2005) - [j23]Eric D. Scheeff, Philip E. Bourne:
Structural Evolution of the Protein Kinase-Like Superfamily. PLoS Comput. Biol. 1(5) (2005) - [c15]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 - 2004
- [j22]Philip E. Bourne, John D. Westbrook, Helen M. Berman:
The Protein Data Bank and lessons in data management. Briefings Bioinform. 5(1): 23-30 (2004) - [j21]Werner G. Krebs, Philip E. Bourne:
Statistically rigorous automated protein annotation. Bioinform. 20(7): 1066-1073 (2004) - [j20]Dmitry Pekurovsky, Ilya N. Shindyalov, Philip E. Bourne:
A case study of high-throughput biological data processing on parallel platforms. Bioinform. 20(12): 1940-1947 (2004) - [j19]Werner G. Krebs, Philip E. Bourne:
Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. J. Bioinform. Comput. Biol. 2(1): 61-76 (2004) - [j18]Yuting Jia, T. Gregory Dewey, Ilya N. Shindyalov, Philip E. Bourne:
A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE. J. Comput. Biol. 11(5): 787-799 (2004) - [j17]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 Res. 32(Database-Issue): 223-225 (2004) - [j16]Chittibabu Guda, Sifang Lu, Eric D. Scheeff, Philip E. Bourne, Ilya N. Shindyalov:
CE-MC: a multiple protein structure alignment server. Nucleic Acids Res. 32(Web-Server-Issue): 100-103 (2004) - [j15]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 Gener. Comput. 22(2): 127-136 (2004) - [c14]Philip E. Bourne:
The Future of Bioinformatics. APBC 2004: 3 - [c13]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 - [c12]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 - [c11]Sean D. Mooney, Philip E. Bourne, Patricia C. Babbitt:
Session Introduction. Pacific Symposium on Biocomputing 2004: 372-374 - [c10]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 - [e2]Philip E. Bourne, Dan Gusfield:
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 [contents] - 2003
- [j14]Peng Yang, Paul A. Craig, David S. Goodsell, Philip E. Bourne:
BioEditor - Simplifying Macromolecular Structure Annotation. Bioinform. 19(7): 897-898 (2003) - [c9]Philip E. Bourne:
High Performance Computational Biology - Past Progress and Future Promise. CSB 2003: 13 - [c8]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 - [c7]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 - 2002
- [j13]Douglas S. Greer, John D. Westbrook, Philip E. Bourne:
An ontology driven architecture for derived representations of macromolecular structure. Bioinform. 18(9): 1280-1281 (2002) - [j12]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 Res. 30(1): 245-248 (2002) - [j11]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 Res. 30(1): 409-411 (2002) - [c6]Julia V. Ponomarenko, Philip E. Bourne, Ilya N. Shindyalov:
Building an automated classification of DNA-binding protein domains. ECCB 2002: 192-201 - 2001
- [j10]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 Res. 29(1): 214-218 (2001) - [j9]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 Res. 29(1): 228-229 (2001) - [j8]Wilfred W. Li, Boojala V. B. Reddy, Ilya N. Shindyalov, Philip E. Bourne:
CKAAPs DB: a conserved key amino acid positions database. Nucleic Acids Res. 29(1): 329-331 (2001) - [c5]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 - 2000
- [j7]John D. Westbrook, Philip E. Bourne:
STAR/mmCIF: An ontology for macromolecular structure. Bioinform. 16(2): 159-168 (2000) - [j6]Philip E. Bourne, Michael Gribskov:
ISMB-2000: Bioinformatics enters a new millennium. Bioinform. 16(9): 749 (2000) - [j5]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 Res. 28(1): 235-242 (2000) - [e1]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:
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 [contents]
1990 – 1999
- 1999
- [j4]Helge Weissig, Philip E. Bourne:
An analysis of the Protein Data Bank in search of temporal and global trends. Bioinform. 15(10): 807-831 (1999) - [c4]Greg B. Quinn, H.-P. Wang, David Martínez, Philip E. Bourne:
Developing Protein Documentaries and Other Multimedia Presentations for Molecular Biology. Pacific Symposium on Biocomputing 1999: 380-391 - 1997
- [j3]Ilya N. Shindyalov, Philip E. Bourne:
Protein data representation and query using optimized data decomposition. Comput. Appl. Biosci. 13(5): 487-496 (1997) - [c3]John Biggs, Calton Pu, Philip E. Bourne:
Code Generation through Annotation of Macromolecular Structure Data. ISMB 1997: 52-55 - 1995
- [c2]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 - 1994
- [j2]Peisen Zhang, Eric A. Schon, Stuart G. Fischer, Eftihia Cayanis, Janie Weiss, Susan Kistler, Philip E. Bourne:
An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA. Comput. Appl. Biosci. 10(3): 309-317 (1994) - [j1]Weider Chang, Ilya N. Shindyalov, Calton Pu, Philip E. Bourne:
Design and application of PDBlib, a C++ macromolecular class library. Comput. Appl. Biosci. 10(6): 575-586 (1994) - [c1]Weider Chang, Ilya N. Shindyalov, Calton Pu, Philip E. Bourne:
Design and Application of a C++ Macromolecular Class Library. ISMB 1994: 70-77
Coauthor Index
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