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Items: 1 to 50 of 235

1.

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

Koleck TA, Dreisbach C, Bourne PE, Bakken S.

J Am Med Inform Assoc. 2019 Apr 1;26(4):364-379. doi: 10.1093/jamia/ocy173.

PMID:
30726935
2.

Ten Simple Rules for avoiding and resolving conflicts with your colleagues.

Lewitter F, Bourne PE, Attwood TK.

PLoS Comput Biol. 2019 Jan 18;15(1):e1006708. doi: 10.1371/journal.pcbi.1006708. eCollection 2019 Jan. No abstract available.

3.

Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants.

Zhao Z, Xie L, Bourne PE.

J Chem Inf Model. 2019 Jan 28;59(1):453-462. doi: 10.1021/acs.jcim.8b00458. Epub 2019 Jan 11.

PMID:
30582689
4.

One thousand simple rules.

Bourne PE, Lewitter F, Markel S, Papin JA.

PLoS Comput Biol. 2018 Dec 20;14(12):e1006670. doi: 10.1371/journal.pcbi.1006670. eCollection 2018 Dec. No abstract available.

5.

The Small β-Barrel Domain: A Survey-Based Structural Analysis.

Youkharibache P, Veretnik S, Li Q, Stanek KA, Mura C, Bourne PE.

Structure. 2019 Jan 2;27(1):6-26. doi: 10.1016/j.str.2018.09.012. Epub 2018 Nov 1. Review.

PMID:
30393050
6.

Ten simple rules when considering retirement.

Bourne PE.

PLoS Comput Biol. 2018 Oct 4;14(10):e1006411. doi: 10.1371/journal.pcbi.1006411. eCollection 2018 Oct. No abstract available.

7.

Structural biology meets data science: does anything change?

Mura C, Draizen EJ, Bourne PE.

Curr Opin Struct Biol. 2018 Oct;52:95-102. doi: 10.1016/j.sbi.2018.09.003. Epub 2018 Sep 27. Review.

PMID:
30267935
8.

Cloud computing applications for biomedical science: A perspective.

Navale V, Bourne PE.

PLoS Comput Biol. 2018 Jun 14;14(6):e1006144. doi: 10.1371/journal.pcbi.1006144. eCollection 2018 Jun.

9.

Progress with covalent small-molecule kinase inhibitors.

Zhao Z, Bourne PE.

Drug Discov Today. 2018 Mar;23(3):727-735. doi: 10.1016/j.drudis.2018.01.035. Epub 2018 Jan 11. Review.

10.

Ten simple rules in considering a career in academia versus government.

Bourne PE.

PLoS Comput Biol. 2017 Oct 5;13(10):e1005729. doi: 10.1371/journal.pcbi.1005729. eCollection 2017 Oct. No abstract available.

11.

Developing international open science collaborations: Funder reflections on the Open Science Prize.

Kittrie E, Atienza AA, Kiley R, Carr D, MacFarlane A, Pai V, Couch J, Bajkowski J, Bonner JF, Mietchen D, Bourne PE.

PLoS Biol. 2017 Aug 1;15(8):e2002617. doi: 10.1371/journal.pbio.2002617. eCollection 2017 Aug.

12.

Building the biomedical data science workforce.

Dunn MC, Bourne PE.

PLoS Biol. 2017 Jul 17;15(7):e2003082. doi: 10.1371/journal.pbio.2003082. eCollection 2017 Jul.

13.

Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome.

Zhao Z, Xie L, Bourne PE.

PLoS One. 2017 Jun 19;12(6):e0179936. doi: 10.1371/journal.pone.0179936. eCollection 2017.

14.

Ten simple rules to consider regarding preprint submission.

Bourne PE, Polka JK, Vale RD, Kiley R.

PLoS Comput Biol. 2017 May 4;13(5):e1005473. doi: 10.1371/journal.pcbi.1005473. eCollection 2017 May. No abstract available.

15.

Big Data Science: Opportunities and Challenges to Address Minority Health and Health Disparities in the 21st Century.

Zhang X, Pérez-Stable EJ, Bourne PE, Peprah E, Duru OK, Breen N, Berrigan D, Wood F, Jackson JS, Wong DWS, Denny J.

Ethn Dis. 2017 Apr 20;27(2):95-106. doi: 10.18865/ed.27.2.95. eCollection 2017 Spring.

16.

Should biomedical research be like Airbnb?

Bonazzi VR, Bourne PE.

PLoS Biol. 2017 Apr 7;15(4):e2001818. doi: 10.1371/journal.pbio.2001818. eCollection 2017 Apr.

17.

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

Gao J, Prlic A, Bi C, Bluhm WF, Dimitropoulos D, Xu D, Bourne PE, Rose PW.

Bioinformatics. 2017 Jul 1;33(13):2047-2049. doi: 10.1093/bioinformatics/btx101.

18.

Determining Cysteines Available for Covalent Inhibition Across the Human Kinome.

Zhao Z, Liu Q, Bliven S, Xie L, Bourne PE.

J Med Chem. 2017 Apr 13;60(7):2879-2889. doi: 10.1021/acs.jmedchem.6b01815. Epub 2017 Apr 4.

19.

Life is three-dimensional, and it begins with molecules.

Bourne PE.

PLoS Biol. 2017 Mar 16;15(3):e2002041. doi: 10.1371/journal.pbio.2002041. eCollection 2017 Mar.

20.

Harnessing Big Data for Systems Pharmacology.

Xie L, Draizen EJ, Bourne PE.

Annu Rev Pharmacol Toxicol. 2017 Jan 6;57:245-262. doi: 10.1146/annurev-pharmtox-010716-104659. Epub 2016 Oct 13. Review.

21.

How open science helps researchers succeed.

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.

Elife. 2016 Jul 7;5. pii: e16800. doi: 10.7554/eLife.16800.

22.

SCIENTIFIC COMMUNITY. Preprints for the life sciences.

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.

Science. 2016 May 20;352(6288):899-901. doi: 10.1126/science.aaf9133. No abstract available.

PMID:
27199406
23.

The FAIR Guiding Principles for scientific data management and stewardship.

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.

Sci Data. 2016 Mar 15;3:160018. doi: 10.1038/sdata.2016.18.

24.

Systems biology of the structural proteome.

Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO.

BMC Syst Biol. 2016 Mar 11;10:26. doi: 10.1186/s12918-016-0271-6.

25.

Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach.

Zhao Z, Xie L, Xie L, Bourne PE.

J Med Chem. 2016 May 12;59(9):4326-41. doi: 10.1021/acs.jmedchem.5b02041. Epub 2016 Mar 17.

26.

Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology.

Zhao Z, Martin C, Fan R, Bourne PE, Xie L.

BMC Bioinformatics. 2016 Feb 18;17:90. doi: 10.1186/s12859-016-0941-9.

27.

The NIH Big Data to Knowledge (BD2K) initiative.

Bourne PE, Bonazzi V, Dunn M, Green ED, Guyer M, Komatsoulis G, Larkin J, Russell B.

J Am Med Inform Assoc. 2015 Nov;22(6):1114. doi: 10.1093/jamia/ocv136. No abstract available.

28.

Perspective: Sustaining the big-data ecosystem.

Bourne PE, Lorsch JR, Green ED.

Nature. 2015 Nov 5;527(7576):S16-7. doi: 10.1038/527S16a. No abstract available.

PMID:
26536219
29.

Developing multi-target therapeutics to fine-tune the evolutionary dynamics of the cancer ecosystem.

Xie L, Bourne PE.

Front Pharmacol. 2015 Sep 24;6:209. doi: 10.3389/fphar.2015.00209. eCollection 2015. No abstract available.

30.

Let's Make Gender Diversity in Data Science a Priority Right from the Start.

Berman FD, Bourne PE.

PLoS Biol. 2015 Jul 27;13(7):e1002206. doi: 10.1371/journal.pbio.1002206. eCollection 2015 Jul.

31.

Zeta Inhibitory Peptide Disrupts Electrostatic Interactions That Maintain Atypical Protein Kinase C in Its Active Conformation on the Scaffold p62.

Tsai LC, Xie L, Dore K, Xie L, Del Rio JC, King CC, Martinez-Ariza G, Hulme C, Malinow R, Bourne PE, Newton AC.

J Biol Chem. 2015 Sep 4;290(36):21845-56. doi: 10.1074/jbc.M115.676221. Epub 2015 Jul 17.

32.

Toward effective software solutions for big biology.

Prins P, de Ligt J, Tarasov A, Jansen RC, Cuppen E, Bourne PE.

Nat Biotechnol. 2015 Jul;33(7):686-7. doi: 10.1038/nbt.3240. No abstract available.

PMID:
26154002
33.

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

Bourne PE, Brenner SE, Eisen MB.

PLoS Comput Biol. 2015 Jun 24;11(6):e1004317. doi: 10.1371/journal.pcbi.1004317. eCollection 2015 Jun. No abstract available.

34.

DOIs for DICOM raw images: enabling science reproducibility.

Bourne PE.

Radiology. 2015 Apr;275(1):3-4. doi: 10.1148/radiol.15150144. No abstract available.

35.

Ten simple rules for lifelong learning, according to Hamming.

Erren TC, Slanger TE, Groß JV, Bourne PE, Cullen P.

PLoS Comput Biol. 2015 Feb 26;11(2):e1004020. doi: 10.1371/journal.pcbi.1004020. eCollection 2015 Feb. No abstract available.

36.

Confronting the ethical challenges of big data in public health.

Bourne PE.

PLoS Comput Biol. 2015 Feb 9;11(2):e1004073. doi: 10.1371/journal.pcbi.1004073. eCollection 2015 Feb. No abstract available.

37.

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

Bliven SE, Bourne PE, Prlić A.

Bioinformatics. 2015 Apr 15;31(8):1316-8. doi: 10.1093/bioinformatics/btu823. Epub 2014 Dec 12.

38.

Achievements and challenges in structural bioinformatics and computational biophysics.

Samish I, Bourne PE, Najmanovich RJ.

Bioinformatics. 2015 Jan 1;31(1):146-50. doi: 10.1093/bioinformatics/btu769. Epub 2014 Dec 8.

39.

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

Rose PW, Prlić 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.

Nucleic Acids Res. 2015 Jan;43(Database issue):D345-56. doi: 10.1093/nar/gku1214. Epub 2014 Nov 26.

40.

Ten simple rules for writing a PLOS ten simple rules article.

Dashnow H, Lonsdale A, Bourne PE.

PLoS Comput Biol. 2014 Oct 23;10(10):e1003858. doi: 10.1371/journal.pcbi.1003858. eCollection 2014 Oct. No abstract available.

41.

MixGF: spectral probabilities for mixture spectra from more than one peptide.

Wang J, Bourne PE, Bandeira N.

Mol Cell Proteomics. 2014 Dec;13(12):3688-97. doi: 10.1074/mcp.O113.037218. Epub 2014 Sep 15.

42.

Ten simple rules for better figures.

Rougier NP, Droettboom M, Bourne PE.

PLoS Comput Biol. 2014 Sep 11;10(9):e1003833. doi: 10.1371/journal.pcbi.1003833. eCollection 2014 Sep. No abstract available.

43.

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

Quinn GB, Bi C, Christie CH, Pang K, Prlić A, Nakane T, Zardecki C, Voigt M, Berman HM, Bourne PE, Rose PW.

Bioinformatics. 2015 Jan 1;31(1):126-7. doi: 10.1093/bioinformatics/btu596. Epub 2014 Sep 2.

44.

Ten simple rules for approaching a new job.

Bourne PE.

PLoS Comput Biol. 2014 Jun 26;10(6):e1003660. doi: 10.1371/journal.pcbi.1003660. eCollection 2014 Jun. No abstract available.

45.

Towards structural systems pharmacology to study complex diseases and personalized medicine.

Xie L, Ge X, Tan H, Xie L, Zhang Y, Hart T, Yang X, Bourne PE.

PLoS Comput Biol. 2014 May 15;10(5):e1003554. doi: 10.1371/journal.pcbi.1003554. eCollection 2014 May. Review.

46.

Systematic detection of internal symmetry in proteins using CE-Symm.

Myers-Turnbull D, Bliven SE, Rose PW, Aziz ZK, Youkharibache P, Bourne PE, Prlić A.

J Mol Biol. 2014 May 29;426(11):2255-68. doi: 10.1016/j.jmb.2014.03.010. Epub 2014 Mar 26.

47.

What Big Data means to me.

Bourne PE.

J Am Med Inform Assoc. 2014 Mar-Apr;21(2):194. doi: 10.1136/amiajnl-2014-002651. No abstract available.

48.

Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra.

Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N.

Mol Cell Proteomics. 2014 Apr;13(4):1128-36. doi: 10.1074/mcp.M113.035758. Epub 2014 Feb 3.

49.

A turn-key approach for large-scale identification of complex posttranslational modifications.

Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N.

J Proteome Res. 2014 Mar 7;13(3):1190-9. doi: 10.1021/pr400368u. Epub 2014 Jan 29.

50.

Quantifying reproducibility in computational biology: the case of the tuberculosis drugome.

Garijo D, Kinnings S, Xie L, Xie L, Zhang Y, Bourne PE, Gil Y.

PLoS One. 2013 Nov 27;8(11):e80278. doi: 10.1371/journal.pone.0080278. eCollection 2013.

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