Philip E. Bourne

According to our database1, Philip E. Bourne authored at least 154 papers between 1994 and 2019.

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Bibliography

2019
Natural language processing of symptoms documented in free-text narratives of electronic health records: a systematic review.
JAMIA, 2019

A systematic review of natural language processing and text mining of symptoms from electronic patient-authored text data.
I. J. Medical Informatics, 2019

2018
Cloud computing applications for biomedical science: A perspective.
PLoS Computational Biology, 2018

2017
Ten simple rules to consider regarding preprint submission.
PLoS Computational Biology, 2017

Ten simple rules in considering a career in academia versus government.
PLoS Computational Biology, 2017

BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank.
Bioinformatics, 2017

2016
Systems biology of the structural proteome.
BMC Systems Biology, 2016

Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology.
BMC Bioinformatics, 2016

2015
Ten Simple Rules for Lifelong Learning, According to Hamming.
PLoS Computational Biology, 2015

Ten Years of PLoS Computational Biology: A Decade of Appreciation and Innovation.
PLoS Computational Biology, 2015

Confronting the Ethical Challenges of Big Data in Public Health.
PLoS Computational Biology, 2015

Perspective: Sustaining the big-data ecosystem.
Nature, 2015

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.
Nucleic Acids Research, 2015

The NIH Big Data to Knowledge (BD2K) initiative.
JAMIA, 2015

Editor's Choice: Achievements and challenges in structural bioinformatics and computational biophysics.
Bioinformatics, 2015

RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank.
Bioinformatics, 2015

Detection of circular permutations within protein structures using CE-CP.
Bioinformatics, 2015

Big data in biomedicine - An NIH perspective.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

2014
Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine.
PLoS Computational Biology, 2014

Ten Simple Rules for Better Figures.
PLoS Computational Biology, 2014

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article.
PLoS Computational Biology, 2014

Ten Simple Rules for Approaching a New Job.
PLoS Computational Biology, 2014

What Big Data means to me.
JAMIA, 2014

Anti-Infectious Drug Repurposing Using an Integrated Chemical Genomics and Structural Systems Biology Approach.
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

2013
Ten Simple Rules for Cultivating Open Science and Collaborative R&D.
PLoS Computational Biology, 2013

Let's Make Those Book Chapters Open Too!
PLoS Computational Biology, 2013

Learning How to Run a Lab: Interviews with Principal Investigators.
PLoS Computational Biology, 2013

The RCSB Protein Data Bank: new resources for research and education.
Nucleic Acids Research, 2013

The reaming of life: based on the 2010 Jim Gray eScience Award Lecture.
Concurrency and Computation: Practice and Experience, 2013

Antibacterial mechanisms identified through structural systems pharmacology.
BMC Systems Biology, 2013

The era of open.
Proceedings of the 9th International Symposium on Open Collaboration, Hong Kong, China, August 05, 2013

2012
Topic Pages: PLoS Computational Biology Meets Wikipedia.
PLoS Computational Biology, 2012

Ten Simple Rules to Protect Your Intellectual Property.
PLoS Computational Biology, 2012

Ten Simple Rules To Commercialize Scientific Research.
PLoS Computational Biology, 2012

Ten Simple Rules for Starting a Company.
PLoS Computational Biology, 2012

A Review of 2011 for PLoS Computational Biology.
PLoS Computational Biology, 2012

Seven Years; It's Time for a Change.
PLoS Computational Biology, 2012

Immune epitope database analysis resource.
Nucleic Acids Research, 2012

SuperTarget goes quantitative: update on drug-target interactions.
Nucleic Acids Research, 2012

BioJava: an open-source framework for bioinformatics in 2012.
Bioinformatics, 2012

An integrated workflow for proteome-wide off-target identification and polypharmacology drug design.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

2011
Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir.
PLoS Computational Biology, 2011

Teaching Bioinformatics at the Secondary School Level.
PLoS Computational Biology, 2011

A Review of 2010 for PLoS Computational Biology.
PLoS Computational Biology, 2011

Ten Simple Rules for Building and Maintaining a Scientific Reputation.
PLoS Computational Biology, 2011

Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia.
PLoS Computational Biology, 2011

The RCSB Protein Data Bank: redesigned web site and web services.
Nucleic Acids Research, 2011

IEDB-3D: structural data within the immune epitope database.
Nucleic Acids Research, 2011

PROMISCUOUS: a database for network-based drug-repositioning.
Nucleic Acids Research, 2011

Correction to "A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing".
Journal of Chemical Information and Modeling, 2011

A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing.
Journal of Chemical Information and Modeling, 2011

Improving The Future of Research Communications and e-Scholarship (Dagstuhl Perspectives Workshop 11331).
Dagstuhl Manifestos, 2011

Coarse-graining the electrostatic potential via distributed multipole expansions.
Computer Physics Communications, 2011

Cobweb: a Java applet for network exploration and visualisation.
Bioinformatics, 2011

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank.
Database, 2011

2010
The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications.
PLoS Computational Biology, 2010

A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology.
PLoS Computational Biology, 2010

A Review of 2009 for PLoS Computational Biology.
PLoS Computational Biology, 2010

PLoS Computational Biology Conference Postcards from PSB 2010.
PLoS Computational Biology, 2010

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model.
PLoS Computational Biology, 2010

Will Widgets and Semantic Tagging Change Computational Biology?
PLoS Computational Biology, 2010

What Do I Want from the Publisher of the Future?
PLoS Computational Biology, 2010

SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison.
Nucleic Acids Research, 2010

Integration of open access literature into the RCSB Protein Data Bank using BioLit.
BMC Bioinformatics, 2010

Word add-in for ontology recognition: semantic enrichment of scientific literature.
BMC Bioinformatics, 2010

dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment.
BMC Bioinformatics, 2010

Pre-calculated protein structure alignments at the RCSB PDB website.
Bioinformatics, 2010

2009
Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors.
PLoS Computational Biology, 2009

Ten Simple Rules To Combine Teaching and Research.
PLoS Computational Biology, 2009

Sm/Lsm Genes Provide a Glimpse into the Early Evolution of the Spliceosome.
PLoS Computational Biology, 2009

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis.
PLoS Computational Biology, 2009

A Review of 2008 for PLoS Computational Biology.
PLoS Computational Biology, 2009

Ten Simple Rules for Chairing a Scientific Session.
PLoS Computational Biology, 2009

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery.
Bioinformatics, 2009

2008
Computational Biology Resources Lack Persistence and Usability.
PLoS Computational Biology, 2008

Ten Simple Rules for Organizing a Scientific Meeting.
PLoS Computational Biology, 2008

Open Access: Taking Full Advantage of the Content.
PLoS Computational Biology, 2008

I Am Not a Scientist, I Am a Number.
PLoS Computational Biology, 2008

Immune epitope database analysis resource (IEDB-AR).
Nucleic Acids Research, 2008

SuperTarget and Matador: resources for exploring drug-target relationships.
Nucleic Acids Research, 2008

BioLit: integrating biological literature with databases.
Nucleic Acids Research, 2008

Superimposé: a 3D structural superposition server.
Nucleic Acids Research, 2008

ElliPro: a new structure-based tool for the prediction of antibody epitopes.
BMC Bioinformatics, 2008

Session Introduction.
Proceedings of the Biocomputing 2008, 2008

Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks.
Proceedings of the Biocomputing 2008, 2008

2007
In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators.
PLoS Computational Biology, 2007

Ten Simple Rules for a Successful Collaboration.
PLoS Computational Biology, 2007

The International Society for Computational Biology 10th Anniversary.
PLoS Computational Biology, 2007

Ten Simple Rules for Graduate Students.
PLoS Computational Biology, 2007

Ten Simple Rules for Doing Your Best Research, According to Hamming.
PLoS Computational Biology, 2007

Ten Simple Rules for a Good Poster Presentation.
PLoS Computational Biology, 2007

Developing Computational Biology.
PLoS Computational Biology, 2007

Ten Simple Rules for Making Good Oral Presentations.
PLoS Computational Biology, 2007

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites.
BMC Bioinformatics, 2007

Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2.
BMC Bioinformatics, 2007

High-throughput identification of interacting protein-protein binding sites.
BMC Bioinformatics, 2007

Con-Struct Map: a comparative contact map analysis tool.
Bioinformatics, 2007

2006
ISMB 2006.
PLoS Computational Biology, 2006

Wiggle - Predicting Functionally Flexible Regions from Primary Sequence.
PLoS Computational Biology, 2006

Biocurators: Contributors to the World of Science.
PLoS Computational Biology, 2006

Ten Simple Rules for Reviewers.
PLoS Computational Biology, 2006

Correction: Ten Simple Rules for Selecting a Postdoctoral Position.
PLoS Computational Biology, 2006

Ten Simple Rules for Selecting a Postdoctoral Position.
PLoS Computational Biology, 2006

Ten Simple Rules for Getting Grants.
PLoS Computational Biology, 2006

One Year of PLoS Computational Biology.
PLoS Computational Biology, 2006

The RCSB PDB information portal for structural genomics.
Nucleic Acids Research, 2006

Curation of complex, context-dependent immunological data.
BMC Bioinformatics, 2006

Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction.
BMC Bioinformatics, 2006

Multipolar representation of protein structure.
BMC Bioinformatics, 2006

The Immune Epitope Database and Analysis Resource.
Proceedings of the Pattern Recognition in Bioinformatics, International Workshop, 2006

ISMB 2006.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005
Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models.
PLoS Computational Biology, 2005

Structural Evolution of the Protein Kinase-Like Superfamily.
PLoS Computational Biology, 2005

PLoS Computational Biology: A New Community Journal.
PLoS Computational Biology, 2005

Ten Simple Rules for Getting Published.
PLoS Computational Biology, 2005

Will a Biological Database Be Different from a Biological Journal?
PLoS Computational Biology, 2005

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema.
Nucleic Acids Research, 2005

The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications.
BMC Bioinformatics, 2005

Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular STructure.
Proceedings of the Biocomputing 2005, 2005

2004
The Encyclopedia of Life Project: Grid Software and Deployment.
New Generation Comput., 2004

CE-MC: a multiple protein structure alignment server.
Nucleic Acids Research, 2004

The distribution and query systems of the RCSB Protein Data Bank.
Nucleic Acids Research, 2004

A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE.
Journal of Computational Biology, 2004

A case study of high-throughput biological data processing on parallel platforms.
Bioinformatics, 2004

Statistically rigorous automated protein annotation.
Bioinformatics, 2004

The Protein Data Bank and lessons in data management.
Briefings in Bioinformatics, 2004

Session Introduction.
Proceedings of the Biocomputing 2004, 2004

The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures.
Proceedings of the Biocomputing 2004, 2004

Grid Portal Interface for Interactive Use and Monitoring of High-Throughput Proteome Annotation.
Proceedings of the Grid Computing in Life Science, 2004

Grid Workflow Software for a High-Throughput Proteome Annotation Pipeline.
Proceedings of the Grid Computing in Life Science, 2004

The Future of Bioinformatics.
Proceedings of the Second Asia-Pacific Bioinformatics Conference (APBC 2004), 2004

2003
BioEditor - Simplifying Macromolecular Structure Annotation.
Bioinformatics, 2003

Parallel Processing on Large Redudant Biological Data Sets: Protein Structures Classification with CEPAR.
Proceedings of the Parallel Computing: Software Technology, 2003

Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

High Performance Computational Biology - Past Progress and Future Promise.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002
The Protein Data Bank: unifying the archive.
Nucleic Acids Research, 2002

CKAAPs DB: a Conserved Key Amino Acid Positions DataBase.
Nucleic Acids Research, 2002

An ontology driven architecture for derived representations of macromolecular structure.
Bioinformatics, 2002

Building an automated classification of DNA-binding protein domains.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002

2001
A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm.
Nucleic Acids Research, 2001

CKAAPs DB: a conserved key amino acid positions database.
Nucleic Acids Research, 2001

The PDB data uniformity project.
Nucleic Acids Research, 2001

A New Algorithm for the Alignment of Multiple Protein Structures Using Monte Carlo Optimization.
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

2000
The Protein Data Bank.
Nucleic Acids Research, 2000

STAR/mmCIF: An ontology for macromolecular structure.
Bioinformatics, 2000

ISMB-2000: Bioinformatics enters a new millennium.
Bioinformatics, 2000

1999
An analysis of the Protein Data Bank in search of temporal and global trends.
Bioinformatics, 1999

Developing Protein Documentaries and Other Multimedia Presentations for Molecular Biology.
Proceedings of the 4th Pacific Symposium on Biocomputing, 1999

1997
Protein data representation and query using optimized data decomposition.
Computer Applications in the Biosciences, 1997

Code Generation through Annotation of Macromolecular Structure Data.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

1995
Design and use of a software framework to obtain information derived from macromolecular structure data.
Proceedings of the 28th Annual Hawaii International Conference on System Sciences (HICSS-28), 1995

1994
An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA.
Computer Applications in the Biosciences, 1994

Design and application of PDBlib, a C++ macromolecular class library.
Computer Applications in the Biosciences, 1994

Design and Application of a C++ Macromolecular Class Library.
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994


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