Philip Bourne

TitleEmeritus Professor
InstitutionUniversity of California San Diego
DepartmentSchool of Pharmacy and Pharmaceutical Science
Address9500 Gilman Drive #0719
La Jolla CA 92093
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    Collapse Research 
    Collapse Research Activities and Funding
    SciVee Pubcasts - New Modes of Scientific Dissemination
    NIH/NCRR R41RR025720Mar 1, 2009 - Mar 31, 2010
    Role: Principal Investigator
    Protein Functional Site Characterization and Analysis
    NIH/NIGMS R01GM078596Jul 1, 2007 - Jun 30, 2011
    Role: Principal Investigator
    ISMB 2005 Conf. Support for Students &Young Scientists
    NIH/NIGMS R13GM075666Jun 1, 2005 - May 31, 2006
    Role: Principal Investigator
    Tools &Data Resources in Support of Structural Genomics
    NIH/NIGMS P01GM063208Apr 1, 2002 - Mar 31, 2009
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Navale V, Bourne P. Cloud computing applications for biomedical science: A perspective. PLoS Comput Biol. 2018 06; 14(6):e1006144. PMID: 29902176.
      View in: PubMed
    2. Bourne P. Ten simple rules in considering a career in academia versus government. PLoS Comput Biol. 2017 Oct; 13(10):e1005729. PMID: 28981499.
      View in: PubMed
    3. Kittrie E, Atienza AA, Kiley R, Carr D, MacFarlane A, Pai V, Couch J, Bajkowski J, Bonner JF, Mietchen D, Bourne P. Developing international open science collaborations: Funder reflections on the Open Science Prize. PLoS Biol. 2017 Aug; 15(8):e2002617. PMID: 28763440.
      View in: PubMed
    4. Dunn MC, Bourne P. Building the biomedical data science workforce. PLoS Biol. 2017 Jul; 15(7):e2003082. PMID: 28715407.
      View in: PubMed
    5. Gao J, Prlic A, Bi C, Bluhm WF, Dimitropoulos D, Xu D, Bourne P, Rose PW. BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. Bioinformatics. 2017 Jul 01; 33(13):2047-2049. PMID: 28334105.
      View in: PubMed
    6. Zhao Z, Xie L, Bourne P. Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome. PLoS One. 2017; 12(6):e0179936. PMID: 28628649.
      View in: PubMed
    7. Bourne P, Polka JK, Vale RD, Kiley R. Ten simple rules to consider regarding preprint submission. PLoS Comput Biol. 2017 May; 13(5):e1005473. PMID: 28472041.
      View in: PubMed
    8. Zhang X, Pérez-Stable EJ, Bourne P, Peprah E, Duru OK, Breen N, Berrigan D, Wood F, Jackson JS, Wong DWS, Denny J. Big Data Science: Opportunities and Challenges to Address Minority Health and Health Disparities in the 21st Century. Ethn Dis. 2017; 27(2):95-106. PMID: 28439179.
      View in: PubMed
    9. Bonazzi VR, Bourne P. Should biomedical research be like Airbnb? PLoS Biol. 2017 Apr; 15(4):e2001818. PMID: 28388615.
      View in: PubMed
    10. Zhao Z, Liu Q, Bliven S, Xie L, Bourne P. Determining Cysteines Available for Covalent Inhibition Across the Human Kinome. J Med Chem. 2017 Apr 13; 60(7):2879-2889. PMID: 28326775.
      View in: PubMed
    11. Bourne P. Life is three-dimensional, and it begins with molecules. PLoS Biol. 2017 Mar; 15(3):e2002041. PMID: 28301467.
      View in: PubMed
    12. Xie L, Draizen EJ, Bourne P. Harnessing Big Data for Systems Pharmacology. Annu Rev Pharmacol Toxicol. 2017 Jan 06; 57:245-262. PMID: 27814027.
      View in: PubMed
    13. Zhao Z, Xie L, Xie L, Bourne P. Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach. J Med Chem. 2016 05 12; 59(9):4326-41. PMID: 26929980.
      View in: PubMed
    14. Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne P, Palsson BO. Systems biology of the structural proteome. BMC Syst Biol. 2016 Mar 11; 10:26. PMID: 26969117; PMCID: PMC4787049.
    15. Zhao Z, Martin C, Fan R, Bourne P, Xie L. Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. BMC Bioinformatics. 2016 Feb 18; 17:90. PMID: 26887654; PMCID: PMC4757998.
    16. Bourne P, Lorsch JR, Green ED. Perspective: Sustaining the big-data ecosystem. Nature. 2015 Nov 05; 527(7576):S16-7. PMID: 26536219.
      View in: PubMed
    17. Bourne P, Bonazzi V, Dunn M, Green ED, Guyer M, Komatsoulis G, Larkin J, Russell B. The NIH Big Data to Knowledge (BD2K) initiative. J Am Med Inform Assoc. 2015 Nov; 22(6):1114. PMID: 26555016; PMCID: PMC5009910 [Available on 11/01/16].
    18. Xie L, Bourne P. Developing multi-target therapeutics to fine-tune the evolutionary dynamics of the cancer ecosystem. Front Pharmacol. 2015; 6:209. PMID: 26441664; PMCID: PMC4585080.
    19. Berman FD, Bourne P. Let's Make Gender Diversity in Data Science a Priority Right from the Start. PLoS Biol. 2015 Jul; 13(7):e1002206. PMID: 26213996; PMCID: PMC4516301.
    20. Tsai LC, Xie L, Dore K, Xie L, Del Rio JC, King CC, Martinez-Ariza G, Hulme C, Malinow R, Bourne P, Newton AC. Zeta Inhibitory Peptide Disrupts Electrostatic Interactions That Maintain Atypical Protein Kinase C in Its Active Conformation on the Scaffold p62. J Biol Chem. 2015 Sep 04; 290(36):21845-56. PMID: 26187466; PMCID: PMC4571940.
    21. Bourne P, Brenner SE, Eisen MB. Ten Years of PLoS Computational Biology: A Decade of Appreciation and Innovation. PLoS Comput Biol. 2015 Jun; 11(6):e1004317. PMID: 26107720; PMCID: PMC4479580.
    22. Bourne P. DOIs for DICOM raw images: enabling science reproducibility. Radiology. 2015 Apr; 275(1):3-4. PMID: 25799330; PMCID: PMC4455617.
    23. Erren TC, Slanger TE, Groß JV, Bourne P, Cullen P. Ten simple rules for lifelong learning, according to Hamming. PLoS Comput Biol. 2015 Feb; 11(2):e1004020. PMID: 25719205; PMCID: PMC4342007.
    24. Bourne P. Confronting the ethical challenges of big data in public health. PLoS Comput Biol. 2015 Feb; 11(2):e1004073. PMID: 25664660; PMCID: PMC4321831.
    25. Bliven SE, Bourne P, Prlic A. Detection of circular permutations within protein structures using CE-CP. Bioinformatics. 2015 Apr 15; 31(8):1316-8. PMID: 25505094; PMCID: PMC4393524.
    26. Samish I, Bourne P, Najmanovich RJ. Achievements and challenges in structural bioinformatics and computational biophysics. Bioinformatics. 2015 Jan 01; 31(1):146-50. PMID: 25488929; PMCID: PMC4271151.
    27. Rose PW, Prlic A, Bi C, Bluhm WF, Christie CH, Dutta S, Green RK, Goodsell DS, Westbrook JD, Woo J, Young J, Zardecki C, Berman HM, Bourne P, Burley SK. The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res. 2015 Jan; 43(Database issue):D345-56. PMID: 25428375; PMCID: PMC4383988.
    28. Dashnow H, Lonsdale A, Bourne P. Ten simple rules for writing a PLOS ten simple rules article. PLoS Comput Biol. 2014 Oct; 10(10):e1003858. PMID: 25340653; PMCID: PMC4207461.
    29. Wang J, Bourne P, Bandeira N. MixGF: spectral probabilities for mixture spectra from more than one peptide. Mol Cell Proteomics. 2014 Dec; 13(12):3688-97. PMID: 25225354; PMCID: PMC4256515.
    30. Rougier NP, Droettboom M, Bourne P. Ten simple rules for better figures. PLoS Comput Biol. 2014 Sep; 10(9):e1003833. PMID: 25210732; PMCID: PMC4161295.
    31. Quinn GB, Bi C, Christie CH, Pang K, Prlic A, Nakane T, Zardecki C, Voigt M, Berman HM, Bourne P, Rose PW. RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. Bioinformatics. 2015 Jan 01; 31(1):126-7. PMID: 25183487; PMCID: PMC4271143.
    32. Bourne P. Ten simple rules for approaching a new job. PLoS Comput Biol. 2014 Jun; 10(6):e1003660. PMID: 24967974; PMCID: PMC4072506.
    33. Xie L, Ge X, Tan H, Xie L, Zhang Y, Hart T, Yang X, Bourne P. Towards structural systems pharmacology to study complex diseases and personalized medicine. PLoS Comput Biol. 2014 May; 10(5):e1003554. PMID: 24830652; PMCID: PMC4022462.
    34. Myers-Turnbull D, Bliven SE, Rose PW, Aziz ZK, Youkharibache P, Bourne P, Prlic A. Systematic detection of internal symmetry in proteins using CE-Symm. J Mol Biol. 2014 May 29; 426(11):2255-68. PMID: 24681267; PMCID: PMC4456030.
    35. Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne P, Bandeira N. Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. Mol Cell Proteomics. 2014 Apr; 13(4):1128-36. PMID: 24493012; PMCID: PMC3977190.
    36. Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne P, Bandeira N. A turn-key approach for large-scale identification of complex posttranslational modifications. J Proteome Res. 2014 Mar 07; 13(3):1190-9. PMID: 24437954; PMCID: PMC3993922.
    37. Ng C, Hauptman R, Zhang Y, Bourne P, Xie L. Anti-infectious drug repurposing using an integrated chemical genomics and structural systems biology approach. Pac Symp Biocomput. 2014; 136-47. PMID: 24297541.
      View in: PubMed
    38. Garijo D, Kinnings S, Xie L, Xie L, Zhang Y, Bourne P, Gil Y. Quantifying reproducibility in computational biology: the case of the tuberculosis drugome. PLoS One. 2013; 8(11):e80278. PMID: 24312207.
      View in: PubMed
    39. Alexandrov T, Bourne P. Learning how to run a lab: interviews with principal investigators. PLoS Comput Biol. 2013; 9(11):e1003349. PMID: 24244147; PMCID: PMC3820502.
    40. Chang RL, Xie L, Bourne P, Palsson BO. Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst Biol. 2013 Oct 10; 7:102. PMID: 24112686; PMCID: PMC3853765.
    41. Masum H, Rao A, Good BM, Todd MH, Edwards AM, Chan L, Bunin BA, Su AI, Thomas Z, Bourne P. Ten simple rules for cultivating open science and collaborative R&D. PLoS Comput Biol. 2013; 9(9):e1003244. PMID: 24086123; PMCID: PMC3784487.
    42. Xie L, Ng C, Ali T, Valencia R, Ferreira BL, Xue V, Tanweer M, Zhou D, Haddad GG, Bourne P, Xie L. Multiscale modeling of the causal functional roles of nsSNPs in a genome-wide association study: application to hypoxia. BMC Genomics. 2013; 14 Suppl 3:S9. PMID: 23819581; PMCID: PMC3665574.
    43. Rose PW, Bi C, Bluhm WF, Christie CH, Dimitropoulos D, Dutta S, Green RK, Goodsell DS, Prlic A, Quesada M, Quinn GB, Ramos AG, Westbrook JD, Young J, Zardecki C, Berman HM, Bourne P. The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res. 2013 Jan; 41(Database issue):D475-82. PMID: 23193259; PMCID: PMC3531086.
    44. Jolly M, Fletcher AC, Bourne P. Ten simple rules to protect your intellectual property. PLoS Comput Biol. 2012; 8(11):e1002766. PMID: 23144604; PMCID: PMC3493459.
    45. Fletcher AC, Bourne P. Ten simple rules to commercialize scientific research. PLoS Comput Biol. 2012; 8(9):e1002712. PMID: 23028299; PMCID: PMC3459878.
    46. Prlic A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne P, Willis S. BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics. 2012 Oct 15; 28(20):2693-5. PMID: 22877863; PMCID: PMC3467744.
    47. Ho Sui SJ, Lo R, Fernandes AR, Caulfield MD, Lerman JA, Xie L, Bourne P, Baillie DL, Brinkman FS. Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence. Int J Antimicrob Agents. 2012 Sep; 40(3):246-51. PMID: 22819149.
      View in: PubMed
    48. Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne P, Nielsen M, Peters B. Immune epitope database analysis resource. Nucleic Acids Res. 2012 Jul; 40(Web Server issue):W525-30. PMID: 22610854; PMCID: PMC3394288.
    49. Wodak SJ, Mietchen D, Collings AM, Russell RB, Bourne P. Topic pages: PLoS Computational Biology meets Wikipedia. PLoS Comput Biol. 2012; 8(3):e1002446. PMID: 22479174; PMCID: PMC3315447.
    50. Fletcher AC, Bourne P. Ten simple rules for starting a company. PLoS Comput Biol. 2012; 8(3):e1002439. PMID: 22479171; PMCID: PMC3315446.
    51. Rana BK, Bourne P, Insel PA. Receptor databases and computational websites for ligand binding. Methods Mol Biol. 2012; 897:1-13. PMID: 22674158.
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    52. Hecker N, Ahmed J, von Eichborn J, Dunkel M, Macha K, Eckert A, Gilson MK, Bourne P, Preissner R. SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1113-7. PMID: 22067455; PMCID: PMC3245174.
    53. Lewitter F, Bourne P. Teaching bioinformatics at the secondary school level. PLoS Comput Biol. 2011 Oct; 7(10):e1002242. PMID: 22046116; PMCID: PMC3203059.
    54. Xie L, Xie L, Kinnings SL, Bourne P. Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annu Rev Pharmacol Toxicol. 2012; 52:361-79. PMID: 22017683.
      View in: PubMed
    55. Wang J, Bourne P, Bandeira N. Peptide identification by database search of mixture tandem mass spectra. Mol Cell Proteomics. 2011 Dec; 10(12):M111.010017. PMID: 21862760; PMCID: PMC3237077.
    56. Gramada A, Bourne P. Coarse-graining the electrostatic potential via distributed multipole expansions. Comput Phys Commun. 2011 Jul 01; 182(7):1455-1462. PMID: 21572587.
      View in: PubMed
    57. Bourne P, Barbour V. Ten simple rules for building and maintaining a scientific reputation. PLoS Comput Biol. 2011 Jun; 7(6):e1002108. PMID: 21738465; PMCID: PMC3127799.
    58. Xie L, Evangelidis T, Xie L, Bourne P. Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir. PLoS Comput Biol. 2011 Apr; 7(4):e1002037. PMID: 21552547; PMCID: PMC3084228.
    59. Kinnings SL, Liu N, Tonge PJ, Jackson RM, Xie L, Bourne P. Correction to "Machine learning-based method to improve docking scoring functions and its application to drug repurposing". J Chem Inf Model. 2011 May 23; 51(5):1195-7. PMID: 21526828; PMCID: PMC3186856.
    60. von Eichborn J, Bourne P, Preissner R. Cobweb: a Java applet for network exploration and visualisation. Bioinformatics. 2011 Jun 15; 27(12):1725-6. PMID: 21486937.
      View in: PubMed
    61. Bluhm WF, Beran B, Bi C, Dimitropoulos D, Prlic A, Quinn GB, Rose PW, Shah C, Young J, Yukich B, Berman HM, Bourne P. Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. Database (Oxford). 2011; 2011:bar003. PMID: 21382834; PMCID: PMC3056270.
    62. Valas RE, Bourne P. The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon. Biol Direct. 2011 Feb 28; 6:16. PMID: 21356104; PMCID: PMC3056875.
    63. Kinnings SL, Liu N, Tonge PJ, Jackson RM, Xie L, Bourne P. A machine learning-based method to improve docking scoring functions and its application to drug repurposing. J Chem Inf Model. 2011 Feb 28; 51(2):408-19. PMID: 21291174; PMCID: PMC3076728.
    64. Kuo GM, Ma JD, Lee KC, Halpert JR, Bourne P, Ganiats TG, Taylor P. Institutional Profile: University of California San Diego Pharmacogenomics Education Program (PharmGenEd™): bridging the gap between science and practice. Pharmacogenomics. 2011 Feb; 12(2):149-53. PMID: 21332308.
      View in: PubMed
    65. Xie L, Xie L, Bourne P. Structure-based systems biology for analyzing off-target binding. Curr Opin Struct Biol. 2011 Apr; 21(2):189-99. PMID: 21292475; PMCID: PMC3070778.
    66. Dickin R, Marden C, Collings AM, Nussinov R, Bourne P. A Review of 2010 for PLoS Computational Biology. PLoS Comput Biol. 2011 Jan 27; 7(1):e1002003. PMID: 21298077; PMCID: PMC3029231.
    67. Bourne P. Ten simple rules for getting ahead as a computational biologist in Academia. PLoS Comput Biol. 2011 Jan 06; 7(1):e1002001. PMID: 21253560; PMCID: PMC3017106.
    68. von Eichborn J, Murgueitio MS, Dunkel M, Koerner S, Bourne P, Preissner R. PROMISCUOUS: a database for network-based drug-repositioning. Nucleic Acids Res. 2011 Jan; 39(Database issue):D1060-6. PMID: 21071407; PMCID: PMC3013657.
    69. Kinnings SL, Xie L, Fung KH, Jackson RM, Xie L, Bourne P. The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol. 2010 Nov 04; 6(11):e1000976. PMID: 21079673; PMCID: PMC2973814.
    70. Rose PW, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Goodsell DS, Prlic A, Quesada M, Quinn GB, Westbrook JD, Young J, Yukich B, Zardecki C, Berman HM, Bourne P. The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 2011 Jan; 39(Database issue):D392-401. PMID: 21036868; PMCID: PMC3013649.
    71. Ponomarenko J, Papangelopoulos N, Zajonc DM, Peters B, Sette A, Bourne P. IEDB-3D: structural data within the immune epitope database. Nucleic Acids Res. 2011 Jan; 39(Database issue):D1164-70. PMID: 21030437; PMCID: PMC3013771.
    72. Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne P. Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics. 2010 Dec 01; 26(23):2983-5. PMID: 20937596; PMCID: PMC3003546.
    73. Chang RL, Xie L, Xie L, Bourne P, Palsson BØ. Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput Biol. 2010 Sep 23; 6(9):e1000938. PMID: 20957118; PMCID: PMC2950675.
    74. Valas RE, Bourne P. Save the tree of life or get lost in the woods. Biol Direct. 2010 Jul 01; 5:44. PMID: 20594329; PMCID: PMC2910001.
    75. Alden K, Veretnik S, Bourne P. dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. BMC Bioinformatics. 2010 Jun 09; 11:310. PMID: 20529369; PMCID: PMC2897830.
    76. Bourne P. What do I want from the publisher of the future? PLoS Comput Biol. 2010 May 27; 6(5):e1000787. PMID: 20523744; PMCID: PMC2877727.
    77. Dupont CL, Butcher A, Valas RE, Bourne P, Caetano-Anollés G. History of biological metal utilization inferred through phylogenomic analysis of protein structures. Proc Natl Acad Sci U S A. 2010 Jun 08; 107(23):10567-72. PMID: 20498051; PMCID: PMC2890839.
    78. Ren J, Xie L, Li WW, Bourne P. SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. Nucleic Acids Res. 2010 Jul; 38(Web Server issue):W441-4. PMID: 20484373; PMCID: PMC2896174.
    79. Prlic A, Martinez MA, Dimitropoulos D, Beran B, Yukich BT, Rose PW, Bourne P, Fink JL. Integration of open access literature into the RCSB Protein Data Bank using BioLit. BMC Bioinformatics. 2010 Apr 29; 11:220. PMID: 20429930.
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    80. Datta RS, Lux MW, Bourne P. PLoS Computational Biology conference postcards from PSB 2010. PLoS Comput Biol. 2010 Apr 29; 6(4):e1000746. PMID: 20442855; PMCID: PMC2861683.
    81. Bourne P, Beran B, Bi C, Bluhm W, Dunbrack R, Prlic A, Quinn G, Rose P, Shah R, Tao W, Weitzner B, Yukich B. Will widgets and semantic tagging change computational biology? PLoS Comput Biol. 2010 Feb 26; 6(2):e1000673. PMID: 20195550; PMCID: PMC2829027.
    82. Fink JL, Fernicola P, Chandran R, Parastatidis S, Wade A, Naim O, Quinn GB, Bourne P. Word add-in for ontology recognition: semantic enrichment of scientific literature. BMC Bioinformatics. 2010 Feb 24; 11:103. PMID: 20181245; PMCID: PMC2837026.
    83. Zhang H, Wang P, Papangelopoulos N, Xu Y, Sette A, Bourne P, Lund O, Ponomarenko J, Nielsen M, Peters B. Limitations of Ab initio predictions of peptide binding to MHC class II molecules. PLoS One. 2010 Feb 17; 5(2):e9272. PMID: 20174654; PMCID: PMC2822856.
    84. Durrant JD, Amaro RE, Xie L, Urbaniak MD, Ferguson MA, Haapalainen A, Chen Z, Di Guilmi AM, Wunder F, Bourne P, McCammon JA. A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol. 2010 Jan 22; 6(1):e1000648. PMID: 20098496; PMCID: PMC2799658.
    85. Yang S, Bourne P. The evolutionary history of protein domains viewed by species phylogeny. PLoS One. 2009 Dec 21; 4(12):e8378. PMID: 20041107; PMCID: PMC2794708.
    86. Bateman A, Bourne P. Ten simple rules for chairing a scientific session. PLoS Comput Biol. 2009 Sep; 5(9):e1000517. PMID: 19779547; PMCID: PMC2738972.
    87. Valas RE, Bourne P. Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life. Biol Direct. 2009 Aug 25; 4:30. PMID: 19706177; PMCID: PMC3224940.
    88. Kinnings SL, Liu N, Buchmeier N, Tonge PJ, Xie L, Bourne P. Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comput Biol. 2009 Jul; 5(7):e1000423. PMID: 19578428; PMCID: PMC2699117.
    89. Xie L, Xie L, Bourne P. 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 Jun 15; 25(12):i305-12. PMID: 19478004; PMCID: PMC2687974.
    90. Xie L, Li J, Xie L, Bourne P. Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. PLoS Comput Biol. 2009 May; 5(5):e1000387. PMID: 19436720; PMCID: PMC2676506.
    91. Valas RE, Yang S, Bourne P. Nothing about protein structure classification makes sense except in the light of evolution. Curr Opin Struct Biol. 2009 Jun; 19(3):329-34. PMID: 19394812; PMCID: PMC2696554.
    92. Vicens Q, Bourne P. Ten simple rules to combine teaching and research. PLoS Comput Biol. 2009 Apr; 5(4):e1000358. PMID: 19390598; PMCID: PMC2661017.
    93. Veretnik S, Wills C, Youkharibache P, Valas RE, Bourne P. Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome. PLoS Comput Biol. 2009 Mar; 5(3):e1000315. PMID: 19282982; PMCID: PMC2650416.
    94. Browne E, Dickin R, Bourne P. A Review of 2008 for PLoS Computational Biology. PLoS Comput Biol. 2009 Jan; 5(1):e1000275. PMID: 19180176; PMCID: PMC2613517.
    95. Bourne P, Fink JL. I am not a scientist, I am a number. PLoS Comput Biol. 2008 Dec; 4(12):e1000247. PMID: 19112480; PMCID: PMC2586848.
    96. Ponomarenko J, Bui HH, Li W, Fusseder N, Bourne P, Sette A, Peters B. ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics. 2008 Dec 02; 9:514. PMID: 19055730; PMCID: PMC2607291.
    97. Gramada A, Bourne P. Resolving a distribution of charge into intrinsic multipole moments: a rankwise distributed multipole analysis. Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Dec; 78(6 Pt 2):066601. PMID: 19256962.
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    98. Karp PD, Sherlock G, Gerlt JA, Sim I, Paulsen I, Babbitt PC, Laderoute K, Hunter L, Sternberg P, Wooley J, Bourne P. Changes to NIH grant system may backfire. Science. 2008 Nov 21; 322(5905):1187-8. PMID: 19023064.
      View in: PubMed
    99. Veretnik S, Fink JL, Bourne P. Computational biology resources lack persistence and usability. PLoS Comput Biol. 2008 Jul 18; 4(7):e1000136. PMID: 18636105; PMCID: PMC2443418.
    100. Corpas M, Gehlenborg N, Janga SC, Bourne P. Ten simple rules for organizing a scientific meeting. PLoS Comput Biol. 2008 Jun 27; 4(6):e1000080. PMID: 18584020; PMCID: PMC2367436.
    101. Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne P, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B. Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res. 2008 Jul 01; 36(Web Server issue):W513-8. PMID: 18515843; PMCID: PMC2447801.
    102. Fink JL, Kushch S, Williams PR, Bourne P. BioLit: integrating biological literature with databases. Nucleic Acids Res. 2008 Jul 01; 36(Web Server issue):W385-9. PMID: 18515836; PMCID: PMC2447735.
    103. Bauer RA, Bourne P, Formella A, Frömmel C, Gille C, Goede A, Guerler A, Hoppe A, Knapp EW, Pöschel T, Wittig B, Ziegler V, Preissner R. Superimpose: a 3D structural superposition server. Nucleic Acids Res. 2008 Jul 01; 36(Web Server issue):W47-54. PMID: 18492720; PMCID: PMC2447795.
    104. Valas RE, Bourne P. Rethinking proteasome evolution: two novel bacterial proteasomes. J Mol Evol. 2008 May; 66(5):494-504. PMID: 18389302; PMCID: PMC3235984.
    105. Xie L, Bourne P. Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A. 2008 Apr 08; 105(14):5441-6. PMID: 18385384; PMCID: PMC2291117.
    106. Bourne P, Fink JL, Gerstein M. Open access: taking full advantage of the content. PLoS Comput Biol. 2008 Mar 28; 4(3):e1000037. PMID: 18369428; PMCID: PMC2275780.
    107. Briedis KM, Starr A, Bourne P. Analysis of the human kinome using methods including fold recognition reveals two novel kinases. PLoS One. 2008 Feb 13; 3(2):e1597. PMID: 18270584; PMCID: PMC2223070.
    108. Caporaso JG, Deshpande N, Fink JL, Bourne P, Cohen KB, Hunter L. Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pac Symp Biocomput. 2008; 640-51. PMID: 18229722; PMCID: PMC2517250.
    109. Gu J, Bourne P. Ten simple rules for graduate students. PLoS Comput Biol. 2007 Nov; 3(11):e229. PMID: 18052537; PMCID: PMC2098857.
    110. Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne P, Bork P, Preissner R. SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res. 2008 Jan; 36(Database issue):D919-22. PMID: 17942422; PMCID: PMC2238858.
    111. Ponomarenko JV, Bourne P. Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol. 2007 Oct 02; 7:64. PMID: 17910770; PMCID: PMC2174481.
    112. Erren TC, Cullen P, Erren M, Bourne P. Ten simple rules for doing your best research, according to Hamming. PLoS Comput Biol. 2007 Oct; 3(10):1839-40. PMID: 17967054; PMCID: PMC2041981.
    113. Xie L, Wang J, Bourne P. In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comput Biol. 2007 Nov; 3(11):e217. PMID: 18052534; PMCID: PMC2098847.
    114. Bourne P, Brenner SE. Developing computational biology. PLoS Comput Biol. 2007 Sep; 3(9):1669. PMID: 17907793; PMCID: PMC1994973.
    115. Chung JL, Beaver JE, Scheeff ED, Bourne P. Con-Struct Map: a comparative contact map analysis tool. Bioinformatics. 2007 Sep 15; 23(18):2491-2. PMID: 17709340.
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    116. Berman HM, Henrick K, Nakamura H, Markley J, Bourne P, Westbrook J. Realism about PDB. Nat Biotechnol. 2007 Aug; 25(8):845-6; author reply 846. PMID: 17687352.
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    117. Chung JL, Wang W, Bourne P. High-throughput identification of interacting protein-protein binding sites. BMC Bioinformatics. 2007 Jun 27; 8:223. PMID: 17594507; PMCID: PMC1925121.
    118. Xie L, Bourne P. A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinformatics. 2007 May 22; 8 Suppl 4:S9. PMID: 17570152; PMCID: PMC1892088.
    119. Erren TC, Bourne P. Ten simple rules for a good poster presentation. PLoS Comput Biol. 2007 May; 3(5):e102. PMID: 17530921; PMCID: PMC1876493.
    120. Bourne P. Ten simple rules for making good oral presentations. PLoS Comput Biol. 2007 Apr 27; 3(4):e77. PMID: 17500596; PMCID: PMC1857815.
    121. Vicens Q, Bourne P. Ten simple rules for a successful collaboration. PLoS Comput Biol. 2007 Mar 30; 3(3):e44. PMID: 17397252; PMCID: PMC1847992.
    122. Beaver JE, Bourne P, Ponomarenko JV. EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB). Immunome Res. 2007 Feb 21; 3:3. PMID: 17313688; PMCID: PMC1810240.
    123. Gu J, Bourne P. Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2. BMC Bioinformatics. 2007 Feb 07; 8:45. PMID: 17286863; PMCID: PMC1800904.
    124. Bourne P, Friedberg I. Ten simple rules for selecting a postdoctoral position. PLoS Comput Biol. 2006 Nov 24; 2(11):e121. PMID: 17121457; PMCID: PMC1664706.
    125. Guda P, Bourne P, Guda C. Conserved motifs in voltage-sensing and pore-forming modules of voltage-gated ion channel proteins. Biochem Biophys Res Commun. 2007 Jan 12; 352(2):292-8. PMID: 17126810.
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    126. Dupont CL, Yang S, Palenik B, Bourne P. Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. Proc Natl Acad Sci U S A. 2006 Nov 21; 103(47):17822-7. PMID: 17098870; PMCID: PMC1635651.
    127. Bourne P, McEntyre J. Biocurators: contributors to the world of science. PLoS Comput Biol. 2006 Oct 27; 2(10):e142. PMID: 17411327; PMCID: PMC1626157.
    128. Bourne P, Korngreen A. Ten simple rules for reviewers. PLoS Comput Biol. 2006 Sep 29; 2(9):e110. PMID: 17009861; PMCID: PMC1584310.
    129. Scheeff ED, Bourne P. Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics. 2006 Sep 14; 7:410. PMID: 16970830; PMCID: PMC1622756.
    130. Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne P, Bryant SH, Dunbrack RL, Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, Heymann B, Jones D, Markley JL, Moult J, Montelione GT, Orengo C, Rossmann MG, Rost B, Saibil H, Schwede T, Standley DM, Westbrook JD. Outcome of a workshop on archiving structural models of biological macromolecules. Structure. 2006 Aug; 14(8):1211-7. PMID: 16955948.
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    131. Vita R, Vaughan K, Zarebski L, Salimi N, Fleri W, Grey H, Sathiamurthy M, Mokili J, Bui HH, Bourne P, Ponomarenko J, de Castro R, Chan RK, Sidney J, Wilson SS, Stewart S, Way S, Peters B, Sette A. Curation of complex, context-dependent immunological data. BMC Bioinformatics. 2006 Jul 12; 7:341. PMID: 16836764; PMCID: PMC1534061.
    132. Holland TA, Veretnik S, Shindyalov IN, Bourne P. Partitioning protein structures into domains: why is it so difficult? J Mol Biol. 2006 Aug 18; 361(3):562-90. PMID: 16863650.
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    133. Gu J, Gribskov M, Bourne P. Wiggle-predicting functionally flexible regions from primary sequence. PLoS Comput Biol. 2006 Jul 14; 2(7):e90. PMID: 16839194; PMCID: PMC1500818.
    134. Gramada A, Bourne P. Multipolar representation of protein structure. BMC Bioinformatics. 2006 May 04; 7:242. PMID: 16674828; PMCID: PMC1483839.
    135. Chung JL, Wang W, Bourne P. Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins. 2006 Mar 15; 62(3):630-40. PMID: 16329107.
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    136. Bourne P, Chalupa LM. Ten simple rules for getting grants. PLoS Comput Biol. 2006 Feb; 2(2):e12. PMID: 16501664; PMCID: PMC1378105.
    137. Neshich G, Bourne P, Brunak S. ISMB 2006. PLoS Comput Biol. 2006 Feb; 2(2):e11. PMID: 16758006; PMCID: PMC1378106.
    138. Kouranov A, Xie L, de la Cruz J, Chen L, Westbrook J, Bourne P, Berman HM. The RCSB PDB information portal for structural genomics. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D302-5. PMID: 16381872; PMCID: PMC1347482.
    139. Scheeff ED, Bourne P. Structural evolution of the protein kinase-like superfamily. PLoS Comput Biol. 2005 Oct; 1(5):e49. PMID: 16244704; PMCID: PMC1261164.
    140. Bourne P. Ten simple rules for getting published. PLoS Comput Biol. 2005 Oct; 1(5):e57. PMID: 16261197; PMCID: PMC1274296.
    141. Sathiamurthy M, Peters B, Bui HH, Sidney J, Mokili J, Wilson SS, Fleri W, McGuinness DL, Bourne P, Sette A. An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. Immunome Res. 2005 Sep 20; 1(1):2. PMID: 16305755; PMCID: PMC1287064.
    142. Xie L, Bourne P. Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput Biol. 2005 Aug; 1(3):e31. PMID: 16118666; PMCID: PMC1188274.
    143. Bourne P, Brenner SE, Eisen MB. PLoS Computational Biology: a new community journal. PLoS Comput Biol. 2005 Jun; 1(1):e4. PMID: 16103905; PMCID: PMC1183510.
    144. Ponomarenko JV, Bourne P, Shindyalov IN. Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology. Proteins. 2005 Mar 01; 58(4):855-65. PMID: 15645518.
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    145. Moreland JL, Gramada A, Buzko OV, Zhang Q, Bourne P. The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. BMC Bioinformatics. 2005 Feb 06; 6:21. PMID: 15694009; PMCID: PMC548701.
    146. Yang S, Doolittle RF, Bourne P. Phylogeny determined by protein domain content. Proc Natl Acad Sci U S A. 2005 Jan 11; 102(2):373-8. PMID: 15630082; PMCID: PMC540256.
    147. Deshpande N, Addess KJ, Bluhm WF, Merino-Ott JC, Townsend-Merino W, Zhang Q, Knezevich C, Xie L, Chen L, Feng Z, Green RK, Flippen-Anderson JL, Westbrook J, Berman HM, Bourne P. The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D233-7. PMID: 15608185; PMCID: PMC540011.
    148. Babbitt PC, Bourne P, Mooney SD. Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure. Pac Symp Biocomput. 2005; 319-21. PMID: 15759637.
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    149. Guda C, Lu S, Scheeff ED, Bourne P, Shindyalov IN. CE-MC: a multiple protein structure alignment server. Nucleic Acids Res. 2004 Jul 01; 32(Web Server issue):W100-3. PMID: 15215359; PMCID: PMC441602.
    150. Veretnik S, Bourne P, Alexandrov NN, Shindyalov IN. Toward consistent assignment of structural domains in proteins. J Mol Biol. 2004 Jun 04; 339(3):647-78. PMID: 15147847.
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    151. Krebs WG, Bourne P. Statistical and visual morph movie analysis of crystallographic mutant selection bias in protein mutation resource data. J Bioinform Comput Biol. 2004 Mar; 2(1):61-75. PMID: 15272433.
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    152. Bourne P, Westbrook J, Berman HM. The Protein Data Bank and lessons in data management. Brief Bioinform. 2004 Mar; 5(1):23-30. PMID: 15153303.
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    153. Krebs WG, Bourne P. Statistically rigorous automated protein annotation. Bioinformatics. 2004 May 01; 20(7):1066-73. PMID: 14764575.
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    154. Jia Y, Dewey TG, Shindyalov IN, Bourne P. A new scoring function and associated statistical significance for structure alignment by CE. J Comput Biol. 2004; 11(5):787-99. PMID: 15700402.
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    155. Bourne P, Addess KJ, Bluhm WF, Chen L, Deshpande N, Feng Z, Fleri W, Green R, Merino-Ott JC, Townsend-Merino W, Weissig H, Westbrook J, Berman HM. The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D223-5. PMID: 14681399; PMCID: PMC308830.
    156. Li WW, Quinn GB, Alexandrov NN, Bourne P, Shindyalov IN. A comparative proteomics resource: proteins of Arabidopsis thaliana. Genome Biol. 2003; 4(8):R51. PMID: 12914659; PMCID: PMC193643.
    157. Yang P, Craig PA, Goodsell D, Bourne P. BioEditor-simplifying macromolecular structure annotation. Bioinformatics. 2003 May 01; 19(7):897-8. PMID: 12724304.
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    158. Bourne P. Free access to publicly funded databases is vital. Nature. 2003 Feb 20; 421(6925):786. PMID: 12594481.
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    159. Weissig H, Bourne P. Other structure-based databases. Methods Biochem Anal. 2003; 44:217-36. PMID: 12647388.
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    160. Reedy BV, Bourne P. Protein structure evolution and the SCOP database. Methods Biochem Anal. 2003; 44:239-48. PMID: 12647389.
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    161. Bourne P. CASP and CAFASP experiments and their findings. Methods Biochem Anal. 2003; 44:501-7. PMID: 12647401.
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    162. Bourne P, Shindyalov IN. Structure comparison and alignment. Methods Biochem Anal. 2003; 44:321-37. PMID: 12647393.
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    163. Krebs WG, Bourne P. Statistical and visual morph movie analysis of crystallographic mutant selection bias in protein mutation resource data. Proc IEEE Comput Soc Bioinform Conf. 2003; 2:180-9. PMID: 16452792.
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    164. Greer DS, Westbrook JD, Bourne P. An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics. 2002 Sep; 18(9):1280-1. PMID: 12217927.
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    165. Reddy BV, Li WW, Bourne P. Use of conserved key amino acid positions to morph protein folds. Biopolymers. 2002 Jul 15; 64(3):139-45. PMID: 12012349.
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    166. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne P, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 2002 Jun; 58(Pt 6 No 1):899-907. PMID: 12037327.
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    167. Weissig H, Bourne P. Protein structure resources. Acta Crystallogr D Biol Crystallogr. 2002 Jun; 58(Pt 6 No 1):908-15. PMID: 12037328.
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    168. Kuller A, Fleri W, Bluhm WF, Smith JL, Westbrook J, Bourne P. A biologist's guide to synchrotron facilities: the BioSync web resource. Trends Biochem Sci. 2002 Apr; 27(4):213-5. PMID: 11943550.
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    169. Ponomarenko JV, Bourne P, Shindyalov IN. Building an automated classification of DNA-binding protein domains. Bioinformatics. 2002; 18 Suppl 2:S192-201. PMID: 12386003.
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    170. Li WW, Reddy BV, Tate JG, Shindyalov IN, Bourne P. CKAAPs DB: a Conserved Key Amino Acid Positions DataBase. Nucleic Acids Res. 2002 Jan 01; 30(1):409-11. PMID: 11752351; PMCID: PMC99066.
    171. Westbrook J, Feng Z, Jain S, Bhat TN, Thanki N, Ravichandran V, Gilliland GL, Bluhm W, Weissig H, Greer DS, Bourne P, Berman HM. The Protein Data Bank: unifying the archive. Nucleic Acids Res. 2002 Jan 01; 30(1):245-8. PMID: 11752306; PMCID: PMC99110.