Philip Bourne

Title(s)Emeritus Professor, School of Pharmacy and Pharmaceutical Science
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Research 
    Collapse Research Activities and Funding
    SciVee Pubcasts - New Modes of Scientific Dissemination
    NIH R41RR025720Mar 1, 2009 - Mar 31, 2010
    Role: Principal Investigator
    Protein Functional Site Characterization and Analysis
    NIH R01GM078596Jul 1, 2007 - Jun 30, 2011
    Role: Principal Investigator
    ISMB 2005 Conf. Support for Students &Young Scientists
    NIH R13GM075666Jun 1, 2005 - May 31, 2006
    Role: Principal Investigator
    Tools &Data Resources in Support of Structural Genomics
    NIH 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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data. BMC Bioinformatics. 2024 Jan 04; 25(1):11. Draizen EJ, Readey J, Mura C, Bourne PE. PMID: 38177985; PMCID: PMC10768222.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    2. Ten simple rules for humane data science. PLoS Comput Biol. 2023 Dec; 19(12):e1011698. Masum H, Bourne PE. PMID: 38127691; PMCID: PMC10734991.
      View in: PubMed   Mentions:    Fields:    
    3. Ten simple rules for managing laboratory information. PLoS Comput Biol. 2023 Dec; 19(12):e1011652. Berezin CT, Aguilera LU, Billerbeck S, Bourne PE, Densmore D, Freemont P, Gorochowski TE, Hernandez SI, Hillson NJ, King CR, Köpke M, Ma S, Miller KM, Moon TS, Moore JH, Munsky B, Myers CJ, Nicholas DA, Peccoud SJ, Zhou W, Peccoud J. PMID: 38060459; PMCID: PMC10703290.
      View in: PubMed   Mentions:    Fields:    
    4. How Ligands Interact with the Kinase Hinge. ACS Med Chem Lett. 2023 Nov 09; 14(11):1503-1508. Zhao Z, Bourne PE. PMID: 37974950; PMCID: PMC10641887.
      View in: PubMed   Mentions:
    5. Policy recommendations to ensure that research software is openly accessible and reusable. PLoS Biol. 2023 07; 21(7):e3002204. McKiernan EC, Barba L, Bourne PE, Carter C, Chandler Z, Choudhury S, Jacobs S, Katz DS, Lieggi S, Plale B, Tananbaum G. PMID: 37478129; PMCID: PMC10396347.
      View in: PubMed   Mentions: 1     Fields:    
    6. Rigid Scaffolds Are Promising for Designing Macrocyclic Kinase Inhibitors. ACS Pharmacol Transl Sci. 2023 Aug 11; 6(8):1182-1191. Zhao Z, Bourne PE. PMID: 37588756; PMCID: PMC10425998.
      View in: PubMed   Mentions: 1  
    7. Ten simple rules for serving as an editor. PLoS Comput Biol. 2023 Mar; 19(3):e1010911. Mura C, Bourne PE. PMID: 36862619; PMCID: PMC9980748.
      View in: PubMed   Mentions:    Fields:    
    8. Analysis of KRAS-Ligand Interaction Modes and Flexibilities Reveals the Binding Characteristics. J Chem Inf Model. 2023 02 27; 63(4):1362-1370. Zhao Z, Bohidar N, Bourne PE. PMID: 36780612.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    9. End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins. PLoS Comput Biol. 2023 01; 19(1):e1010851. Cai T, Xie L, Zhang S, Chen M, He D, Badkul A, Liu Y, Namballa HK, Dorogan M, Harding WW, Mura C, Bourne PE, Xie L. PMID: 36652496; PMCID: PMC9886305.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    10. The curse of the protein ribbon diagram. PLoS Biol. 2022 Dec; 20(12):e3001901. Bourne PE, Draizen EJ, Mura C. PMID: 36508416.
      View in: PubMed   Mentions: 2     Fields:    
    11. Systematic Exploration of Privileged Warheads for Covalent Kinase Drug Discovery. Pharmaceuticals (Basel). 2022 Oct 26; 15(11). Zhao Z, Bourne PE. PMID: 36355497; PMCID: PMC9695834.
      View in: PubMed   Mentions: 2  
    12. From biomedical cloud platforms to microservices: next steps in FAIR data and analysis. Sci Data. 2022 09 08; 9(1):553. Sheffield NC, Bonazzi VR, Bourne PE, Burdett T, Clark T, Grossman RL, Spjuth O, Yates AD. PMID: 36075919; PMCID: PMC9458632.
      View in: PubMed   Mentions: 3     Fields:    
    13. Ten simple rules for organizing a special session at a scientific conference. PLoS Comput Biol. 2022 08; 18(8):e1010395. Chicco D, Bourne PE. PMID: 36006874; PMCID: PMC9409505.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    14. Harnessing systematic protein-ligand interaction fingerprints for drug discovery. Drug Discov Today. 2022 Oct; 27(10):103319. Zhao Z, Bourne PE. PMID: 35850431.
      View in: PubMed   Mentions: 9     Fields:    
    15. Playing catch-up in building an open research commons. Science. 2022 07 15; 377(6603):256-258. Bourne PE, Bonazzi V, Brand A, Carroll B, Foster I, Guha RV, Hanisch R, Keller SA, Kennedy ML, Kirkpatrick C, Mons B, Nusser SM, Stebbins M, Strawn G, Szalay A. PMID: 35857616.
      View in: PubMed   Mentions: 5     Fields:    
    16. Ten simple rules for improving communication among scientists. PLoS Comput Biol. 2022 06; 18(6):e1010130. Bautista C, Alfuraiji N, Drangowska-Way A, Gangwani K, de Flamingh A, Bourne PE. PMID: 35737640; PMCID: PMC9223317.
      View in: PubMed   Mentions: 1     Fields:    
    17. Ten simple rules for good leadership. PLoS Comput Biol. 2022 06; 18(6):e1010133. Bourne PE. PMID: 35679224; PMCID: PMC9182262.
      View in: PubMed   Mentions: 1     Fields:    
    18. Real-world evidence from over one million COVID-19 vaccinations is consistent with reactivation of the varicella-zoster virus. J Eur Acad Dermatol Venereol. 2022 Aug; 36(8):1342-1348. Hertel M, Heiland M, Nahles S, von Laffert M, Mura C, Bourne PE, Preissner R, Preissner S. PMID: 35470920; PMCID: PMC9114991.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCellsPHPublic Health
    19. Ten simple rules for using entrepreneurship skills to improve research careers and culture. PLoS Comput Biol. 2022 04; 18(4):e1009946. Bawn M, Dent D, Bourne PE. PMID: 35395024; PMCID: PMC8992998.
      View in: PubMed   Mentions:    Fields:    
    20. A Comparative Analysis of COVID-19 Vaccines Based on over 580,000 Cases from the Vaccination Adverse Event Reporting System. Vaccines (Basel). 2022 Mar 08; 10(3). Gallo K, Goede A, Mura C, Abel R, Moahamed B, Preissner S, Nahles S, Heiland M, Bourne PE, Preissner R, Mallach M. PMID: 35335040; PMCID: PMC8950485.
      View in: PubMed   Mentions: 3  
    21. Real-world evidence for preventive effects of statins on cancer incidence: A trans-Atlantic analysis. Clin Transl Med. 2022 02; 12(2):e726. Gohlke BO, Zincke F, Eckert A, Kobelt D, Preissner S, Liebeskind JM, Gunkel N, Putzker K, Lewis J, Preissner S, Kortüm B, Walther W, Mura C, Bourne PE, Stein U, Preissner R. PMID: 35184411; PMCID: PMC8858616.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    22. Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants". J Chem Inf Model. 2022 Jan 10; 62(1):223-224. Zhao Z, Xie L, Bourne PE. PMID: 34929085.
      View in: PubMed   Mentions:    Fields:    
    23. Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology. Res Sq. 2021 Dec 01. Cai T, Xie L, Chen M, Liu Y, He D, Zhang S, Mura C, Bourne PE, Xie L. PMID: 34873596; PMCID: PMC8647653.
      View in: PubMed   Mentions:
    24. A Birds-Eye (Re)View of Acid-Suppression Drugs, COVID-19, and the Highly Variable Literature. Front Pharmacol. 2021; 12:700703. Mura C, Preissner S, Preissner R, Bourne PE. PMID: 34456726; PMCID: PMC8385362.
      View in: PubMed   Mentions: 3  
    25. IL-13 is a driver of COVID-19 severity. JCI Insight. 2021 08 09; 6(15). Donlan AN, Sutherland TE, Marie C, Preissner S, Bradley BT, Carpenter RM, Sturek JM, Ma JZ, Moreau GB, Donowitz JR, Buck GA, Serrano MG, Burgess SL, Abhyankar MM, Mura C, Bourne PE, Preissner R, Young MK, Lyons GR, Loomba JJ, Ratcliffe SJ, Poulter MD, Mathers AJ, Day AJ, Mann BJ, Allen JE, Petri WA. PMID: 34185704; PMCID: PMC8410056.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansAnimalsCells
    26. Real-world evidence for improved outcomes with histamine antagonists and aspirin in 22,560 COVID-19 patients. Signal Transduct Target Ther. 2021 07 14; 6(1):267. Mura C, Preissner S, Nahles S, Heiland M, Bourne PE, Preissner R. PMID: 34262013; PMCID: PMC8278809.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    27. Is "bioinformatics" dead? PLoS Biol. 2021 03; 19(3):e3001165. Bourne PE. PMID: 33735179; PMCID: PMC7984605.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    28. IL-13 is a driver of COVID-19 severity. medRxiv. 2021 Mar 01. Donlan AN, Sutherland TE, Marie C, Preissner S, Bradley BT, Carpenter RM, Sturek JM, Ma JZ, Moreau GB, Donowitz JR, Buck GA, Serrano MG, Burgess SL, Abhyankar MM, Mura C, Bourne PE, Preissner R, Young MK, Lyons GR, Loomba JJ, Ratcliffe SJ, Poulter MD, Mathers AJ, Day A, Mann BJ, Allen JE, Petri WA. PMID: 33688686; PMCID: PMC7941663.
      View in: PubMed   Mentions:
    29. Ten simple rules for starting (and sustaining) an academic data science initiative. PLoS Comput Biol. 2021 02; 17(2):e1008628. Parker MS, Burgess AE, Bourne PE. PMID: 33600414; PMCID: PMC7891724.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    30. Computational Prediction of Potential Inhibitors of the Main Protease of SARS-CoV-2. Front Chem. 2020; 8:590263. Abel R, Paredes Ramos M, Chen Q, Pérez-Sánchez H, Coluzzi F, Rocco M, Marchetti P, Mura C, Simmaco M, Bourne PE, Preissner R, Banerjee P. PMID: 33425850; PMCID: PMC7786237.
      View in: PubMed   Mentions: 8  
    31. Evidence for treatment with estradiol for women with SARS-CoV-2 infection. BMC Med. 2020 11 25; 18(1):369. Seeland U, Coluzzi F, Simmaco M, Mura C, Bourne PE, Heiland M, Preissner R, Preissner S. PMID: 33234138; PMCID: PMC7685778.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansCells
    32. Ten simple rules for starting research in your late teens. PLoS Comput Biol. 2020 11; 16(11):e1008403. Mura C, Chalupa M, Newbury AM, Chalupa J, Bourne PE. PMID: 33211694; PMCID: PMC7676678.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    33. Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery. J Proteome Res. 2020 11 06; 19(11):4698-4705. Zhao Z, Bourne PE. PMID: 32946692.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCellsPHPublic Health
    34. Ten simple rules for researchers while in isolation from a pandemic. PLoS Comput Biol. 2020 06; 16(6):e1007946. Goh HH, Bourne PE. PMID: 32584810; PMCID: PMC7316224.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansPHPublic Health
    35. Revealing Acquired Resistance Mechanisms of Kinase-Targeted Drugs Using an on-the-Fly, Function-Site Interaction Fingerprint Approach. J Chem Theory Comput. 2020 May 12; 16(5):3152-3161. Zhao Z, Bourne PE. PMID: 32283024.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    36. Ten simple rules for more objective decision-making. PLoS Comput Biol. 2020 04; 16(4):e1007706. Fletcher AC, Wagner GA, Bourne PE. PMID: 32240159; PMCID: PMC7117647.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    37. Translational Health Disparities Research in a Data-Rich World. Health Equity. 2019; 3(1):588-600. Breen N, Berrigan D, Jackson JS, Wong DWS, Wood FB, Denny JC, Zhang X, Bourne PE. PMID: 31720554; PMCID: PMC6844128.
      View in: PubMed   Mentions: 15  
    38. The Urfold: Structural similarity just above the superfold level? Protein Sci. 2019 12; 28(12):2119-2126. Mura C, Veretnik S, Bourne PE. PMID: 31599042; PMCID: PMC6863707.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    39. Ten simple rules to aid in achieving a vision. PLoS Comput Biol. 2019 10; 15(10):e1007395. Bourne PE. PMID: 31622329; PMCID: PMC6797078.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    40. Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm. PLoS Comput Biol. 2019 04; 15(4):e1006842. Bliven SE, Lafita A, Rose PW, Capitani G, Prlic A, Bourne PE. PMID: 31009453; PMCID: PMC6504099.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    41. Natural language processing of symptoms documented in free-text narratives of electronic health records: a systematic review. J Am Med Inform Assoc. 2019 04 01; 26(4):364-379. Koleck TA, Dreisbach C, Bourne PE, Bakken S. PMID: 30726935; PMCID: PMC6657282.
      View in: PubMed   Mentions: 116     Fields:    Translation:Humans
    42. Addendum: The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2019 03 19; 6(1):6. Wilkinson MD, Dumontier M, Jan Aalbersberg I, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, Hoen PAC', Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B. PMID: 30890711; PMCID: PMC6427092.
      View in: PubMed   Mentions: 31     Fields:    
    43. A systematic review of natural language processing and text mining of symptoms from electronic patient-authored text data. Int J Med Inform. 2019 05; 125:37-46. Dreisbach C, Koleck TA, Bourne PE, Bakken S. PMID: 30914179; PMCID: PMC6438188.
      View in: PubMed   Mentions: 45     Fields:    Translation:Humans
    44. Ten Simple Rules for avoiding and resolving conflicts with your colleagues. PLoS Comput Biol. 2019 01; 15(1):e1006708. Lewitter F, Bourne PE, Attwood TK. PMID: 30657752; PMCID: PMC6338354.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    45. Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants. J Chem Inf Model. 2019 01 28; 59(1):453-462. Zhao Z, Xie L, Bourne PE. PMID: 30582689; PMCID: PMC6441332.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    46. One thousand simple rules. PLoS Comput Biol. 2018 12; 14(12):e1006670. Bourne PE, Lewitter F, Markel S, Papin JA. PMID: 30571692; PMCID: PMC6301566.
      View in: PubMed   Mentions: 3     Fields:    
    47. The Small β-Barrel Domain: A Survey-Based Structural Analysis. Structure. 2019 01 02; 27(1):6-26. Youkharibache P, Veretnik S, Li Q, Stanek KA, Mura C, Bourne PE. PMID: 30393050.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    48. Ten simple rules when considering retirement. PLoS Comput Biol. 2018 10; 14(10):e1006411. Bourne PE. PMID: 30286100; PMCID: PMC6171791.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    49. Structural biology meets data science: does anything change? Curr Opin Struct Biol. 2018 10; 52:95-102. Mura C, Draizen EJ, Bourne PE. PMID: 30267935.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    50. Cloud computing applications for biomedical science: A perspective. PLoS Comput Biol. 2018 06; 14(6):e1006144. Navale V, Bourne PE. PMID: 29902176; PMCID: PMC6002019.
      View in: PubMed   Mentions: 26     Fields:    Translation:Humans
    51. Progress with covalent small-molecule kinase inhibitors. Drug Discov Today. 2018 Mar; 23(3):727-735. Zhao Z, Bourne PE. PMID: 29337202.
      View in: PubMed   Mentions: 52     Fields:    Translation:Humans
    52. An evaluation of service use outcomes in a Recovery College. J Ment Health. 2018 Aug; 27(4):359-366. Bourne P, Meddings S, Whittington A. PMID: 29275749.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    53. Ten simple rules in considering a career in academia versus government. PLoS Comput Biol. 2017 Oct; 13(10):e1005729. Bourne PE. PMID: 28981499; PMCID: PMC5628781.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    54. Developing international open science collaborations: Funder reflections on the Open Science Prize. PLoS Biol. 2017 Aug; 15(8):e2002617. Kittrie E, Atienza AA, Kiley R, Carr D, MacFarlane A, Pai V, Couch J, Bajkowski J, Bonner JF, Mietchen D, Bourne PE. PMID: 28763440; PMCID: PMC5538631.
      View in: PubMed   Mentions: 1     Fields:    
    55. Building the biomedical data science workforce. PLoS Biol. 2017 Jul; 15(7):e2003082. Dunn MC, Bourne PE. PMID: 28715407; PMCID: PMC5517135.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    56. BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. Bioinformatics. 2017 Jul 01; 33(13):2047-2049. Gao J, Prlic A, Bi C, Bluhm WF, Dimitropoulos D, Xu D, Bourne PE, Rose PW. PMID: 28334105; PMCID: PMC5870676.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    57. 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. Zhao Z, Xie L, Bourne PE. PMID: 28628649; PMCID: PMC5476283.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    58. Ten simple rules to consider regarding preprint submission. PLoS Comput Biol. 2017 May; 13(5):e1005473. Bourne PE, Polka JK, Vale RD, Kiley R. PMID: 28472041; PMCID: PMC5417409.
      View in: PubMed   Mentions: 25     Fields:    
    59. Big Data Science: Opportunities and Challenges to Address Minority Health and Health Disparities in the 21st Century. Ethn Dis. 2017; 27(2):95-106. Zhang X, Pérez-Stable EJ, Bourne PE, Peprah E, Duru OK, Breen N, Berrigan D, Wood F, Jackson JS, Wong DWS, Denny J. PMID: 28439179; PMCID: PMC5398183.
      View in: PubMed   Mentions: 57     Fields:    Translation:Humans
    60. Should biomedical research be like Airbnb? PLoS Biol. 2017 04; 15(4):e2001818. Bonazzi VR, Bourne PE. PMID: 28388615; PMCID: PMC5384655.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    61. Determining Cysteines Available for Covalent Inhibition Across the Human Kinome. J Med Chem. 2017 04 13; 60(7):2879-2889. Zhao Z, Liu Q, Bliven S, Xie L, Bourne PE. PMID: 28326775; PMCID: PMC5493210.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    62. Life is three-dimensional, and it begins with molecules. PLoS Biol. 2017 03; 15(3):e2002041. Bourne PE. PMID: 28301467; PMCID: PMC5354241.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    63. Harnessing Big Data for Systems Pharmacology. Annu Rev Pharmacol Toxicol. 2017 01 06; 57:245-262. Xie L, Draizen EJ, Bourne PE. PMID: 27814027; PMCID: PMC5626567.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimals
    64. How open science helps researchers succeed. Elife. 2016 07 07; 5. McKiernan EC, Bourne PE, Brown CT, Buck S, Kenall A, Lin J, McDougall D, Nosek BA, Ram K, Soderberg CK, Spies JR, Thaney K, Updegrove A, Woo KH, Yarkoni T. PMID: 27387362; PMCID: PMC4973366.
      View in: PubMed   Mentions: 119     Fields:    Translation:Humans
    65. SCIENTIFIC COMMUNITY. Preprints for the life sciences. Science. 2016 May 20; 352(6288):899-901. Berg JM, Bhalla N, Bourne PE, Chalfie M, Drubin DG, Fraser JS, Greider CW, Hendricks M, Jones C, Kiley R, King S, Kirschner MW, Krumholz HM, Lehmann R, Leptin M, Pulverer B, Rosenzweig B, Spiro JE, Stebbins M, Strasser C, Swaminathan S, Turner P, Vale RD, VijayRaghavan K, Wolberger C. PMID: 27199406.
      View in: PubMed   Mentions: 36     Fields:    
    66. 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. Zhao Z, Xie L, Xie L, Bourne PE. PMID: 26929980; PMCID: PMC4865454.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    67. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016 Mar 15; 3:160018. Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJ, Groth P, Goble C, Grethe JS, Heringa J, 't Hoen PA, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B. PMID: 26978244; PMCID: PMC4792175.
      View in: PubMed   Mentions: 2922     Fields:    
    68. Systems biology of the structural proteome. BMC Syst Biol. 2016 Mar 11; 10:26. Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO. PMID: 26969117; PMCID: PMC4787049.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    69. Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. BMC Bioinformatics. 2016 Feb 18; 17:90. Zhao Z, Martin C, Fan R, Bourne PE, Xie L. PMID: 26887654; PMCID: PMC4757998.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    70. Perspective: Sustaining the big-data ecosystem. Nature. 2015 Nov 05; 527(7576):S16-7. Bourne PE, Lorsch JR, Green ED. PMID: 26536219.
      View in: PubMed   Mentions: 45     Fields:    Translation:Humans
    71. The NIH Big Data to Knowledge (BD2K) initiative. J Am Med Inform Assoc. 2015 Nov; 22(6):1114. Bourne PE, Bonazzi V, Dunn M, Green ED, Guyer M, Komatsoulis G, Larkin J, Russell B. PMID: 26555016; PMCID: PMC5009910.
      View in: PubMed   Mentions: 35     Fields:    Translation:Humans
    72. Developing multi-target therapeutics to fine-tune the evolutionary dynamics of the cancer ecosystem. Front Pharmacol. 2015; 6:209. Xie L, Bourne PE. PMID: 26441664; PMCID: PMC4585080.
      View in: PubMed   Mentions: 22  
    73. Let's Make Gender Diversity in Data Science a Priority Right from the Start. PLoS Biol. 2015 Jul; 13(7):e1002206. Berman FD, Bourne PE. PMID: 26213996; PMCID: PMC4516301.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    74. 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. Tsai LC, Xie L, Dore K, Xie L, Del Rio JC, King CC, Martinez-Ariza G, Hulme C, Malinow R, Bourne PE, Newton AC. PMID: 26187466; PMCID: PMC4571940.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimalsCells
    75. Toward effective software solutions for big biology. Nat Biotechnol. 2015 Jul; 33(7):686-7. Prins P, de Ligt J, Tarasov A, Jansen RC, Cuppen E, Bourne PE. PMID: 26154002.
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    76. Ten Years of PLoS Computational Biology: A Decade of Appreciation and Innovation. PLoS Comput Biol. 2015 Jun; 11(6):e1004317. Bourne PE, Brenner SE, Eisen MB. PMID: 26107720; PMCID: PMC4479580.
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    77. DOIs for DICOM raw images: enabling science reproducibility. Radiology. 2015 Apr; 275(1):3-4. Bourne PE. PMID: 25799330; PMCID: PMC4455617.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    78. Ten simple rules for lifelong learning, according to Hamming. PLoS Comput Biol. 2015 Feb; 11(2):e1004020. Erren TC, Slanger TE, Groß JV, Bourne PE, Cullen P. PMID: 25719205; PMCID: PMC4342007.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    79. Confronting the ethical challenges of big data in public health. PLoS Comput Biol. 2015 Feb; 11(2):e1004073. Bourne PE. PMID: 25664660; PMCID: PMC4321831.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansPHPublic Health
    80. Detection of circular permutations within protein structures using CE-CP. Bioinformatics. 2015 Apr 15; 31(8):1316-8. Bliven SE, Bourne PE, Prlic A. PMID: 25505094; PMCID: PMC4393524.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    81. Achievements and challenges in structural bioinformatics and computational biophysics. Bioinformatics. 2015 Jan 01; 31(1):146-50. Samish I, Bourne PE, Najmanovich RJ. PMID: 25488929; PMCID: PMC4271151.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    82. 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. 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 PE, Burley SK. PMID: 25428375; PMCID: PMC4383988.
      View in: PubMed   Mentions: 244     Fields:    Translation:Cells
    83. Ten simple rules for writing a PLOS ten simple rules article. PLoS Comput Biol. 2014 Oct; 10(10):e1003858. Dashnow H, Lonsdale A, Bourne PE. PMID: 25340653; PMCID: PMC4207461.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    84. MixGF: spectral probabilities for mixture spectra from more than one peptide. Mol Cell Proteomics. 2014 Dec; 13(12):3688-97. Wang J, Bourne PE, Bandeira N. PMID: 25225354; PMCID: PMC4256515.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimals
    85. Ten simple rules for better figures. PLoS Comput Biol. 2014 Sep; 10(9):e1003833. Rougier NP, Droettboom M, Bourne PE. PMID: 25210732; PMCID: PMC4161295.
      View in: PubMed   Mentions: 29     Fields:    Translation:Humans
    86. 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. Quinn GB, Bi C, Christie CH, Pang K, Prlic A, Nakane T, Zardecki C, Voigt M, Berman HM, Bourne PE, Rose PW. PMID: 25183487; PMCID: PMC4271143.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    87. Ten simple rules for approaching a new job. PLoS Comput Biol. 2014 Jun; 10(6):e1003660. Bourne PE. PMID: 24967974; PMCID: PMC4072506.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    88. Towards structural systems pharmacology to study complex diseases and personalized medicine. PLoS Comput Biol. 2014 May; 10(5):e1003554. Xie L, Ge X, Tan H, Xie L, Zhang Y, Hart T, Yang X, Bourne PE. PMID: 24830652; PMCID: PMC4022462.
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    89. Systematic detection of internal symmetry in proteins using CE-Symm. J Mol Biol. 2014 May 29; 426(11):2255-68. Myers-Turnbull D, Bliven SE, Rose PW, Aziz ZK, Youkharibache P, Bourne PE, Prlic A. PMID: 24681267; PMCID: PMC4456030.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    90. What Big Data means to me. J Am Med Inform Assoc. 2014 Mar-Apr; 21(2):194. Bourne PE. PMID: 24509599; PMCID: PMC3932474.
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    91. Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. Mol Cell Proteomics. 2014 Apr; 13(4):1128-36. Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. PMID: 24493012; PMCID: PMC3977190.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    92. A turn-key approach for large-scale identification of complex posttranslational modifications. J Proteome Res. 2014 Mar 07; 13(3):1190-9. Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. PMID: 24437954; PMCID: PMC3993922.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    93. Anti-infectious drug repurposing using an integrated chemical genomics and structural systems biology approach. Pac Symp Biocomput. 2014; 136-47. Ng C, Hauptman R, Zhang Y, Bourne PE, Xie L. PMID: 24297541; PMCID: PMC6322395.
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    94. Quantifying reproducibility in computational biology: the case of the tuberculosis drugome. PLoS One. 2013; 8(11):e80278. Garijo D, Kinnings S, Xie L, Xie L, Zhang Y, Bourne PE, Gil Y. PMID: 24312207; PMCID: PMC3842296.
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    95. Learning how to run a lab: interviews with principal investigators. PLoS Comput Biol. 2013; 9(11):e1003349. Alexandrov T, Bourne PE. PMID: 24244147; PMCID: PMC3820502.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    96. Antibacterial mechanisms identified through structural systems pharmacology. BMC Syst Biol. 2013 Oct 10; 7:102. Chang RL, Xie L, Bourne PE, Palsson BO. PMID: 24112686; PMCID: PMC3853765.
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    97. Ten simple rules for cultivating open science and collaborative R&D. PLoS Comput Biol. 2013; 9(9):e1003244. Masum H, Rao A, Good BM, Todd MH, Edwards AM, Chan L, Bunin BA, Su AI, Thomas Z, Bourne PE. PMID: 24086123; PMCID: PMC3784487.
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    98. Biodiversity data should be published, cited, and peer reviewed. Trends Ecol Evol. 2013 Aug; 28(8):454-61. Costello MJ, Michener WK, Gahegan M, Zhang ZQ, Bourne PE. PMID: 23756105.
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    99. 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. Xie L, Ng C, Ali T, Valencia R, Ferreira BL, Xue V, Tanweer M, Zhou D, Haddad GG, Bourne PE, Xie L. PMID: 23819581; PMCID: PMC3665574.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    100. The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res. 2013 Jan; 41(Database issue):D475-82. 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 PE. PMID: 23193259; PMCID: PMC3531086.
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    101. Communication of scientific information: is it time to reassess? Clin Chem. 2013 Apr; 59(4):604-11. Rifai N, Sack J, Keller MA, Acharya A, Bourne PE, Rossner M, Wills S. PMID: 23160064.
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    102. Ten simple rules to protect your intellectual property. PLoS Comput Biol. 2012; 8(11):e1002766. Jolly M, Fletcher AC, Bourne PE. PMID: 23144604; PMCID: PMC3493459.
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    103. Ten simple rules to commercialize scientific research. PLoS Comput Biol. 2012; 8(9):e1002712. Fletcher AC, Bourne PE. PMID: 23028299; PMCID: PMC3459878.
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    104. BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics. 2012 Oct 15; 28(20):2693-5. 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 PE, Willis S. PMID: 22877863; PMCID: PMC3467744.
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    105. Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence. Int J Antimicrob Agents. 2012 Sep; 40(3):246-51. Ho Sui SJ, Lo R, Fernandes AR, Caulfield MD, Lerman JA, Xie L, Bourne PE, Baillie DL, Brinkman FS. PMID: 22819149; PMCID: PMC5511546.
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    106. Immune epitope database analysis resource. Nucleic Acids Res. 2012 Jul; 40(Web Server issue):W525-30. Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne PE, Nielsen M, Peters B. PMID: 22610854; PMCID: PMC3394288.
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    107. Topic pages: PLoS Computational Biology meets Wikipedia. PLoS Comput Biol. 2012; 8(3):e1002446. Wodak SJ, Mietchen D, Collings AM, Russell RB, Bourne PE. PMID: 22479174; PMCID: PMC3315447.
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    108. Ten simple rules for starting a company. PLoS Comput Biol. 2012; 8(3):e1002439. Fletcher AC, Bourne PE. PMID: 22479171; PMCID: PMC3315446.
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    109. Receptor databases and computational websites for ligand binding. Methods Mol Biol. 2012; 897:1-13. Rana BK, Bourne PE, Insel PA. PMID: 22674158.
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    110. SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1113-7. Hecker N, Ahmed J, von Eichborn J, Dunkel M, Macha K, Eckert A, Gilson MK, Bourne PE, Preissner R. PMID: 22067455; PMCID: PMC3245174.
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    111. Teaching bioinformatics at the secondary school level. PLoS Comput Biol. 2011 Oct; 7(10):e1002242. Lewitter F, Bourne PE. PMID: 22046116; PMCID: PMC3203059.
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    112. Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annu Rev Pharmacol Toxicol. 2012; 52:361-79. Xie L, Xie L, Kinnings SL, Bourne PE. PMID: 22017683.
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    113. Peptide identification by database search of mixture tandem mass spectra. Mol Cell Proteomics. 2011 Dec; 10(12):M111.010017. Wang J, Bourne PE, Bandeira N. PMID: 21862760; PMCID: PMC3237077.
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    114. Coarse-graining the electrostatic potential via distributed multipole expansions. Comput Phys Commun. 2011 Jul 01; 182(7):1455-1462. Gramada A, Bourne PE. PMID: 21572587; PMCID: PMC3090642.
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    115. Ten simple rules for building and maintaining a scientific reputation. PLoS Comput Biol. 2011 Jun; 7(6):e1002108. Bourne PE, Barbour V. PMID: 21738465; PMCID: PMC3127799.
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    116. 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. Xie L, Evangelidis T, Xie L, Bourne PE. PMID: 21552547; PMCID: PMC3084228.
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    117. 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. Kinnings SL, Liu N, Tonge PJ, Jackson RM, Xie L, Bourne PE. PMID: 21526828; PMCID: PMC3186856.
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    118. Cobweb: a Java applet for network exploration and visualisation. Bioinformatics. 2011 Jun 15; 27(12):1725-6. von Eichborn J, Bourne PE, Preissner R. PMID: 21486937.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    119. Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. Database (Oxford). 2011; 2011:bar003. Bluhm WF, Beran B, Bi C, Dimitropoulos D, Prlic A, Quinn GB, Rose PW, Shah C, Young J, Yukich B, Berman HM, Bourne PE. PMID: 21382834; PMCID: PMC3056270.
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    120. 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. Valas RE, Bourne PE. PMID: 21356104; PMCID: PMC3056875.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    121. 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. Kinnings SL, Liu N, Tonge PJ, Jackson RM, Xie L, Bourne PE. PMID: 21291174; PMCID: PMC3076728.
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    122. 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. Kuo GM, Ma JD, Lee KC, Halpert JR, Bourne PE, Ganiats TG, Taylor P. PMID: 21332308.
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    123. Structure-based systems biology for analyzing off-target binding. Curr Opin Struct Biol. 2011 Apr; 21(2):189-99. Xie L, Xie L, Bourne PE. PMID: 21292475; PMCID: PMC3070778.
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    124. A Review of 2010 for PLoS Computational Biology. PLoS Comput Biol. 2011 Jan 27; 7(1):e1002003. Dickin R, Marden C, Collings AM, Nussinov R, Bourne PE. PMID: 21298077; PMCID: PMC3029231.
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    125. Ten simple rules for getting ahead as a computational biologist in Academia. PLoS Comput Biol. 2011 Jan 06; 7(1):e1002001. Bourne PE. PMID: 21253560; PMCID: PMC3017106.
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    126. PROMISCUOUS: a database for network-based drug-repositioning. Nucleic Acids Res. 2011 Jan; 39(Database issue):D1060-6. von Eichborn J, Murgueitio MS, Dunkel M, Koerner S, Bourne PE, Preissner R. PMID: 21071407; PMCID: PMC3013657.
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    127. The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol. 2010 Nov 04; 6(11):e1000976. Kinnings SL, Xie L, Fung KH, Jackson RM, Xie L, Bourne PE. PMID: 21079673; PMCID: PMC2973814.
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    128. The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 2011 Jan; 39(Database issue):D392-401. 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 PE. PMID: 21036868; PMCID: PMC3013649.
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    129. IEDB-3D: structural data within the immune epitope database. Nucleic Acids Res. 2011 Jan; 39(Database issue):D1164-70. Ponomarenko J, Papangelopoulos N, Zajonc DM, Peters B, Sette A, Bourne PE. PMID: 21030437; PMCID: PMC3013771.
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    130. Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics. 2010 Dec 01; 26(23):2983-5. Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE. PMID: 20937596; PMCID: PMC3003546.
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    131. 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. Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ. PMID: 20957118; PMCID: PMC2950675.
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    132. Save the tree of life or get lost in the woods. Biol Direct. 2010 Jul 01; 5:44. Valas RE, Bourne PE. PMID: 20594329; PMCID: PMC2910001.
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    133. 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. Alden K, Veretnik S, Bourne PE. PMID: 20529369; PMCID: PMC2897830.
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    134. What do I want from the publisher of the future? PLoS Comput Biol. 2010 May 27; 6(5):e1000787. Bourne PE. PMID: 20523744; PMCID: PMC2877727.
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    135. 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. Dupont CL, Butcher A, Valas RE, Bourne PE, Caetano-Anollés G. PMID: 20498051; PMCID: PMC2890839.
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    136. 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. Ren J, Xie L, Li WW, Bourne PE. PMID: 20484373; PMCID: PMC2896174.
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    137. Integration of open access literature into the RCSB Protein Data Bank using BioLit. BMC Bioinformatics. 2010 Apr 29; 11:220. Prlic A, Martinez MA, Dimitropoulos D, Beran B, Yukich BT, Rose PW, Bourne PE, Fink JL. PMID: 20429930; PMCID: PMC2880030.
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    138. PLoS Computational Biology conference postcards from PSB 2010. PLoS Comput Biol. 2010 Apr 29; 6(4):e1000746. Datta RS, Lux MW, Bourne PE. PMID: 20442855; PMCID: PMC2861683.
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    139. Will widgets and semantic tagging change computational biology? PLoS Comput Biol. 2010 Feb 26; 6(2):e1000673. Bourne PE, Beran B, Bi C, Bluhm W, Dunbrack R, Prlic A, Quinn G, Rose P, Shah R, Tao W, Weitzner B, Yukich B. PMID: 20195550; PMCID: PMC2829027.
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    140. Word add-in for ontology recognition: semantic enrichment of scientific literature. BMC Bioinformatics. 2010 Feb 24; 11:103. Fink JL, Fernicola P, Chandran R, Parastatidis S, Wade A, Naim O, Quinn GB, Bourne PE. PMID: 20181245; PMCID: PMC2837026.
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    141. Limitations of Ab initio predictions of peptide binding to MHC class II molecules. PLoS One. 2010 Feb 17; 5(2):e9272. Zhang H, Wang P, Papangelopoulos N, Xu Y, Sette A, Bourne PE, Lund O, Ponomarenko J, Nielsen M, Peters B. PMID: 20174654; PMCID: PMC2822856.
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    142. A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol. 2010 Jan 22; 6(1):e1000648. Durrant JD, Amaro RE, Xie L, Urbaniak MD, Ferguson MA, Haapalainen A, Chen Z, Di Guilmi AM, Wunder F, Bourne PE, McCammon JA. PMID: 20098496; PMCID: PMC2799658.
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    143. The evolutionary history of protein domains viewed by species phylogeny. PLoS One. 2009 Dec 21; 4(12):e8378. Yang S, Bourne PE. PMID: 20041107; PMCID: PMC2794708.
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    144. Ten simple rules for chairing a scientific session. PLoS Comput Biol. 2009 Sep; 5(9):e1000517. Bateman A, Bourne PE. PMID: 19779547; PMCID: PMC2738972.
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    145. Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life. Biol Direct. 2009 Aug 25; 4:30. Valas RE, Bourne PE. PMID: 19706177; PMCID: PMC3224940.
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    146. 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. Kinnings SL, Liu N, Buchmeier N, Tonge PJ, Xie L, Bourne PE. PMID: 19578428; PMCID: PMC2699117.
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    147. 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. Xie L, Xie L, Bourne PE. PMID: 19478004; PMCID: PMC2687974.
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    148. 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. Xie L, Li J, Xie L, Bourne PE. PMID: 19436720; PMCID: PMC2676506.
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    149. Nothing about protein structure classification makes sense except in the light of evolution. Curr Opin Struct Biol. 2009 Jun; 19(3):329-34. Valas RE, Yang S, Bourne PE. PMID: 19394812; PMCID: PMC2696554.
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    150. Ten simple rules to combine teaching and research. PLoS Comput Biol. 2009 Apr; 5(4):e1000358. Vicens Q, Bourne PE. PMID: 19390598; PMCID: PMC2661017.
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    151. Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome. PLoS Comput Biol. 2009 Mar; 5(3):e1000315. Veretnik S, Wills C, Youkharibache P, Valas RE, Bourne PE. PMID: 19282982; PMCID: PMC2650416.
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    152. A Review of 2008 for PLoS Computational Biology. PLoS Comput Biol. 2009 Jan; 5(1):e1000275. Browne E, Dickin R, Bourne PE. PMID: 19180176; PMCID: PMC2613517.
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    153. I am not a scientist, I am a number. PLoS Comput Biol. 2008 Dec; 4(12):e1000247. Bourne PE, Fink JL. PMID: 19112480; PMCID: PMC2586848.
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    154. ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics. 2008 Dec 02; 9:514. Ponomarenko J, Bui HH, Li W, Fusseder N, Bourne PE, Sette A, Peters B. PMID: 19055730; PMCID: PMC2607291.
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    155. 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. Gramada A, Bourne PE. PMID: 19256962.
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    156. Changes to NIH grant system may backfire. Science. 2008 Nov 21; 322(5905):1187-8. Karp PD, Sherlock G, Gerlt JA, Sim I, Paulsen I, Babbitt PC, Laderoute K, Hunter L, Sternberg P, Wooley J, Bourne PE. PMID: 19023064.
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    157. Computational biology resources lack persistence and usability. PLoS Comput Biol. 2008 Jul 18; 4(7):e1000136. Veretnik S, Fink JL, Bourne PE. PMID: 18636105; PMCID: PMC2443418.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    158. Ten simple rules for organizing a scientific meeting. PLoS Comput Biol. 2008 Jun 27; 4(6):e1000080. Corpas M, Gehlenborg N, Janga SC, Bourne PE. PMID: 18584020; PMCID: PMC2367436.
      View in: PubMed   Mentions: 17     Fields:    
    159. Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res. 2008 Jul 01; 36(Web Server issue):W513-8. Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B. PMID: 18515843; PMCID: PMC2447801.
      View in: PubMed   Mentions: 161     Fields:    
    160. BioLit: integrating biological literature with databases. Nucleic Acids Res. 2008 Jul 01; 36(Web Server issue):W385-9. Fink JL, Kushch S, Williams PR, Bourne PE. PMID: 18515836; PMCID: PMC2447735.
      View in: PubMed   Mentions: 15     Fields:    
    161. Superimpose: a 3D structural superposition server. Nucleic Acids Res. 2008 Jul 01; 36(Web Server issue):W47-54. Bauer RA, Bourne PE, Formella A, Frömmel C, Gille C, Goede A, Guerler A, Hoppe A, Knapp EW, Pöschel T, Wittig B, Ziegler V, Preissner R. PMID: 18492720; PMCID: PMC2447795.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    162. Rethinking proteasome evolution: two novel bacterial proteasomes. J Mol Evol. 2008 May; 66(5):494-504. Valas RE, Bourne PE. PMID: 18389302; PMCID: PMC3235984.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    163. 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. Xie L, Bourne PE. PMID: 18385384; PMCID: PMC2291117.
      View in: PubMed   Mentions: 120     Fields:    Translation:Cells
    164. Open access: taking full advantage of the content. PLoS Comput Biol. 2008 Mar 28; 4(3):e1000037. Bourne PE, Fink JL, Gerstein M. PMID: 18369428; PMCID: PMC2275780.
      View in: PubMed   Mentions: 8     Fields:    
    165. Analysis of the human kinome using methods including fold recognition reveals two novel kinases. PLoS One. 2008 Feb 13; 3(2):e1597. Briedis KM, Starr A, Bourne PE. PMID: 18270584; PMCID: PMC2223070.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    166. Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pac Symp Biocomput. 2008; 640-51. Caporaso JG, Deshpande N, Fink JL, Bourne PE, Cohen KB, Hunter L. PMID: 18229722; PMCID: PMC2517250.
      View in: PubMed   Mentions: 19     Fields:    
    167. TRANSLATING BIOLOGY: TEXT MINING TOOLS THAT WORK. Pac Symp Biocomput. 2008 Jan 01; 13:551-555. Cohen KB, Yu H, Bourne PE, Hirschman L. PMID: 20827444; PMCID: PMC2934913.
      View in: PubMed   Mentions: 6     Fields:    
    168. Ten simple rules for graduate students. PLoS Comput Biol. 2007 Nov; 3(11):e229. Gu J, Bourne PE. PMID: 18052537; PMCID: PMC2098857.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    169. SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res. 2008 Jan; 36(Database issue):D919-22. 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 PE, Bork P, Preissner R. PMID: 17942422; PMCID: PMC2238858.
      View in: PubMed   Mentions: 234     Fields:    
    170. Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol. 2007 Oct 02; 7:64. Ponomarenko JV, Bourne PE. PMID: 17910770; PMCID: PMC2174481.
      View in: PubMed   Mentions: 94     Fields:    Translation:Cells
    171. Ten simple rules for doing your best research, according to Hamming. PLoS Comput Biol. 2007 Oct; 3(10):1839-40. Erren TC, Cullen P, Erren M, Bourne PE. PMID: 17967054; PMCID: PMC2041981.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    172. In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comput Biol. 2007 Nov; 3(11):e217. Xie L, Wang J, Bourne PE. PMID: 18052534; PMCID: PMC2098847.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    173. Developing computational biology. PLoS Comput Biol. 2007 Sep; 3(9):1669. Bourne PE, Brenner SE. PMID: 17907793; PMCID: PMC1994973.
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    174. Con-Struct Map: a comparative contact map analysis tool. Bioinformatics. 2007 Sep 15; 23(18):2491-2. Chung JL, Beaver JE, Scheeff ED, Bourne PE. PMID: 17709340.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    175. Realism about PDB. Nat Biotechnol. 2007 Aug; 25(8):845-6; author reply 846. Berman HM, Henrick K, Nakamura H, Markley J, Bourne PE, Westbrook J. PMID: 17687352.
      View in: PubMed   Mentions: 4     Fields:    
    176. High-throughput identification of interacting protein-protein binding sites. BMC Bioinformatics. 2007 Jun 27; 8:223. Chung JL, Wang W, Bourne PE. PMID: 17594507; PMCID: PMC1925121.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    177. 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. Xie L, Bourne PE. PMID: 17570152; PMCID: PMC1892088.
      View in: PubMed   Mentions: 61     Fields:    Translation:Cells
    178. Ten simple rules for a good poster presentation. PLoS Comput Biol. 2007 May; 3(5):e102. Erren TC, Bourne PE. PMID: 17530921; PMCID: PMC1876493.
      View in: PubMed   Mentions: 16     Fields:    
    179. Ten simple rules for making good oral presentations. PLoS Comput Biol. 2007 Apr 27; 3(4):e77. Bourne PE. PMID: 17500596; PMCID: PMC1857815.
      View in: PubMed   Mentions: 26     Fields:    
    180. Ten simple rules for a successful collaboration. PLoS Comput Biol. 2007 Mar 30; 3(3):e44. Vicens Q, Bourne PE. PMID: 17397252; PMCID: PMC1847992.
      View in: PubMed   Mentions: 39     Fields:    
    181. 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. Beaver JE, Bourne PE, Ponomarenko JV. PMID: 17313688; PMCID: PMC1810240.
      View in: PubMed   Mentions: 22  
    182. Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2. BMC Bioinformatics. 2007 Feb 07; 8:45. Gu J, Bourne PE. PMID: 17286863; PMCID: PMC1800904.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    183. Ten simple rules for selecting a postdoctoral position. PLoS Comput Biol. 2006 Nov 24; 2(11):e121. Bourne PE, Friedberg I. PMID: 17121457; PMCID: PMC1664706.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    184. 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. Guda P, Bourne PE, Guda C. PMID: 17126810.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    185. 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. Dupont CL, Yang S, Palenik B, Bourne PE. PMID: 17098870; PMCID: PMC1635651.
      View in: PubMed   Mentions: 78     Fields:    Translation:AnimalsCells
    186. Biocurators: contributors to the world of science. PLoS Comput Biol. 2006 Oct 27; 2(10):e142. Bourne PE, McEntyre J. PMID: 17411327; PMCID: PMC1626157.
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    187. Ten simple rules for reviewers. PLoS Comput Biol. 2006 Sep 29; 2(9):e110. Bourne PE, Korngreen A. PMID: 17009861; PMCID: PMC1584310.
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    188. Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics. 2006 Sep 14; 7:410. Scheeff ED, Bourne PE. PMID: 16970830; PMCID: PMC1622756.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    189. Outcome of a workshop on archiving structural models of biological macromolecules. Structure. 2006 Aug; 14(8):1211-7. Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, 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. PMID: 16955948.
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    190. Curation of complex, context-dependent immunological data. BMC Bioinformatics. 2006 Jul 12; 7:341. Vita R, Vaughan K, Zarebski L, Salimi N, Fleri W, Grey H, Sathiamurthy M, Mokili J, Bui HH, Bourne PE, Ponomarenko J, de Castro R, Chan RK, Sidney J, Wilson SS, Stewart S, Way S, Peters B, Sette A. PMID: 16836764; PMCID: PMC1534061.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimals
    191. Partitioning protein structures into domains: why is it so difficult? J Mol Biol. 2006 Aug 18; 361(3):562-90. Holland TA, Veretnik S, Shindyalov IN, Bourne PE. PMID: 16863650.
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    192. Wiggle-predicting functionally flexible regions from primary sequence. PLoS Comput Biol. 2006 Jul 14; 2(7):e90. Gu J, Gribskov M, Bourne PE. PMID: 16839194; PMCID: PMC1500818.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    193. Multipolar representation of protein structure. BMC Bioinformatics. 2006 May 04; 7:242. Gramada A, Bourne PE. PMID: 16674828; PMCID: PMC1483839.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    194. Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins. 2006 Mar 15; 62(3):630-40. Chung JL, Wang W, Bourne PE. PMID: 16329107.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    195. Ten simple rules for getting grants. PLoS Comput Biol. 2006 Feb; 2(2):e12. Bourne PE, Chalupa LM. PMID: 16501664; PMCID: PMC1378105.
      View in: PubMed   Mentions: 18     Fields:    
    196. ISMB 2006. PLoS Comput Biol. 2006 Feb; 2(2):e11. Neshich G, Bourne PE, Brunak S. PMID: 16758006; PMCID: PMC1378106.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    197. The RCSB PDB information portal for structural genomics. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D302-5. Kouranov A, Xie L, de la Cruz J, Chen L, Westbrook J, Bourne PE, Berman HM. PMID: 16381872; PMCID: PMC1347482.
      View in: PubMed   Mentions: 154     Fields:    Translation:HumansCells
    198. Structural evolution of the protein kinase-like superfamily. PLoS Comput Biol. 2005 Oct; 1(5):e49. Scheeff ED, Bourne PE. PMID: 16244704; PMCID: PMC1261164.
      View in: PubMed   Mentions: 127     Fields:    Translation:HumansAnimalsCells
    199. Ten simple rules for getting published. PLoS Comput Biol. 2005 Oct; 1(5):e57. Bourne PE. PMID: 16261197; PMCID: PMC1274296.
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    200. 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. Sathiamurthy M, Peters B, Bui HH, Sidney J, Mokili J, Wilson SS, Fleri W, McGuinness DL, Bourne PE, Sette A. PMID: 16305755; PMCID: PMC1287064.
      View in: PubMed   Mentions: 19  
    201. Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput Biol. 2005 Aug; 1(3):e31. Xie L, Bourne PE. PMID: 16118666; PMCID: PMC1188274.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    202. PLoS Computational Biology: a new community journal. PLoS Comput Biol. 2005 Jun; 1(1):e4. Bourne PE, Brenner SE, Eisen MB. PMID: 16103905; PMCID: PMC1183510.
      View in: PubMed   Mentions: 2     Fields:    
    203. Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology. Proteins. 2005 Mar 01; 58(4):855-65. Ponomarenko JV, Bourne PE, Shindyalov IN. PMID: 15645518.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    204. The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. BMC Bioinformatics. 2005 Feb 06; 6:21. Moreland JL, Gramada A, Buzko OV, Zhang Q, Bourne PE. PMID: 15694009; PMCID: PMC548701.
      View in: PubMed   Mentions: 102     Fields:    Translation:HumansCells
    205. Phylogeny determined by protein domain content. Proc Natl Acad Sci U S A. 2005 Jan 11; 102(2):373-8. Yang S, Doolittle RF, Bourne PE. PMID: 15630082; PMCID: PMC540256.
      View in: PubMed   Mentions: 99     Fields:    Translation:AnimalsCells
    206. 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. 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 PE. PMID: 15608185; PMCID: PMC540011.
      View in: PubMed   Mentions: 146     Fields:    Translation:Cells
    207. Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure. Pac Symp Biocomput. 2005; 319-21. Babbitt PC, Bourne PE, Mooney SD. PMID: 15759637.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    208. CE-MC: a multiple protein structure alignment server. Nucleic Acids Res. 2004 Jul 01; 32(Web Server issue):W100-3. Guda C, Lu S, Scheeff ED, Bourne PE, Shindyalov IN. PMID: 15215359; PMCID: PMC441602.
      View in: PubMed   Mentions: 46     Fields:    Translation:Cells
    209. Toward consistent assignment of structural domains in proteins. J Mol Biol. 2004 Jun 04; 339(3):647-78. Veretnik S, Bourne PE, Alexandrov NN, Shindyalov IN. PMID: 15147847.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    210. A case study of high-throughput biological data processing on parallel platforms. Bioinformatics. 2004 Aug 12; 20(12):1940-7. Pekurovsky D, Shindyalov IN, Bourne PE. PMID: 15044237.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    211. 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. Krebs WG, Bourne PE. PMID: 15272433.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    212. The Protein Data Bank and lessons in data management. Brief Bioinform. 2004 Mar; 5(1):23-30. Bourne PE, Westbrook J, Berman HM. PMID: 15153303.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    213. Statistically rigorous automated protein annotation. Bioinformatics. 2004 May 01; 20(7):1066-73. Krebs WG, Bourne PE. PMID: 14764575.
      View in: PubMed   Mentions: 5     Fields:    
    214. A new scoring function and associated statistical significance for structure alignment by CE. J Comput Biol. 2004; 11(5):787-99. Jia Y, Dewey TG, Shindyalov IN, Bourne PE. PMID: 15700402.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    215. The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D223-5. Bourne PE, 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. PMID: 14681399; PMCID: PMC308830.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansAnimals
    216. The status of structural genomics defined through the analysis of current targets and structures. Pac Symp Biocomput. 2004; 375-86. Bourne PE, Allerston CK, Krebs W, Li W, Shindyalov IN, Godzik A, Friedberg I, Liu T, Wild D, Hwang S, Ghahramani Z, Chen L, Westbrook J. PMID: 14992518.
      View in: PubMed   Mentions: 3     Fields:    
    217. A comparative proteomics resource: proteins of Arabidopsis thaliana. Genome Biol. 2003; 4(8):R51. Li WW, Quinn GB, Alexandrov NN, Bourne PE, Shindyalov IN. PMID: 12914659; PMCID: PMC193643.
      View in: PubMed   Mentions: 6     Fields:    Translation:Animals
    218. The apoptosis database. Cell Death Differ. 2003 Jun; 10(6):621-33. Doctor KS, Reed JC, Godzik A, Bourne PE. PMID: 12761571.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    219. BioEditor-simplifying macromolecular structure annotation. Bioinformatics. 2003 May 01; 19(7):897-8. Yang P, Craig PA, Goodsell D, Bourne PE. PMID: 12724304.
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    220. Free access to publicly funded databases is vital. Nature. 2003 Feb 20; 421(6925):786. Bourne PE. PMID: 12594481.
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    221. Other structure-based databases. Methods Biochem Anal. 2003; 44:217-36. Weissig H, Bourne PE. PMID: 12647388.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    222. Protein structure evolution and the SCOP database. Methods Biochem Anal. 2003; 44:239-48. Reedy BV, Bourne PE. PMID: 12647389.
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    223. CASP and CAFASP experiments and their findings. Methods Biochem Anal. 2003; 44:501-7. Bourne PE. PMID: 12647401.
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    224. Structure comparison and alignment. Methods Biochem Anal. 2003; 44:321-37. Bourne PE, Shindyalov IN. PMID: 12647393.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    225. 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. Krebs WG, Bourne PE. PMID: 16452792.
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    226. An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics. 2002 Sep; 18(9):1280-1. Greer DS, Westbrook JD, Bourne PE. PMID: 12217927.
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    227. Use of conserved key amino acid positions to morph protein folds. Biopolymers. 2002 Jul 15; 64(3):139-45. Reddy BV, Li WW, Bourne PE. PMID: 12012349.
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    228. Science's policy on data deposition. Science. 2002 May 31; 296(5573):1609; author reply 1609. Bourne PE. PMID: 12041531.
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    229. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 2002 Jun; 58(Pt 6 No 1):899-907. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, 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. PMID: 12037327.
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    230. Protein structure resources. Acta Crystallogr D Biol Crystallogr. 2002 Jun; 58(Pt 6 No 1):908-15. Weissig H, Bourne PE. PMID: 12037328.
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    231. A biologist's guide to synchrotron facilities: the BioSync web resource. Trends Biochem Sci. 2002 Apr; 27(4):213-5. Kuller A, Fleri W, Bluhm WF, Smith JL, Westbrook J, Bourne PE. PMID: 11943550.
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    232. CKAAPs DB: a Conserved Key Amino Acid Positions DataBase. Nucleic Acids Res. 2002 Jan 01; 30(1):409-11. Li WW, Reddy BV, Tate JG, Shindyalov IN, Bourne PE. PMID: 11752351; PMCID: PMC99066.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    233. The Protein Data Bank: unifying the archive. Nucleic Acids Res. 2002 Jan 01; 30(1):245-8. Westbrook J, Feng Z, Jain S, Bhat TN, Thanki N, Ravichandran V, Gilliland GL, Bluhm W, Weissig H, Greer DS, Bourne PE, Berman HM. PMID: 11752306; PMCID: PMC99110.
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    234. Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins. Proteins. 2001 Feb 01; 42(2):148-63. Reddy BV, Li WW, Shindyalov IN, Bourne PE. PMID: 11119639.
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    235. Protein-nucleic acid interactions. Folding and binding. Curr Opin Struct Biol. 2001 Feb; 11(1):9-10. Bourne P, Murray-Rust J, Lakey JH. PMID: 11179884.
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    236. CKAAPs DB: a conserved key amino acid positions database. Nucleic Acids Res. 2001 Jan 01; 29(1):329-31. Li WW, Reddy BV, Shindyalov IN, Bourne PE. PMID: 11125128; PMCID: PMC29811.
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    237. A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. Nucleic Acids Res. 2001 Jan 01; 29(1):228-9. Shindyalov IN, Bourne PE. PMID: 11125099; PMCID: PMC29823.
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    238. Design and implementation of a collaborative molecular graphics environment. J Mol Graph Model. 2001; 19(3-4):280-7, 369-73. Tate JG, Moreland JL, Bourne PE. PMID: 11449565.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    239. A new algorithm for the alignment of multiple protein structures using Monte Carlo optimization. Pac Symp Biocomput. 2001; 275-86. Guda C, Scheeff ED, Bourne PE, Shindyalov IN. PMID: 11262947.
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    240. The Protein Data Bank and the challenge of structural genomics. Nat Struct Biol. 2000 Nov; 7 Suppl:957-9. Berman HM, Bhat TN, Bourne PE, Feng Z, Gilliland G, Weissig H, Westbrook J. PMID: 11103999.
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    241. Engineering and design membrane proteins lipids. Web alert. Curr Opin Struct Biol. 2000 Aug; 10(4):397-8. Bourne PE, Murray-Rust J, Lakey JH. PMID: 10981624.
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    242. Bioinformatics meets data mining: time to dance? Trends Biotechnol. 2000 Jun; 18(6):228-30. Bourne PE. PMID: 10928784.
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    243. An alternative view of protein fold space. Proteins. 2000 Feb 15; 38(3):247-60. Shindyalov IN, Bourne PE. PMID: 10713986.
      View in: PubMed   Mentions: 46     Fields:    Translation:Cells
    244. STAR/mmCIF: an ontology for macromolecular structure. Bioinformatics. 2000 Feb; 16(2):159-68. Westbrook JD, Bourne PE. PMID: 10842738.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    245. Common EF-hand motifs in cholinesterases and neuroligins suggest a role for Ca2+ binding in cell surface associations. Protein Sci. 2000 Jan; 9(1):180-5. Tsigelny I, Shindyalov IN, Bourne PE, Südhof TC, Taylor P. PMID: 10739260; PMCID: PMC2144444.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    246. The Protein Data Bank. Nucleic Acids Res. 2000 Jan 01; 28(1):235-42. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. PMID: 10592235; PMCID: PMC102472.
      View in: PubMed   Mentions: 11765     Fields:    Translation:Cells
    247. An analysis of the Protein Data Bank in search of temporal and global trends. Bioinformatics. 1999 Oct; 15(10):807-31. Weissig H, Bourne PE. PMID: 10705434.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    248. Development of Internet-based multimedia applications. Trends Biochem Sci. 1999 Aug; 24(8):321-4. Quinn GB, Taylor A, Wang HP, Bourne PE. PMID: 10431177.
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    249. Developing protein documentaries and other multimedia presentations for molecular biology. Pac Symp Biocomput. 1999; 380-91. Quinn G, Wang HP, Martinez D, Bourne PE. PMID: 10380212.
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    250. Catalysis and regulation. Proteins. Web alert. Curr Opin Struct Biol. 1998 Dec; 8(6):673-4. Murray-Rust J, Lakey JH, Bourne PE. PMID: 10026004.
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    251. Macromolecular structure databases: past progress and future challenges. Acta Crystallogr D Biol Crystallogr. 1998 Nov 01; 54(Pt 6 Pt 1):1085-94. Weissig H, Shindyalov IN, Bourne PE. PMID: 10089484.
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    252. Carbohydrates and glycoconjugates biophysical methods. Curr Opin Struct Biol. 1998 Oct; 8(5):543-4. Lakey JH, Bourne PE, Murray-Rust J. PMID: 9890778.
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    253. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 1998 Sep; 11(9):739-47. Shindyalov IN, Bourne PE. PMID: 9796821.
      View in: PubMed   Mentions: 683     Fields:    Translation:Cells
    254. Lipids engineering and design membrane proteins. Web alert. Curr Opin Struct Biol. 1998 Aug; 8(4):411-2. Bourne PE, Murray-Rust J, Lakey JH. PMID: 9729729.
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    255. Macromolecular assemblages theory and simulation. Web alert. Curr Opin Struct Biol. 1998 Apr; 8(2):137-8. Lakey JH, Bourne PE, Murray-Rust J. PMID: 9631284.
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    256. Protein-nucleic acid interactions folding and binding. Web alert. Curr Opin Struct Biol. 1998 Feb; 8(1):9-10. Bourne PE, Murray-Rust J, Lakey JH. PMID: 9519289.
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    257. Web alert. Catalysis and regulation. Proteins. Curr Opin Struct Biol. 1997 Dec; 7(6):765. Murray-Rust J, Lakey JH, Bourne PE. PMID: 9836855.
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    258. The protein kinase resource. Trends Biochem Sci. 1997 Nov; 22(11):444-6. Smith CM, Shindyalov IN, Veretnik S, Gribskov M, Taylor SS, Ten Eyck LF, Bourne PE. PMID: 9397688.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimals
    259. Protein data representation and query using optimized data decomposition. Comput Appl Biosci. 1997 Oct; 13(5):487-96. Shindyalov IN, Bourne PE. PMID: 9367122.
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    260. Web alert. Theory and simulation. Macromolecular assemblages. Curr Opin Struct Biol. 1997 Apr; 7(2):285. Lakey JH, Bourne PE, Murray-Rust J. PMID: 9094338.
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    261. Web alert. Folding and binding. Protein-nucleic acid interactions. Curr Opin Struct Biol. 1997 Feb; 7(1):135. Bourne PE, Murray-Rust J, Lakey JH. PMID: 9032070.
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    262. Macromolecular Crystallographic Information File. Methods Enzymol. 1997; 277:571-90. Bourne PE, Berman HM, McMahon B, Watenpaugh KD, Westbrook JD, Fitzgerald PM. PMID: 18488325.
      View in: PubMed   Mentions: 52     Fields:    
    263. Design and application of PDBlib, a C++ macromolecular class library. Comput Appl Biosci. 1994 Dec; 10(6):575-86. Chang W, Shindyalov IN, Pu C, Bourne PE. PMID: 7704656.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    264. Macromolecular query language (MMQL): prototype data model and implementation. Protein Eng. 1994 Nov; 7(11):1311-22. Shindyalov IN, Chang W, Pu C, Bourne PE. PMID: 7700863.
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    265. An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA. Comput Appl Biosci. 1994 Jun; 10(3):309-17. Zhang P, Schon EA, Fischer SG, Cayanis E, Weiss J, Kistler S, Bourne PE. PMID: 7922688.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    266. Design and application of a C++ macromolecular class library. Proc Int Conf Intell Syst Mol Biol. 1994; 2:70-7. Chang W, Shindyalov IN, Pu C, Bourne PE. PMID: 7584420.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    267. A CPU benchmark for protein crystallographic refinement. Comput Biol Med. 1990; 20(4):219-30. Bourne PE, Hendrickson WA. PMID: 2225778.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    268. PRONUC: a software package for the analysis of protein and nucleic acid sequences. Comput Methods Programs Biomed. 1987 Feb; 24(1):27-36. Bourne PE, Desai N. PMID: 3829646.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    269. Erabutoxin b. Initial protein refinement and sequence analysis at 0.140-nm resolution. Eur J Biochem. 1985 Dec 16; 153(3):521-7. Bourne PE, Sato A, Corfield PW, Rosen LS, Birken S, Low BW. PMID: 4076189.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    270. Helix packing and subunit conformation in horse spleen apoferritin. Nature. 1980 Nov 20; 288(5788):298-300. Clegg GA, Stansfield RF, Bourne PE, Harrison PM. PMID: 7432529.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    271. The structure and heavy-metal-ion-binding sites of horse spleen apoferritin. Biochem Soc Trans. 1980 Oct; 8(5):654-5. Clegg GA, Stansfield RF, Bourne PE, Harrison PM. PMID: 7450277.
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