Publications

2014

  • Y. Zhang, L. Xie, L. Xie & P.E.Bourne 2014 The Plasmodium falciparum Drugome and its Polypharmacological Implications PLoS ONE, in preparation.
  • C. Krishna, Li Xie, C. DerMarderossian & P.E. Bourne 2013 Combating Chagas Disease Through Inhibition of Tiam1, a Rho GTPase Guanine Nucleotide Exchange Factor, in preparation.
  • N.P.Rougier & P.E.Bourne 2014 Ten Simple Rules for Better Visuals, PLOS Comp. Biol. submitted.
  • P.E.Bourne 2014 What Big Data Means to Me, J. Am. Med. Inform. Assoc. 2014;21:194 [PDF].
  • L. Xie, L. Xie & P.E. Bourne 2014 Structural Systems Pharmacology for Complex Diseases and Personalized Medicine (Review) PLOS Comp. Biol. accepted.
  • J. Wang, V.G. Anania, J. Knott, J. Rush, J.R Lill, P.E. Bourne & N. Bandeira 2014 A Turn-key Approach for Large-scale Identification of Complex Post-translational Modifications, J. Proteomics Research 13 (3): 1190-1199 [PDF].
  • J. Wang, V.G. Anania, J. Knott, J. Rush, J.R Lill, P.E. Bourne & N. Bandeira 2014 Combinatorial Approach for Large-scale Identification of Linked Peptides from MS/MS Spectra, Mol. Cell. Proteomics 13(4):1128-36.[PDF]
  • P.E. Bourne 2014 Ten Simple Rules for Approaching a Job Interview, PLOS Comp. Biol., accepted.
  • D. Myers-Turnbull, S.E. Bliven, P.W. Rose, Z.K. Azizd, P. Youkharibache, P.E. Bourne &, Andreas Prlic, 2014 Systematic Detection of Internal Symmetry in Proteins using CE-Symm, J. Mol. Biol ,http://dx.doi.org/10.1016/j.jmb.2014.03.010. [PDF]
  • J. Wang, P.E. Bourne & N. Bandeira 2014 MixGF: Spectral Probabilities for Mixture Spectra from More Than One Peptide, Mol. Cell Proteomics, accepted.
  • C. Ng, Y.Zhang, P.E. Bourne & L. Xie 2014 Anti-infectious Drug Repurposing Usingan Integrated Chemical Genomics and Structural Systems Biology Approach, Pacific Symposium on Biocomputing, 19:136-47. [PDF]

2013

  • T. Alexandrov & P.E. Bourne 2013 Learning How to Run a Lab: Interviews with principle Investigators, PLOS Comp. Biol., 9(11): e1003349. [PDF].
  • R. Chang, P.E.Bourne & B.O. Palsson 2013 Antibacterial Mechanisms Identified through Structural Systems Pharmacology BMC Systems Biology, 7:102 [PDF].
  • H. Masum, A. Rao, B.M. Good, M.H. Todd, A.M. Edwards, L. Chan, B.A. Bunin, A.I. Su, Z. Thomas, P.E. Bourne 2013 Ten Simple Rules for Cultivating Open Science and Collaborative R&D PLOS Comp. Biol. 9(9) e1003244 [PDF].
  • E. Kolker, I. Altintas, P.E. Bourne et al. 2013 In Praise of Open Research Measures Nature 498, 170. [PDF].
  • M.J. Costello, W.K. Michener, M. Gahegan, Z-Q. Zhang, & P.E. Bourne 2013 Biodiversity Data Should be Published, Cited and Peer Reviewed Trends in Ecology and Evolution, http://dx.doi.org/10.1016/j.tree.2013.05.002 [PDF].
  • L. Xie, T. Ali, R. Valencia, B.L. Ferreira. V. Xue, M. Tanweer, D. Zhou, G.G. Hahhah, P.E. Bourne & L. Xie 2013 Multiscale Modeling of the Causal Functional Roles of nsSNPs in a Genome-wide Association Study: Application to Hypoxia BMC Genomics 14(Suppl 3):S9 doi:10.1186/1471-2164-14-S3-S9 [PDF].
  • D. Garijo, S. Kinnings, L. Xie, L. Xie, P.E. Bourne & Y. Gil 2013 Quantifying Reproducability in Computational Biology: The Case of the Tuberculosis Drugome.PLOS ONE,8(11): e80278 [PDF].
  • P.E. Bourne 2013 Lets Make Those Book Chapters Open Too! PLOS Comp. Biol. 9(2) e1002941 [PDF].

2012

  • N. Rifai, J. Sack, M.A. Keller, A. Acharya, P.E. Bourne, M. Rossner, and S. Wills 2012 Communication of Scientific Information: is it Time to Reassess? Clinical Chemistry, 59:4 [PDF].
  • M. Jolly, A.C. Fletcher & P.E. Bourne 2012 Ten Simple Rules to Protect Your Intellectual Property. PLoS Comp. Biol. 8(11): e1002766 [PDF].
  • P.W. Rose, C. Bi, W.F. Bluhm, D. Dimitropoulos, D.S. Goodsell, A. Prlic, M. Quesada, G.B. Quinn, A. Ramos, J.D. Westbrook, J. Young, C. Zardecki, H.M. Berman & P.E. Bourne 2012 An Update on the RCSB Protein Data Bank. NAR 1;41(D1):D475-D482 [PDF].
  • P.E. Bourne 2012 Seven Years; Its Time for a Change. PLoS Comp. Biol. 8(10): e1002728 [PDF].
  • A.C. Fletcher & P.E. Bourne 2012 Ten Simple Rules to Commercialize Scientific Research PLoS Comp. Biol. 8(9): e1002712 [PDF].
  • A. Prlic, A. Yates, S.E. Bliven, P.W. Rose, J. Jacobsen, P.V. Troshin, M. Chapman, J. Gao, C.H. Koh, S. Foisy, R. Holland, G. Rimsa, M.L.Heuer, H. Brandstatter–Muller, P.E. Bourne & S. Willis 2012 BioJava: An Open-source Framework for Bioinformatics in 2012, Bioinformatics. 10.1093/bioinformatics/bts494 [PDF].
  • P.E. Bourne 2012 The Reaming of Life: Based on the 2010 Jim Gray eScience Award Lecture. Concurrency and Computation: Practice and Experience, 25(4), 445-453. [PDF].
  • Y. Kim, J. Ponomarenko, Z. Zhu, D. Tamang, P. Wang, J. Greenbaum, A. Sette, O. Lund, P.E. Bourne, M. Nielsen, & B. Peters 2012 Immune Epitope Database Analysis Resource NAR 40(W1): W525-530, [PDF].
  • S.J. Wodak, D. Mietchen, A.M. Collings, R.B. Russell & P.E. Bourne 2012 PLoS Computational Biology Meets Wikipedia PLoS Comp. Biol. 8(3): e1002446 [PDF].
  • P.E. Bourne 2012 The RCSB Protein Data Bank: An Interview with Phil. Bourne, Associate Director RCSB Protein Data Bank. Interviewed by Wendy Warr J. Comput. Aided Mol. Des. 26:165-167 [PDF].
  • M.J. Costello, W.K. Michener, M. Gahegan, Z-Q. Zhang, P.E. Bourne & V. Chavan 2012 Quality Assurance and Intellectual Property Rights in Advancing Diodiversity Data Publication Global Biodiversity Information Facility Pp. 33, ISBN: 87-92020-49-6 [PDF].
  • A.C. Fletcher & P.E. Bourne 2012 Ten Simple Rules for Starting a Company PLoS Comp Biol.8(3): e1002439 [PDF].
  • R. Dicken, C.J. Hall, L.K. Taylor, A.M. Collins, R. Nussinov & P.E. Bourne 2012 A Review of 2011 for PLoS Computational Biology PLoS Comp Biol. 8(1): e10022387 [PDF].
  • L. Xie, S.L. Kinnings, L. Xie and P.E. Bourne 2012 Predicting the Polypharmacology of Drugs: Identifying New Uses Through Cheminformatics, Structural Informatics and Molecular Modeling-based Approaches in Drug Repurposing M. Barrett and D. Frail (Eds.) Chap. 7, 163-194, Wiley and Sons [book].
  • B.K. Rana, P.E. Bourne and P. Insel 2012 Receptor Databases and Computational Websites for Ligand Binding. Receptor Binding Techniques,Methods in Molecular Biology A.P. Davenport (Ed.). Springer. 897:1-13 [PDF].
  • S.J. Ho Sui, R. Lo, A.R. Fernandes, M.DG.Caulfield, J.A Lerman, L. Xie, P.E. Bourne, D.L.Baillie and F.S.L.Brinkman 2012 Raloxifene Attenuates Pseudomonas aeruginosa Pyocyanin Production and Virulence. Int. J. of Antimicrobial Agents (40)3: 246-251 [PDF].
  • L. Xie, L. Xie, S.L. Kinnings and P.E. Bourne 2012 Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs, Annual Review of Pharmacology and Toxicology 52: 361-379 [PDF].
  • N. Hecker, J. Ahmed, J. von Eichborn , M. Dunkel, K. Macha, A. Eckert, M.K. Gilson, P.E. Bourne, and R. Preissner 2012 SuperTarget goes quantitative: update on drug-target interactions Nucleic Acids Res. 40 (D1) D1113-D1117 [PDF].

2011

  • P.E. Bourne, T.W. Clark, R. Dale, A. de Waard, I. Herman, E.H. Hovy and D. Shotton (eds.), on behalf of the Force11 community 2011. Improving the Future of Research Communication and e-Scholarship. Dagstuhl Perspectives Workshop 11331. 10.4230/DagMan.1.1.41 [PDF].
  • P.E.Bourne 2011 Digital research/analog publishing - one scientist's view Serials 24(2) 119-122 [PDF].
  • F. Lewitter and P.E. Bourne 2011 Teaching Bioinformatics at the Secondary School Level PLoS Comp Biol 7(10): e1002242. [PDF].
  • P.E. Bourne and V. Barbour 2011 Ten Simple Rules for Building and Maintaining a Scientific Reputation PLoS Comp Biol 7(6) e1002108 [PDF].
  • J. Wang, P.E. Bourne, N. Bandeira 2011 Peptide Identification by Database Search of Mixture Tandem Mass Spectra Mol. Cell Proteomics [PDF]
  • J. von Eichborn, P.E. Bourne and R. Priessner 2011 Cobweb: A Java Applet for Network Exploration and Visualization Bioiformatics 7(12):1725-6 [PDF]
  • P.W. Rose, W.F. Bluhm, B. Beran, C. Bi, D. Dimitropoulos, D.S. Goodsell, A. Prlic, G.B. Quinn, B. Yukich, H.M. Berman & P.E. Bourne 2011, The RCSB Protein Data Bank: Site Functionality and Bioinformatics Use Cases. National Cancer Institute, Nature Pathways Interaction Database doi:10.1038/pid.2011.1 [PDF]
  • L. Xie, L. Xie and P.E.Bourne 2011 Structure-based Systems Biology for Analyzing Off-target Binding. Curr. Opinions. in Struct. Biol. 21:1-11. [PDF]
  • W.F. Bluhm, B. Beran, C. Bi, D. Dimitropoulos, A. Prlic, G. Quinn, P.W. Rose, C. Shah, B. Yukich, H.M. Berman, P.E. Bourne 2011 Quality Assurance for the Query and Distribution Systems of the RCSB Protein Data Bank, Database doi: 10.1093/database/bar003 [PDF]
  • P.E. Bourne, B. Beran, C. Bi, W.F. Bluhm, D. Dimitropoulos, Z. Feng, D.S. Goodsell, A. Prlic, G. Quinn, P.W. Rose, J. Westbrook, B. Yukich, J. Young, C. Zardecki, and H.M.Berman, 2011 The Evolution of the RCSB Protein Data Bank Website. WIRE Computational Molecular Science, DOI: 10.1002/wcms.57 [PDF].
  • R.E. Valas and P.E. Bourne 2011 The Origin of the Derived Superkingdom: How a Gram-positive Bacterium Crossed the Desert to Become an Archaeon, Biology Direct 6:16 [PDF].
  • G.M. Kuo, J.D. Ma, K.C. Lee and P.E. Bourne 2011 Telemedicine, Genomics and Personalized Medicine: Synergies and Challenges Current Pharmacogenomics and Personalized Medicine 9(1), 6-13 [PDF]
  • S.L. Kinnings, N. Liu, P.J. Tonge, R.M. Jackson, L. Xie and P.E.Bourne 2011 A Machine Learning Based Method to Improve Docking Scoring Functions and its Application to Drug Repurposing J. Chem. Info. Model. 51(2), 408-419 [PDF] [correction]
  • L. Xie, T. Evangelidis, L. Xie and P.E. Bourne 2011 Drug Discovery Using Chemical Systems Biology: Weak inhibition of multiple kinases may contribute to the anti-cancer effect of Nelfinavir PLoS Comp. Biol. 7(4) e1002037 [PDF]. [Science 2011 332(6030) 648-649 [PDF]]
  • A. Gramada and P.E. Bourne 2011 Coarse-graining the Electrostatic Potential via Distributed Multipole Expansions. Comp. Phys. Communications, 182, 1455-1462. [PDF].
  • G.M. Kuo, J.D. Ma, K.C.Lee, J.R. Halpert, P.E. Bourne, T.G. Ganiats and P.W. Taylor, 2011 Instititional Profile: University of California San Diego Pharmacogenomics Education Program (PharmGenEd): Bridging the Gap Between Science and Practice. Pharmacogenomics 12(2), 149-153 [PDF].
  • R. Dicken, C. Marden, A.M.Collins, R. Nussinov and P.E. Bourne 2011 A Review of 2010 for PLoS Compuational Biology, PLoS Comp. Biol., 7(1) e1002003 [PDF]
  • P.E. Bourne 2011 Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS Comp. Biol. 7(1) e1002001. [PDF]
  • J. von Eichborn, M.S. Murgueitio, M. Dunkel, S. Koerner, P.E. Bourne and R. Preissner 2011 PROMISCUOUS: A Database for Network-based Drug Repositioning, NAR 39 D1060-6 [PDF]
  • P.W. Rose, B. Beran, C. Bi, W.F. Bluhm, D. Dimitropoulos, D.S. Goodsell, A. Prlic, M. Quesada, G. Quinn, J.D. Westbrook, J. Young, B. Yukich, C. Zardecki, H.M. Berman, P.E. Bourne 2011 The RCSB Protein Data Bank: Redesigned Website and Web Services NAR 39 D392-401 [PDF]
  • J. Ponomarenko, N. Papangelopoulos, D.M Zajonc, B. Peters, A. Sette, P.E. Bourne 2011 IEDB-3D: Structural Data within the Immune Epitope Database NAR 39, D1164-70 [PDF]

2010

  • G.B Quinn, G. Berger and P.E. Bourne 2010 Data Encapsulation and Mobile Access to the Protein Data Bank m-Science Sensing, Computing and Dissemination Eds E Canessa and M Zennaro, ICTP, Italy ISBN 92-95003-43-8, p189-203. [PDF]
  • A. Prlic, S. Bliven, P.W. Rose, W.F. Bluhm, C. Bizon, A.Godzik, P.E. Bourne 2010 Precalculated Protein Structure Alignments at the RCSB PDB website. Bioinformatics 10.1093/bioinformatics/btq572. [PDF]
  • P.E. Bourne 2010 What Do I Want from the Publisher of the Future? PLoS Comp Biol 6(5): e1000787. [PDF]
  • J. Ren, L. Xie, W. Li & P.E. Bourne 2010 SMAP-WS: A Parallel Web Service for Structural Proteomic-wide Ligand-Binding Site Comparison. NAR, doi: 10.1093/nar/gkq400 [PDF]
  • R.E. Valas & P.E. Bourne 2010 Save the Tree of Life or Get Lost in the Woods Biology Direct, 5:44 [PDF].
  • K. Alden, S. Veretnik, P.E.Bourne 2010 dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. BMC Bioinformatics, 11:310 [PDF].
  • S.L. Kinnings, L. Xie, K.H.Fung, R.M. Jackson, L. Xie and P.E. Bourne 2010 The Mycbacterium tuberculosis Drugome and its Pharmaceutical Implications. PLoS Comp. Biol. 6(11): e1000976. [PDF].
  • C. L. Dupont, A Butcher, R.E. Valas, P.E. Bourne, and G. Caetano-Anolles 2010 History of Biological Metal Utilization Inferred Through Phylogenetic Analysis of Protein Structures PNAS, 107(23), 10567-72 [PDF].
  • R.L Chang, L. Xie, L. Xie, P.E. Bourne B.O. Palsson 2010 Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model. Plos Comp. Biol. 6(9): e1000938 [PDF].
  • P.E. Bourne, K. Briedis, C. Dupont, R. Valas, S. Yang 2010 Genome Evolution Studied through Protein Structure in Evolutionary Genomics and Systems Biology G. Caetano-Anolles (Ed.) Wiley-Blackwell Inc. p153-164.[PDF]
  • R.S. Datta, M.W. Lux and P.E. Bourne. 2010 PLoS Computational Biology Postcards from PSB 2010 PLoS Comp. Biol.6(4) e1000746 [PDF]
  • H. Zhang, P. Wang, N. Papangelopoulos, Y. Xu, A. Sette, P.E. Bourne, O. Lund, J. Ponomarenko, M. Nielsen and B. Peters 2010 Limitations of ab initio Predictions of Peptide Binding to MHC class II Molecules PLoS ONE 5(2): e9272 [PDF].
  • A. Prlic, M.A. Martinez, B.T. Yukich, D. Dimitropoulos, B. Beran, P.W. Rose, P.E. Bourne, J.L. Fink 2010 Integration of Open Access Literature into the RCSB Protein Data Bank Using BioLit. BMC Bioinformatics 11:220 [PDF].
  • J.L. Fink, P. Fernicola, R. Chandran, S. Parastatidis, A. Wade, O. Naim, G.B. Quinn & P.E. Bourne 2010 Word Add-in for Ontology Recognition: Semantic Enrichment of Scientific Literature. BMC Bioinformatics 11:103. [PDF].
  • P.E. Bourne, B. Beran, C. Bi, W. Bluhm, R. Dunbrack, A. Prlic, G. Quinn, P. Rose, R. Shah, W. Tao, B. Weitzner, Ben Yukich 2010 Will Widgets and Semantic Tagging Change Computational Biology? PLoS Comp. Biol. 6(2) e1000673 [PDF].
  • R. Dickin, C. Marden, C. Nancarrow & P.E. Bourne 2010 A Review of 2009 for PLoS Computational Biology PLoS Comp. Biol. 6(2) e1000687 [PDF].
  • J.D. Durant, R.E. Amaro, L. Xie, M.D. Urbaniak, M.A.J. Ferguson, A. Haapalainen, Z-J. Chen, A.M. Di Guilmi, F. Wunder, A. Tersteegen. P.E. Bourne & J.A. McCammon 2010 A Multidimensional Strategy to Detect Secondary Pharmacological Targets in the Absence of Global Structure and Sequence Homology PLoS Comp Biol. 6(1): e1000648 [PDF].

2009

  • J Hodlin, C.D. Bishop, F.A. Sharp and R.E. Valas 2009 A Creative Celebration of Evolution Nature 461:733 [PDF]
  • A. Bateman & P.E. Bourne 2009 Ten Simple Rules for Chairing a Scientific Session PLoS Comp. Biol. 5(9):e1000517 [PDF]
  • R.E. Valas & P.E. Bourne 2009 Structural Analysis of Polarizing Indels: An Emerging Consensus on the Root of the Tree of Life. Biology Direct. 4(1) 30 [PDF]
  • H. Asher & P.E. Bourne 2009 Drivers of Change - Emergent Information and Biotechnologies in Pharmacy Informatics P.H. Anderson, S.M. McGuinness & P.E. Bourne (Eds.) Taylor & Francis Chapter 2, pp 7-19.
  • P.E. Bourne 2009 Computer and Informatics Basics in Pharmacy Informatics P.H. Anderson, S.M. McGuinness & P.E. Bourne (Eds.) Taylor & Francis, Chapter 3, pp23-35.
  • P.E. Bourne & S.M. McGuinness 2009 Controlled Vocabularies in Pharmacy Informatics P.H. Anderson, S.M. McGuinness & P.E. Bourne (Eds.) Taylor & Francis, Chapter 4, pp37-52.
  • P.E. Bourne 2009 Pharmaceutical Sciences in a Virtual World in Pharmacy Informatics P.H. Anderson, S.M. McGuinness & P.E. Bourne (Eds.) Taylor & Francis Chapter 17, pp251-259.
  • P.O. Anderson, S.M. McGuinness & P.E. Bourne 2009 What is Pharmacy Informatics in in Pharmacy Informatics P.H. Anderson, S.M. McGuinness & P.E. Bourne (Eds.) Taylor & Francis, Chapter 1, pp3-5.
  • R.E. Valas, S. Yang and P.E. Bourne 2009 Nothing in Protein Structure Classification Makes Sense Except in the Light of Evolution Current Opinions in Structural Biology 19:1-6 [PDF]Structural Bioinformatics
  • Q. Vicens and P.E. Bourne 2009 Ten Simple Rules for Combining Teaching and Research PLoS Comp. Biol. 5(4): e1000358 [PDF]
  • J.L. Fink, H. Weissig and P.E. Bourne 2009 Other Structure Based Databases in Structural Bioinformatics 2nd Edition J. Gu and P.E. Bourne (Eds.) John Wiley and Sons NJ 321-338. [PDF]
  • M.A. Marti-Renom, E. Capriotti, I.N. Shindyalov and P.E. Bourne 2009 Structure Comparison and Alignment in Structural Bioinformatics 2nd Edition J. Gu and P.E. Bourne (Eds.) John Wiley and Sons NJ 397-417. [PDF]
  • S. Yang, R. Valas and P.E. Bourne 2009 Evolution Studies Through Protein Structure in Structural Bioinformatics 2nd Edition J. Gu and P.E. Bourne (Eds.) John Wiley and Sons NJ 559-571. [PDF]
  • J. Gu and P.E. Bourne 2009 CASP and Other Community-wide Assessments to Advance the Field of Structure Prediction in Structural Bioinformatics 2nd Edition J. Gu and P.E. Bourne (Eds.) John Wiley and Sons NJ 665-678. [PDF]
  • S.L Kinnings, N. Buchmeier, N. Liu, P.J. Tonge L. Xie and P.E. Bourne 2009 Discovery of Novel Drug Leads to Treat Multi-drug and Extensively Drug Resistant Tuberculosis by Repositioning Safe Pharmaceuticals: A Chemical Genomics Approach with Subsequent Biological Validation. PLoS Comp. Biol. 5(7) e1000423. [PDF]
  • L. Xie, L. Xie and P.E. Bourne 2009 A Unified Statistical Model to Support Local Sequence Order Independent Similarity Searching for Ligand-binding Sites and Its Application in Genome-based Drug Discovery 2009 Bioinformatics 25(12) 305-312 [PDF].
  • S. Yang and P.E.Bourne 2009 The Evolutionary History of Protein Domains Viewed by Species Phylogeny, PLoS ONE, 4(12): e8378 [PDF].
  • L. Xie, J. Li, L. Xie, and P.E.Bourne 2009 Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors, PLoS Comp. Biol.. 5(5) e1000387 [PDF] MiniReview in Genome Biol [PDF]
  • S. Veretnik, C. Wills, P. Youkharibache, R. Valas & P.E. Bourne 2009 Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome, PLoS Comp. Biol.5(3) e10000315 [PDF]
  • E. Browne, R. Dickin, P.E. Bourne 2009 A Review of 2008 for PLoS Computational Biology PLoS Comp. Biol. 5(1) e1000275 [PDF]

2008

  • P.E. Bourne and J.L. Fink 2008 I am Not a Scientist I am a Number PLoS Comp. Biol. (Perspective),4(12):e1000247 [PDF]
  • J.V. Ponomarenko, H-H. Bui, W. Li, N. Fusseder, P.E. Bourne, A. Sette and B. Peters 2008 ElliPro: A New Structure-based Tool for the Prediction of Antibody Epitopes, BMC Bioinformatics 9:514 [PDF].
  • A. Gramada and P.E.Bourne 2008 Resolving a Distribution of Charge into Intrinsic Multipole Moments: A Rankwise Distributed Multipole Analysis. Physical Review E,78, 066601 [PDF].
  • P.D. Karp, G. Sherlock, J.A. Gerlt, I. Sim, I. Paulsen, P.C. Babbitt, K. Laderoute, L. Hunter, P. Sternberg, J. Wooley, P.E.Bourne 2008 Changes to NIH Grant System May Backfire Science 322(5905) 1187-1188. [PDF]
  • M. Corpas, N. Gehlenborg, S. Chandra Janga and P. E. Bourne 2008 Ten Simple Rules for Organizing a Scientific Meeting PLoS Comp. Biol. 4(5) e10000024. [PDF]
  • S.Veretnik, J.L.Fink, and P.E. Bourne 2008 Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. . 4(7): e1000136 [PDF].
  • P.E.Bourne and L.M.Chalupa 2008 A New Approach to Scientific Dissemination Materials Today 11(6) 48 [PDF].
  • R. Bauer, P.E. Bourne, A. Formella, C. Frommel, G. Cornelius G. Christoph, G. Andrean, A. Aysam, A. Hoppe, E-W Knapp, T. Poschel, B. Wittig, V. Ziegler, R. Preissner 2008 Superimpose: A 3D structural superposition server NAR 36(S2) W47-54 [PDF].
  • J.L.Fink, S. Kushch, P. Williams & P.E.Bourne 2008 BioLit: Integrating Biological Literature with Databases NAR 36(S2) W385-389 [PDF].
  • Q. Zhang, P. Wang, Y. Kim, P. Haste-Andersen, J. Beaver, P.E. Bourne, H-H. Bui, S. Buus, S. Frankild, J. Greenbaum, O. Lund, C. Lundegaard, M. Nielsen, J. Ponomarenko, A. Sette, Z. Zhu, B. Peters 2008 Immune Epitope Database Analysis Resource (IEDB-AR) NAR. 36(S2) W513-W518 [PDF].
  • P.E.Bourne, J.L.Fink, M.Gerstein 2008 Open Access: Taking Full Advantage of the Content PLoS Comp. Biol. (Editorial) 4(3) e1000037 [PDF].
  • L. Xie and P.E. Bourne 2008 Detecting Evolutionary Linkages Across Fold and Functional Space with Sequence Order Independent Profile-profile Alignments. PNAS, 105(14) 5441-5446 [PDF].
  • R. Valas and P.E. Bourne 2008 Rethinking Proteasome Evolution: Two Novel Bacterial Proteasomes. J. Mol. Evol. 66(5) 494-504 [PDF] [Video].
  • K. Briedis, A. Starr and P.E. Bourne 2008 Analysis of the Human Kinome Using Methods Including Fold Recognition Reveals Two Novel Kinases PLoS ONE, 3(2): e1597 [PDF].
  • J.G. Caporaso, N. Deshpande, J.L. Fink, P.E. Bourne, K.B. Cohen and L. Hunter 2008 Intrinsic Evaluation of Text Mining Systems May Not Predict Performance on Realistic Tasks. Pacific Symposium on Biocomputing, 640-651 [PDF].
  • S. Gunther, M. Kuhn, M. Dunkel, M. Campillos, C. Senger, E. Petsalaki, J. Ahmed, E. Garcia Urdiales, A. Gewiess, L. Juhl Jensen, R. Schneider, R. Skoblo, R.B. Russell, P.E. Bourne, P. Bork and R. Preissner 2007 SuperTarget and Matador: Resources for exploring drug-target relationships NAR, 36:D919-922 [PDF].

2007

  • J. Gu and P.E.Bourne 2007 Ten Simple Rules for Graduate Students. PLoS Comp. Biol. 3(11) e229. [PDF]
  • L. Xie, J. Wang and P.E.Bourne 2007 In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Esterogen Receptor Modulators. PLoS Comp. Biol., 3(11) e217 [PDF].
  • T.C. Erren, P. Cullen, M. Erren and P.E.Bourne 2007 Ten Simple Rules for Doing Your Best Research, According to Hamming PLoS Comp. Biol., 3(10): e213 [PDF]
  • P.E. Bourne and S.E. Brenner 2007 Developing Computational Biology 3(9):e157 [PDF]
  • J. Ponomarenko and P.E.Bourne 2007 Antibody-Protein Interactions: Benchmark Datasets and Prediction Tools Evaluation BMC Structural Biology 7(1):64 [HTML] [Video].
  • J-L Chung, J. Beaver, E.D. Scheeff and P.E. Bourne 2007 Con-Struct Map: a Comparative Contact Map Analysis Tool Bioinformatics 23:2491-2492 [PDF].
  • J.L. Fink and P.E.Bourne 2007 Reinventing Scholarly Communication for the Electronic Age. CT Watch, 3(3) 26-31 [HTML]
  • H.M. Berman, K. Hendrick, H. Nakamura, J. Markley, P.E. Bourne, J. Westbrook (2007) Realism about PDB Nature Biotechnology, 25(8) 845-6. [PDF]
  • L. Hunter, R.B.Altman and P.E. Bourne 2007 The International Society for Computational Biology 10th Anniversary PLoS Comp. Biol. 3(6) e135 [PDF]
  • J-L Chung, W Wang and P.E.Bourne 2007 High-throughput identification of Interacting Protein-Protein Binding Sites. BMC Bioinformatics, 8(1): 223 [PDF].
  • L. Xie and P.E. Bourne 2007 A Robust and Efficient Algorithm for the Shape Description of Protein Structures and Its Application in Predicting Ligand Binding Sites BMC Bioinformatics, 8(Suppl 4):S9 [PDF].
  • P.E. Bourne 2007 Ten Simple Rules for Making Good Oral Presentations, PLoS Comp. Biol., 3(4)e77 [PDF] [Video].
  • J.E Beaver, P.E Bourne and J.V Ponomarenko 2007 EpitopeViewer: a Java Application for the Visualization and Analysis of Immune Epitopes in the IEDB database. Immunome Research, 3(1):3 [PDF].
  • Q. Vicens and P.E.Bourne 2007 Ten Simple Rules for Collaboration PLoS Comp. Biol., 3(3) e44 [PDF].
  • P.E. Bourne and A. Godzik 2007 Structural Genomics in Bioinformatics – From Genomes to Therapies T. Lengauer (Ed.) Wiley-VCH. p419-438. [PDF]
  • J. Gu and P.E.Bourne 2007 Allosteric Fluctuation Transitions as Applied to Cyclin Dependent Kinase 2 BMC Bioinformatics 8(1):45. [PDF]

2006

  • P Guda, P.E. Bourne and C. Guda 2006 Conserved Motifs in Voltahge-sensing and Pore-forming Modules of Voltage-gated Ion Channel Proteins Biochem. Biophys. Res. Com. 352(2) 292-8 [PDF].
  • P.E. Bourne and I. Friedberg 2006 Ten Simple Rules for Getting a Post Doc. PLoS Comp. Biol., (Editorial), 2(11) e121. [PDF]
  • A.Sette, H.H.Bui, J.Sidney, P.E.Bourne, S. Buus, W. Fleri, R.Kubo, O.Lund, D.Nemazee, J.V.Ponomarenko, M.Sathiamurthy, S. Stweart, S.Way, S.S.Wilson and B. Peters 2006 The Immune Epitope Database and Analysis Resource Pattern Recognition in Bioinformatics, Springer, Jagath C. Rajapakse, Limsoon Wong, Raj Acharya (Eds) [PDF]
  • C.L. Dupont, S.Yang, B. Palenik and P.E.Bourne 2006 Modern Proteomes Contain Putative Imprints of Ancient Shifts in Trace Metal Geochemistry PNAS, 103(47) 17822-17827 [PDF] [Video].
  • P.E.Bourne and J. McEntyre 2006 Biocurators: Contributors to the World of Science PLoS Comp. Biol., (Editorial) 2(10) e142 [PDF].
  • E.D Scheeff and P.E. Bourne 2006 Application of Protein Structure Alignments to Iterated Hidden Markov Model Protocols for Structure Prediction. BMC Bioinformatics, 7:410 [html].
  • H.M. Berman, S.K. Burley, W. Chiu, A. Sali, A. Adzhubei, P.E. Bourne, S.H. Bryant, R.L. Dunbrack, Jr., K. Fidelis, J. Frank, A. Godzik, K. Henrick, A. Joachimiak, B. Heymann, D. Jones, J.L. Markley, John Moult, G.T. Montelione, C. Orengo, M.G. Rossmann, B. Rost,21 H. Saibil, T. Schwede, D.M. Standley, J.D. Westbrook 2006 Acrhiving Structural Models of Biological Macromolecules. Structure, 14:1211-1217. [PDF]
  • P.E.Bourne and A. Korngreen 2006 Ten Simple Rules for Reviewers. PLoS Comp. Biol., (Editorial), 2(9) e110 [HTML]
  • P.E.Bourne 2006 One Year of PLoS Computational Biology PLoS Comp. Biol., (Editorial) 2(8):e111. [PDF]
  • P.E. Bourne and S. Brunak 2006 ISMB 2006 (Editorial) Bioinformatics 22(14):e1-2 [PDF]
  • R. Vita, K. Vaughan, L. Zarebski, N. Salimi, W. Fleri, H. Grey, M. Sathiamurthy, J. Mokili, H-H. Bui, P.E Bourne, J. Ponomarenko, R. DE Castro Jr, R.K Chan, J. Sidney, S.S Wilson, S. Stewart, S. Way, B. Peters and A. Sette 2006 Curation of Complex, Content-dependant Immunological Data BMC Bioinformatics, 7(1), 341 [HTML]
  • J. Gu, M. Gribskov and P.E. Bourne 2006 Wiggle – Predicting Functionally Flexible Regions from Primary Sequence PLoS Comp. Biol., 2(7) e90. [PDF][Video]
  • T. Holland, S. Veretnik, I.N. Shindyalov, P.E. Bourne 2006 A Benchmark for Domain Assignment from Protein 3-dimensional Structure and it’s Applications J. Mol. Biol., 361(3), 562-590. [HTML].
  • A. Gramada and P.E. Bourne 2006 Multipolar Representation of Protein Structure BMC Bioinformatics, 7:242 [HTML][Video].
  • J-L Chung, W. Wang and P.E. Bourne 2006 Exploiting Sequence and Structure Homology to Identify Protein-Protein Binding Sites Proteins: Structure, Function and Bioinformatics 62(3) 630-640. [PDF].
  • P.E.Bourne and L.M.Chalupa 2006 Ten Simple Rules for Getting a Grant PLoS Comp. Biol., (Editorial) 2(2) e12 [pdf] [Video].
  • A. Kouranov, L. Xie, J. de la Cruz, L. Chen, J. Westbrook, P.E. Bourne and H.M. Berman 2006 The RCSB PDB Information Portal for Structural Genomics Nucleic Acids Research, 34 D302-5. [HTML]

2005

  • E. Scheeff and P.E. Bourne 2005 Structural Evolution of the Protein Kinase-Like Superfamily PLoS Comp. Biol. 1(5): e49. [open access] [Video]
  • P.E. Bourne, W.F. Bluhm, N. Deshpande, Q. Zhang, K. Burkhardt, H.M. Berman, J.L. Flippen-Anderson 2005 The Protein Data Bank. The Encyclopedia of Medicinal Chemistry Accepted.
  • P.E. Bourne 2005 Ten Simple Rules for Getting Published PLoS Comp. Biol. 1(5) e57. [open access][Video]
  • M. Sathiamurthy, B. Peters, H. Bui, J. Sidney, J.Mokili, S.S. Wilson, W. Fleri, D.L. McGuinness, P.E. Bourne and A. Sette 2005 An Ontology for Immune Epitopes: Application to the Design of a Broad Scope Database of Immune Reactivities Immunome Research 1:2 [Open Access]
  • P.E. Bourne 2005 In the Future will a Biological Database Really be Different from a Biological Journal? PLoS Comp. Biol. 1(3) e34 [PDF]
  • P.M.D. Fitzgerald, J. Westbrook, P.E. Bourne, B. McMahon, K.D. Watenpaugh, and H.M. Berman 2003 The Macromolecular Crystallographic Information File (mmCIF) The International Tables for X-ray Crystallography Volume G. In Press. [PDF]
  • L. Xie and P.E. Bourne 2005 Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets and Homology Models. PLoS Comp Biol 1(3) e31. [PDF]
  • B. Peters, J. Sidney, P.E. Bourne, H-H Bui, S. Buus, G. Doh, W. Fleri, M. Kronenberg, R. Kubo, O. Lund, D. Nemazee, J.V. Ponomarenko, M. Sathiamurthy, S. Schoenberger, S. Stewart, P. Surko, S. Way, S. Wilson, A. Sette 2005 The Design and Implementation of the Immune Epitope Data Base and Analysis Resource Immunogenetics. 57(5): 326-36 [PDF]
  • P.E. Bourne, S.E. Brenner, M.B. Eisen (2005) PLoS Computational Biology: A New Community Journal. PLoS Comp Biol 1(1): e4 [HTML]
  • B. Peters, J. Sidney, P.E. Bourne, H-H Bui, S. Buus, G. Doh, W. Fleri, M. Kronenberg, R. Kubo, O. Lund, D. Nemazee, J.V. Ponomarenko, M. Sathiamurthy, S. Schoenberger, S. Stewart, P. Surko, S. Way, S. Wilson, A. Sette 2005 The Immune Epitope Database and Analysis Resource: From Vision to Blueprint. PLoS Biology, 3(3) e91. [PDF]
  • Shahab, A., Chuon, D., Suzumura, T., Li, W. W., Byrnes, R. W.,Tanaka, K., Ang, L., Matsuoka, S., Bourne, P. E., Miller, M. A. & Arzberger, P. W. 2005. Grid Portal Interface for Interactive Use and Monitoring of High-Throughput Proteome Annotation. Lecture Notes In Computer Science, 3370:53-67. [PDF]
  • Birnbaum, A., Hayes, J., Li, W. W., Miller, M. A., Arzberger, P.W., Bourne, P. E. & Casanova, H. 2005. Grid Workflow Software for High-Throughput Proteome Annotation Pipeline. Lecture Notes In Computer Science, 3370: 68-61. [PDF]
  • J.L. Moreland, A.Gramada, O.V. Buzko, Q. Zhang and P.E. Bourne 2005 The Molecular Biology Toolkit (mbt): A Modular Platform for Developing Molecular Visualization Applications. BMC Bioinformatics, 6:21. [PDF] [Open Access]
  • J.V. Ponomarenko, P.E. Bourne and I.N. Shindyalov 2005 Assigning New GO Annotations to Protein Data Bank Sequences by Structural Homology Proteins: Structure, Function and Bioinformatics 58: 855-865. [PDF]
  • Q. Zhang, S. Veretnik and P.E.Bourne 2005 Structural Bioinformatics in Bioinformatics Technologies, pp. 15-40, Ed. Y-P.P. Chen, Springer-Verlag, Berlin.
  • S. Yang, R.F. Doolittle and P.E. Bourne 2005 Phylogeny Determined through Protein Domain Content Proc. Nat. Acad. Sci. (USA) 102(2): 373-378. [PDF] [Supplimental Material] [Editor’s choice Science]
  • N. Deshpande, K.J. Addess, W.F. Bluhm, J.C. Merino-Ott, W.Townsend-Merino, Q. Zhang, C. Knezevich, L. Chen, Z. Feng, R. Kramer Green, J.L. Flippen-Anderson, J. Westbrook, H.M. Berman and P.E. Bourne 2005 The RCSB Protein Data Bank: A Redesigned Query System and Relational Database Based on the mmCIF Schema Nucleic Acids Research. 33: D233-D237. [PDF]
  • PC Babbitt, PE Bourne, SD Mooney 2005 Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure. Pacific Symposium on Biocomputing 319-321. [PDF]

2004

  • P.E.Bourne 2004. Protein Resources in Encyclopedia of Biological Chemistry, Eds W.J. Lennarz & M.D. Lane, Elsevier, Oxford, Vol. 3 pp 478-483.
  • Li, W. W., Byrnes, R. W., Hayes, J., Birnbaum, A., Reyes, V. M., Shahab,A., Mosley, C., Pekurovsky, D., Quinn, G. B., Shindyalov, I. N., Casanova, H., Ang, L., Berman, F., Arzberger, P. W., Miller, M. A. & Bourne, P. E. 2004. The Encyclopedia of Life Project: Grid Software and Deployment. New Generation Computing, 22: 127-136.
  • Y. Jia, G.T. Dewey, I.N. Shindyalov and P.E. Bourne 2004 A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE. J. Comp. Biol. 11(5) 787-799. [PDF]
  • W.G Krebs and P.E. Bourne 2004 Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. J. Bioinformatics and Computational Biology, 2(1) 61-75. [PDF]
  • C. Guda, S. Lu, E.D. Scheeff, P.E. Bourne and I.N. Shindyalov 2004 CE-MC: A multiple protein structure alignment server. Nucleic Acids Research, 32 W100-W103. [PDF]
  • S. Verentik, P.E. Bourne, N.N. Alexandrov, I.N. Shindyalov 2004. Towards consistent assignment of structural domains in proteins. Journal of Molecular Biology, 339(3), 647-678 [PDF].
  • D. Pekurovsky, I.N. Shindyalov, P.E. Bourne 2004 High Throughput Biological Data Processing on Massively Parallel Computers. A Case Study of Pairwise Structure Comparison and Alignment Using the Combinatorial Extension (CE) Algorithm. Bioinformatics, 20(12) 1940-1947 [PDF].
  • P.E. Bourne, J. Westbrook and H.M. Berman 2004. The Protein Data Bank and Lessons Learned in Data Management. Briefings in Bioinformatics. 5(1), 23-30. [PDF]
  • W.G. Krebs and P.E. Bourne 2004 Statistically Rigorous Automated Protein Annotation Bioinformatics 10(7) 1066-1073 [PDF]
  • H.M. Berman, P.E. Bourne and J. Westbrook 2004 The Protein Data Bank: A Case Study in the Management of Community Data. Current Proteomics 1, 49-57. [PDF]
  • P.E. Bourne, K.J. Addess, W.F. Bluhm, L. Chen, N. Deshpande, Z. Feng3, R. Kramer Green, J. C. Merino-Ott, W. Townsend-Merino, H. Weissig, J. Westbrook, H. M. Berman 2004. The Distribution and Query Systems of the RCSB Protein Data Bank Nucleic Acids Research, 32, D223-225 [PDF]
  • P.E. Bourne, C.K.J. Allerston, W. Krebs, W. Li, I.N Shindyalov, A. Godzik, I. Friedberg, T. Liu, D. Wild, S. Hwang, Z. Ghahramani L. Chen, and J. Westbrook 2004. The Status of Structural Genomics through the analysis of current targets and structures. 2004 Pacific Symposium on Biocomputing 404-416. [html]

2003

  • Structural BioinformaticsP.E. Bourne 2003 The Status of Structural Genomics Targets 2(5) 181-1182 (Editorial). [PDF]
  • W.G Krebs and P.E. Bourne 2003 Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. Proceedings of the 2003 IEEE Computer Society Bioinformatics Conference Proceedings 180-189 [PDF]
  • W.W. Li1, G.B. Quinn, N. N. Alexandrov, P.E. Bourne and I.N. Shindyalov 2003 Proteins of Arabidopsis thaliana (PAT) database: A resource for comparative proteomics Genome Biology 4(8), R51 [PDF]
  • K.S. Doctor, J. Reed, A. Godzik and P.E.Bourne 2003 The Apoptosis Database Cell Death and Differentiation 10(6), 621-633. [PDF]
  • P. Yang, P.A. Craig, D. Goodsell and P.E. Bourne 2003 BioEditor - Simplifying Macromolecular Structure Annotation Bioinformatics 19(7) 897-898. [PDF]
  • P.E.Bourne 2003 Free access to publicly funded databases is vital Nature 421, 786 [PDF]
  • H.M. Berman, P.E. Bourne, J.D. Westbrook and C. Zardecki 2003 The Protein Data Bank pp 389-406 from Structure (ed.) Chasman Marcel Decker Inc. NY.
  • K. Baldridge and P.E. Bourne 2003 The New Biology and the Grid. Chapter 40 pp 907-922 from Grid Computing - Making the Global Infrastructure a Reality (eds) F.Berman, G. Fox and T.Hey Wiley, New York.

2002

  • J.V. Ponaramenko, I.N. Shindyalov and P.E. Bourne 2002 Building an Automated Classification of DNA-binding Protein Domains Bioinformatics 18:S192-201.[pdf]
  • P Craig, P Yang and PE Bourne 2002 BioEditor A Tool for Structure Annotation FASEB J 16 (5): A741-A742.
  • P.E. Bourne 2002 Science's Policy on Data Deposition. Science 296, 1609 (Letter)
  • I.N. Shindyalov and P.E. Bourne 2002 New Insights into Protein Fold Space and Sequence-Structure Relationships. Structure Prediction:Bioinformtic Approach, Chapter 17, pp 417-428, Ed. I. Tsigelny. Int'l University Line, La Jolla, CA.
  • Chittibabu Guda, Eric D. Scheeff, Philip E. Bourne, and Ilya N. Shindyalov 2002, Comparative Analysis of Protein Structure: New Concepts and Approaches for Multiple Structure Alignment. Structure Prediction:Bioinformtic Approach. Chapter 19, pp 449-459. Ed. I. Tsigelny, Int'l University Line, La Jolla, CA.
  • Eric D. Scheeff, Philip E. Bourne, and Ilya N. Shindyalov 2002 Comparative Analysis of Protein Structure: Automated vs. Manual Alignment of the Protein Kinase Family. Protein Structure Prediction:Bioinformtic Approach, Chapter 20, pp 463-475. Ed. I. Tsigelny, Int'l University Line, La Jolla, CA.
  • H.M. Berman, T. Battistuz, T.N.Bhat, W.F. Bluhm, P.E. Bourne, K. Burkhardt, Z. Feng, G.L. Gilliland, L. Iype, S. Jain, P. Fagan, J. Marvin, V. Ravichandran, B. Schneider, N. Thanki, D. Padilla, H. Weissig, J.D. Westbrook, C. Zardecki 2002 The Protein Data Bank Acta Cryst. D58, 899-907. [pdf]
  • I.N. Shindyalov and P.E. Bourne 2002 Structure Structure Comparison and Alignment Structural Bioinformatics Chapter 16 Ed. H. Weissig and P.E. Bourne Wiley and Associates, NY.
  • H. Wessig and P.E. Bourne 2002 Other Structure Based Databases Structural Bioinformatics Chapter 11 Ed. H. Weissig and P.E. Bourne Wiley and Associates, NY.
  • B.V.B Reddy and P.E. Bourne 2002 A User's Perspective on the Structure Classification of Proteins (SCOP) Structural Bioinformatics Chapter 12 Ed. H. Weissig and P.E. Bourne Wiley and Associates, NY.
  • H.M. Berman, D. Goodsell and P.E. Bourne 2002 Proteins Sturctures: From Famine to Feast American Scientist 90: 350-359. [synopsis] [Full PDF]
  • DS. Greer, JD. Westbrook and PE. Bourne 2002 An Ontology Driven Architecture for Derived Representations of Macromolecular Structure Bioinformatics 18: 1280-128 [pdf].
  • BVB Reddy, W. Li, and P.E.Bourne 2002 Conserved Key Amino Acid Positions Used to Morph Protein Folds Biopolymers 64(3):139-145. [pdf]
  • H.Weissig and P.E. Bourne 2002 Macromolecular Structure Databases Acta Cryst. D 58(6) 908-915. [pdf]
  • A. Kuller, W. Fleri, W.F. Bluhm, J.L. Smith, J. Westbrook and P.E.Bourne 2001. BioSync: A Biologist's Guide to Synchrotron Resources TIBS 27(4):213-215 [pdf].
  • J. Westbrook, Z.Feng, S. Jain, T.N.Bhat, N. Thanki, V.Ravichandran, G.L.Gilliland, W.Bluhm, H. Weissig, D.S.Greer, P.E.Bourne, and H.M.Berman 2002 The Protein Data Bank: Unifying the Archive. Nucleic Acids Research, 30:245-248. [pdf]
  • W. Li, BVB Reddy, J. Tate, IN Shindyalov and P.E.Bourne 2002 CKAAPs DB: A Conserved Key Amino Acid Positions Database. Nucleic Acids Research 30: 409-411. [pdf]

2001

  • D.Greer, J. Westbrook, and P.E.Bourne 2001 OpenMMS: An Ontology Driven Architecture for Macromolecular Structure Objects in Bio- and Chem-informatics (OIBC)
  • A. Kuller, W. Fleri, W.F. Bluhm, J.L. Smith, J. Westbrook and P.E.Bourne 2001. BioSync: A Biologist's Guide to Synchrotron Resources Nature Structure Biology 8(8) 663.
  • I.N.Shindyalov and P.E.Bourne 2001 Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS’01). The Sequence-Structure Space and Data Redundancy in the Protein Data Bank. 139-145.
  • D.S. Greer, J. Westbrook, P.E. Bourne 2001 Proceedings NETTAB - Network Tools and Applications in Biology CORBA and XML: Towards a Bioinformatics Integrated Network Environment. An Ontology Driven Architecture for Macromolecular Structure.
  • J.G. Tate, J. Moreland, and P.E. Bourne 2001 J. Mol. Graphics 19, 280-287. Design and Implementation of of a Collaborative Molecular Graphics Environment.[PDF file]
  • B.V.B Reddy, W. Li, I.N. Shindyalov, and P.E. Bourne 2001 Proteins: Structure, Function and Genetics 42(2) 148-163. Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins. [PDF file]
  • H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne 2001 International Tables for Crystallography Volume F: Crystallography of Biological Macromolecules Rossmann, M.G. and Arnold, E. Editors Dordrecht: Kluwer Academic Publishers, The Netherlands pp. 675-681. The Protein Data Bank 1999-.
  • W.W.Li, B.V.B. Reddy, I.N. Shindyalov and P.E. Bourne 2001 Nucleic Acid Research, 29(1) 329-331. CKAAPs DB: A Conserved Key Amino Acid Position Database. [PDF file]
  • I.N. Shindyalov and P.E.Bourne 2001 Nucleic Acid Research, 29(1) 228-229. CE: A Resource to Compute and Review 3-D Protein Structure Alignments. [PDF file]
  • P.M.D Fitzgerald, J. Westbrook, P.E. Bourne, B. McMahon, K. Watenpaugh, H.M. Berman 2001 The International Tables for X-ray Crystallography, In Press, The Macromolecular Crystallographic Information File.
  • H.M. Berman, T.N. Bhat, P.E. Bourne, G. Gilliland, H.Weissig, and J. Westbrook 2001 Nucleic Acid Research, 29(1) 214-218, The PDB Uniformity Project [PDF file].
  • C. Guda, E.D. Scheeff, P.E. Bourne and I.N. Shindyalov 2001 Pacific Symposium on Biocomputing 6: 275-286. A New Algorithm for Alignment of Multiple Protein Structures Using Monte Carlo Optimization. [PDF file]

2000

  • P.E. Bourne and Michael Gribskov 2000 Bioinformatics Editorial 16 749. ISMB2000: Bioinformatics Enters a New Millennium. Nucleic Acids Research
  • P.E. Bourne 2000 Encyclopedia of Life Sciences Macmillian Reference Ltd. Primary Protein and Nucleic Acid Three-dimensional Databases.
  • H.M. Berman, T.N. Bhat, P.E. Bourne, G. Gilliland, H.Weissig, and J. Westbrook 2000 Nature Structure Biology, 7sup. 957-959. The Protein Data Bank and the Challenge of Structural Genomics [PDF file]
  • J.D. Westbrook and P.E. Bourne 2000 Bioinformatics 16(2) 159-168. STAR/mmCIF: An Extensive Ontology for Macromolecular Structure and Beyond. [PDF File].
  • P.E. Bourne 2000 Trends in Biotechnology 2000 18(6), 228-230. Bioinformatics Meets Data Mining, Time to Dance? A Report of the Data Mining Conference held at the EBI from Nov. 10-12, 1999. [PDF file]
  • I.N. Shindyalov and P.E. Bourne 2000 Proteins: Structure, Function and Genetics 38(3), 247-260. An Alternative View of Protein Fold Space. [PDF file]
  • H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne Nucleic Acid Research 2000 28(1), 235-242. The Protein Data Bank. [PDF file]
  • I. Tsigelny1, I. N. Shindyalov, P. E. Bourne, T. Südhof and P. Taylor Protein Science 2000 9(1) 180-185 Common EF-hand Motifs in Cholinesterases and Neuroligins Suggest a Role for CA2+ Binding in Cell Surface Associations. [PDF file]

1999

  • M. Gribskov, P.E. Bourne, C.M Smith PKR - The Protein Kinase Resource Genetics Databases Ed. Martin J. Bishop Hardcourt Press pp 241-246.
  • M.P. Ponomarenko, I.N. Shindyalov, P.E. Bourne, and N.A. Kolchanov LIKENESS: a real-time system for searching and aligning protein spatial structures. Biofizika. 1999. V. 44. N. 5. pp. 821-831 (Russ).
  • P.E.Bourne Bioinformatics 15(9) 715-716. Editorial
  • J.G. Tate, J. Moreland and P.E. Bourne J. App. Cryst. 32, 1026-1027. MSG (Molecular Scene Generator): A Web-based Application for the Visualization of Macromolecular Structures. [PDF file]
  • G. Quinn, A. Taylor, H-P Wang and P.E. Bourne 1999 TIBS 24 321-324. Development of Internet-based Multimedia Applications. [PDF file]
  • H. Weissig, and P.E. Bourne 1999 Bioinformatics 15(10) 807-831. An Analysis of the Protein Data Bank in Search of Temporal and Global Trends. [PDF]
  • G. Quinn, H-P. Wang, D. Martinez, P.E.Bourne 1999 Pacific Symposium on Biocomputing Developing Protein Documentaries and other Multimedia Presentations for Molecular Biology. Ed. R Altman, K. Dunker, L.Hunter, T. Klein, and K. Lauderdale pp. 380-391. [PDF File] Update on client-side speech synthesis [PDF File].

1998

  • M.P. Ponomarenko, N.A. Kolchanov, I.N. Shindyalov and P.E. Bourne Proc. First Int. Conf. on Bioinformatics of Gene Regulation Novosibirsk Russia 37-374. Likeness: A System Searching for and Aligning Similar Protein Conformations.
  • R. Holstein, J. McMullen, and P.E. Bourne Digital Press MA 1998 ISBN: 1555581552 In Press Unix for Openvms Users.
  • D. Hart and P.E.Bourne Prentice Hall NJ 1998, ISBN: 0135200164 In Press A Cookbook for Serving the Internet - Mac Version.
  • I.N. Shindyalov and P.E. Bourne Protein Engineering 1998, 11(9) 739-747. Protein Structure Alignment by Incremental Combinatorial Extension of the Optimum Path. [PDF File]
  • P.E.Bourne and I.N. Shindyalov 1998 Proceedings of ACHE-98. Ed. D.P. Doctor, D.M. Quinn, R.L. Rotundo, and P. Taylor. A Database of Pairwise Aligned 3-D Structures for the Aceytlcholinesterases, Lipases and Other Homologous Proteins p 455-460. Plenum Press NY.
  • H. Weissig, I.N. Shindyalov, and P.E. Bourne Acta Cryst 1998 D54 1085-1094. Macromolecular Structure Databases: Past Progress and Future Challenges. [PDF file]
  • P.E. Bourne, M. Gribskov, G. Johnson, J. Moreland, and H. Weissig Pacific Symposium on Biocomputing 1998 Ed. R Altman, K. Dunker, L.Hunter, and T. Klein pp.118-129. A Prototype Molecular Interactive Collaborative Environment (MICE). [compressed PostScript 0.12MB] [uncompressed PostScript 0.4MB]
  • W. Chang and P.E. Bourne J. App. Cryst. 1998 31, 505 - 509. CIF Applications: A New Approach for Representing and Manipulating STAR Files.
  • H.J. Bernstein, F.C. Bernstein, and P.E. Bourne J. App. Cryst. 1998, .31, 282 - 295. CIF Applications. pdb2cif: Translating PDB Entires into mmCIF Format.

1997

  • P.E.Bourne Prentice Hall NJ 1997, ISBN 0-13-519992-1 A Cookbook for Serving the Internet - UNIX Version.
  • P.E.Bourne, H.M.Berman, B. McMahon, K. Watenpaugh, J. Westbrook and P.M.D. Fitzgerald. Methods in Enzymology. 1997 277, 571-590. The Macromolecular CIF Dictionary [PDF] (mmCIF).
  • J. Biggs, C. Pu, and P.E. Bourne Fifth International Conference on Intelligent Systems for Molecular Biololgy Ed. T. Gaasterland et al. 1997, 52-55. AAAI Press. Code Generation Through Annotation of Macromolecular Structure Data Postscript [.25MB]
  • I.N.Shindyalov and P.E. Bourne CABIOS 1997, 13, 487-496. Protein Data Representation and Query Using Optimized Data Decomposition. [PDF file .07MB]
  • P.E. Bourne, C. Smith, I.N. Shindyalov, and H. Weissig ACA Transactions ed. G. Gilliland and H.Berman 1997 32 21-31 What Does Database Federation Mean to Crystallography? [compressed Postscript 0.5MB][PDF]
  • C. Smith, M. Gribskov, I.N. Shindyalov, S.S Taylor, L. Ten Eyck, S. Veretnik, P.E.Bourne TIBS 1997, 22(11) 444-446. The Protein Kinase Resource (PKR).
  • M.P. Ponomorenko, I.N. Shindyalov and P.E. Bourne Proteins 1997, Accepted. 3-D Homology of Proteins by Comformational Likeness.

1996

1995

  • I.N.Shindyalov, J.Cooper, W.Chang and P.E.Bourne Proceedings of the 28th Annual Hawaii International Conference on System Sciences (1995), 207-217 IEEE Computer Society Press. Design and Use of a Software Framework to Obtain Information Derived from Macromolecular Structure Data.
  • I.N.Shindyalov and P.E.Bourne J. App. Cryst. 1995, 28(6) 847-852. WPDB A PC-based Tool for Analyzing Protein Structure.

1994

  • W.Chang, I.N.Shindyalov, C.Pu, and P.E.Bourne, CABIOS (1994) 10(6), 575-586. Design and Application of PDBlib, a C++ Macromolecular Class Library.
  • P.Zhang, E.A.Schon, S.G.Fischer, E. Cayanis, J. Weiss, S. Kistler and P.E.Bourne, CABIOS (1994) 10(3), 309-317. An Algorithm Based on Graph Theory for the Assembly of Contigs in the Physical Mapping of DNA.
  • W.Chang, I.N.Shindyalov, C.Pu, and P.E.Bourne, Proceedings of the Second International Conference on Intelligent Systems in Molecular Biology (1994) 70-77. Design and Application of a C++ Macromolecular Class Library.
  • I.N.Shindyalov, W.Chang, C. Pu, and P.E.Bourne Protein Engineering (1994) 7(11), 1311-1322. MMQL An Object Oriented Macromolecular Query Language: Prototype Data Model and Implementation.