Philip Bourne

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Phil Bourne
Phil E Bourne.jpg
Philip Eric Bourne
Born
Philip Eric Bourne

1953 (age 70–71) [1]
Alma mater Flinders University (PhD)
Known for
Spouse
Roma Chalupa
​
(m. 1983)​
Children
  • Scott Bourne (b. 1985)
  • Melanie Bourne (b. 1997)
Awards
Scientific career
Fields Data Science
Computational Biology
Scholarly communication [9]
Bioinformatics
Institutions
Thesis Crystal structure analyses : metal complexes of biological interest and the stereochemistry of substituted phonylbicyclooctanes  (1979)
Notable students Werner G. Krebs
Website datascience.virginia.edu/people/phil-bourne

Philip Eric Bourne (born 1953) is an Australian bioinformatician, [10] non-fiction writer, [2] and businessman. [4] He is currently Stephenson Chair of Data Science and Director of the School of Data Science and Professor of Biomedical Engineering [11] and was the first associate director for Data Science at the National Institutes of Health, where his projects include managing the Big Data to Knowledge initiative, and formerly Associate Vice Chancellor at UCSD. [12] He has contributed to textbooks and is a strong supporter of open-access literature and software. His diverse interests have spanned structural biology, medical informatics, information technology, structural bioinformatics, scholarly communication and pharmaceutical sciences. [10] His papers are highly cited, and he has an h-index above 80. [13] [14] [9]

Contents

Education

Bourne was trained as a physical chemist in the mid to late 1970s and obtained his PhD in 1979 [1] at the Flinders University.

Career and research

After his PhD, Bourne moved to the University of Sheffield to do postdoctoral research during 1979–1981, [15] followed by a move to Columbia University, New York, in 1981. In 1995 he moved to University of California, San Diego, where he was a Professor in the Department of Pharmacology. In 2014, he moved to NIH to become its associate director for Data Science. In January 2017, it was announced that he had accepted a position as director of University of Virginia's Data Science Institute. [16]

He is known for writing the book Unix for VMS Users (1990) [2] and for being co-developer of the Combinatorial Extension algorithm for the three-dimensional alignment of protein structures, [17] together with I. Shindyalov (1998). In 1999 he became co-director of the Protein Data Bank. [18] He was president of the ISCB (2002–2003). [19] He is a fellow of the American Medical Informatics Association since 2002. [20] He is founding Editor in Chief of PLoS Computational Biology (2005-). In 2007 he co-founded SciVee. [4] Bourne is an editor of the popular Ten Simple Rules series of editorials published in the PLoS Computational Biology journal. [21] He has served as the Associate Vice Chancellor for Innovation and Industrial Alliances [12] and a professor of pharmacology at the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego (UCSD). [22] [23] He is an advisor to the Hypothes.is project [24] and associate director for Data Science at the National Institutes of Health where his projects include managing the Big Data to Knowledge initiative. [25] [26]

Publications

Bourne is author of numerous scientific articles and book chapters and editor of the Structural Bioinformatics textbook. [27] [28] and Pharmacy Informatics [29] Other publications [9] include:

Awards and honors

Bourne was elected Fellow of the AAAS under Pharmaceutical Sciences in 2011 [5] and Fellow of the International Society for Computational Biology (ISCB) in 2011. [6] In 2010 he won Microsoft's Jim Gray e-Science award [7] and in 2009 won the Benjamin Franklin Award (2009). [8] [30]

Personal life

Bourne has been married since 1983 to Roma Chalupa and they have two children: Scott Bourne (1985-) and Melanie Bourne (1997-).[ citation needed ] His interests include motorcycles, [31] flying, and hiking

Related Research Articles

The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). These structural data are obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication. Global access to the data is provided by the websites of the wwPDB member organisations.

<span class="mw-page-title-main">UTOPIA (bioinformatics tools)</span>

UTOPIA is a suite of free tools for visualising and analysing bioinformatics data. Based on an ontology-driven data model, it contains applications for viewing and aligning protein sequences, rendering complex molecular structures in 3D, and for finding and using resources such as web services and data objects. There are two major components, the protein analysis suite and UTOPIA documents.

<span class="mw-page-title-main">Janet Thornton</span> British bioinformatician and academic

Dame Janet Maureen Thornton, is a senior scientist and director emeritus at the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL). She is one of the world's leading researchers in structural bioinformatics, using computational methods to understand protein structure and function. She served as director of the EBI from October 2001 to June 2015, and played a key role in ELIXIR.

<span class="mw-page-title-main">Helen M. Berman</span> American chemist

Helen Miriam Berman is a Board of Governors Professor of Chemistry and Chemical Biology at Rutgers University and a former director of the RCSB Protein Data Bank. A structural biologist, her work includes structural analysis of protein-nucleic acid complexes, and the role of water in molecular interactions. She is also the founder and director of the Nucleic Acid Database, and led the Protein Structure Initiative Structural Genomics Knowledgebase.

<span class="mw-page-title-main">Søren Brunak</span> Danish bioinformatics professor, scientist

Søren Brunak is a Danish biological and physical scientist working in bioinformatics, systems biology, and medical informatics. He is a professor of Disease Systems Biology at the University of Copenhagen and professor of bioinformatics at the Technical University of Denmark. As Research Director at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen Medical School, he leads a research effort where molecular-level systems biology data are combined with phenotypic data from the healthcare sector, such as electronic patient records, registry information, and biobank questionnaires. A major aim is to understand the network biology basis for time-ordered comorbidities and discriminate between treatment-related disease correlations and other comorbidities in disease trajectories. Søren Brunak also holds a position as a Medical Informatics Officer at Rigshospitalet, the Capital Region of Denmark.

Anders Krogh is a bioinformatician at the University of Copenhagen, where he leads the university's bioinformatics center. He is known for his pioneering work on the use of hidden Markov models in bioinformatics, and is co-author of a widely used textbook in bioinformatics. In addition, he also co-authored one of the early textbooks on neural networks. His current research interests include promoter analysis, non-coding RNA, gene prediction and protein structure prediction.

<span class="mw-page-title-main">International Society for Computational Biology</span> Scholarly society

The International Society for Computational Biology (ISCB) is a scholarly society for researchers in computational biology and bioinformatics. The society was founded in 1997 to provide a stable financial home for the Intelligent Systems for Molecular Biology (ISMB) conference and has grown to become a larger society working towards advancing understanding of living systems through computation and for communicating scientific advances worldwide.

<span class="mw-page-title-main">Lawrence Hunter</span>

Lawrence E. Hunter is a Professor and Director of the Center for Computational Pharmacology and of the Computational Bioscience Program at the University of Colorado School of Medicine and Professor of Computer Science at the University of Colorado Boulder. He is an internationally known scholar, focused on computational biology, knowledge-driven extraction of information from the primary biomedical literature, the semantic integration of knowledge resources in molecular biology, and the use of knowledge in the analysis of high-throughput data, as well as for his foundational work in computational biology, which led to the genesis of the major professional organization in the field and two international conferences.

Protein function prediction methods are techniques that bioinformatics researchers use to assign biological or biochemical roles to proteins. These proteins are usually ones that are poorly studied or predicted based on genomic sequence data. These predictions are often driven by data-intensive computational procedures. Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of publications, phylogenetic profiles, phenotypic profiles, and protein-protein interaction. Protein function is a broad term: the roles of proteins range from catalysis of biochemical reactions to transport to signal transduction, and a single protein may play a role in multiple processes or cellular pathways.

<span class="mw-page-title-main">ProtCID</span>

The Protein Common Interface Database (ProtCID) is a database of similar protein-protein interfaces in crystal structures of homologous proteins.

<span class="mw-page-title-main">Cyrus Chothia</span> English biochemist (1942–2019)

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<span class="mw-page-title-main">David T. Jones (scientist)</span> British bioinformatician

David Tudor Jones is a Professor of Bioinformatics, and Head of Bioinformatics Group in the University College London. He is also the director in Bloomsbury Center for Bioinformatics, which is a joint Research Centre between UCL and Birkbeck, University of London and which also provides bioinformatics training and support services to biomedical researchers. In 2013, he is a member of editorial boards for PLoS ONE, BioData Mining, Advanced Bioinformatics, Chemical Biology & Drug Design, and Protein: Structure, Function and Bioinformatics.

<span class="mw-page-title-main">Alfonso Valencia</span>

Alfonso Valencia is a Spanish biologist, ICREA Professor, current director of the Life Sciences department at Barcelona Supercomputing Center. and of Spanish National Bioinformatics Institute (INB-ISCIII). From 2015-2018, he was President of the International Society for Computational Biology. His research is focused on the study of biomedical systems with computational biology and bioinformatics approaches.

<span class="mw-page-title-main">Gary Stormo</span> American geneticist (born 1950)

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<span class="mw-page-title-main">Alex Bateman</span> British bioinformatician

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<span class="mw-page-title-main">Janet Kelso</span> South African bioinformatician

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References

  1. 1 2 Bourne, Philip Eric (1979). Crystal structure analyses : metal complexes of biological interest and the stereochemistry of substituted phonylbicyclooctanes (PhD thesis). Flinders University. OCLC   708090572.
  2. 1 2 3 4 Bourne, Phil E (1990). Unix for VMS Users . Digital Press Newton, MA, USA. ISBN   1-55558-034-3.
  3. ↑ Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.; Weissig, H.; Shindyalov, I.; Bourne, P. (2000). "The Protein Data Bank". Nucleic Acids Research. 28 (1): 235–242. doi:10.1093/nar/28.1.235. PMC   102472 . PMID   10592235.
  4. 1 2 3 Fink, JL; Bourne, PE (2007). "Reinventing Scholarly Communication for the Electronic Age". CTWatch Quarterly. 3 (3).
  5. 1 2 "Dr. Phil Bourne elected AAAS Fellow under Pharmaceutical Sciences". Pharmacy.ucsd.edu. Retrieved 2011-02-27.
  6. 1 2 "ISCB fellows". Archived from the original on 2015-03-28. Retrieved 2011-08-15.
  7. 1 2 "Philip E. Bourne wins Microsoft's 2010 Jim Gray eScience Award". Eurekalert.org. 2010-10-18. Retrieved 2011-02-27.
  8. 1 2 "Benjamin Franklin Award". Bioinformatics.org. Retrieved 2011-02-27.
  9. 1 2 3 Philip Bourne publications indexed by Google Scholar OOjs UI icon edit-ltr-progressive.svg
  10. 1 2 Philip Bourne publications indexed by the Scopus bibliographic database. (subscription required)
  11. ↑ "Philip e. Bourne". 6 July 2017.
  12. 1 2 "Archived copy" (PDF). Archived from the original (PDF) on 2012-07-31. Retrieved 2012-07-02.{{cite web}}: CS1 maint: archived copy as title (link)
  13. ↑ page at the University of Virginia
  14. ↑ bournes old website
  15. ↑ Clegg, G. A.; Stansfield, R. F. D.; Bourne, P. E.; Harrison, P. M. (1980). "Helix packing and subunit conformation in horse spleen apoferritin". Nature. 288 (5788): 298–300. Bibcode:1980Natur.288..298C. doi:10.1038/288298a0. PMID   7432529. S2CID   4335735.
  16. ↑ "UVA Names NIH Researcher as New Director of Data Science Institute". 11 January 2017.
  17. ↑ Shindyalov, I. N.; Bourne, P. E. (1998). "Protein structure alignment by incremental combinatorial extension (CE) of the optimal path". Protein Engineering Design and Selection. 11 (9): 739–747. doi: 10.1093/protein/11.9.739 . PMID   9796821.
  18. ↑ Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.; Weissig, H.; Shindyalov, I.; Bourne, P. (2000). "The Protein Data Bank". Nucleic Acids Research. 28 (1): 235–242. doi:10.1093/nar/28.1.235. PMC   102472 . PMID   10592235.
  19. ↑ "ISCB — Past Presidents". Archived from the original on August 28, 2015. Retrieved September 3, 2015.
  20. ↑ Greenes, R. A.; Madsen, E.; Miller, R. A. (2003). "American College of Medical Informatics Fellows and International Associates, 2002". Journal of the American Medical Informatics Association. 10 (3): 281–286. doi:10.1197/jamia.M1326. PMC   400512 .
  21. ↑ Ten Simple Rules
  22. ↑ http://www.sdsc.edu/pb/ The Bourne lab web page
  23. ↑ http://www.sdsc.edu/~bourne/CV.pdf Philip E. Bourne Ph.D. CV
  24. ↑ Hypothes.is official website
  25. ↑ NIH Names Dr. Philip E. Bourne First Associate Director for Data Science
  26. ↑ Margolis, R.; Derr, L.; Dunn, M.; Huerta, M.; Larkin, J.; Sheehan, J.; Guyer, M.; Green, E. D. (2014). "The National Institutes of Health's Big Data to Knowledge (BD2K) initiative: capitalizing on biomedical big data". Journal of the American Medical Informatics Association. 21 (6): 957–8. doi:10.1136/amiajnl-2014-002974. ISSN   1067-5027. PMC   4215061 . PMID   25008006.
  27. 1 2 Bourne, Philip E.; Weissig, Helga (2003). Structural Bioinformatics. John Wiley & Sons.
  28. 1 2 Gu, Jenny; Bourne, Philip E. (March 2009). Structural Bioinformatics (2nd ed.). Wiley-Blackwell. ISBN   978-0-470-18105-8.
  29. 1 2 Anderson, Philip O.; Bourne, Philip E. (December 2009). Pharmacy Informatics. CRC Press. ISBN   978-1-4200-7175-7.
  30. ↑ "The Bourne Commendation: Open Access Evangelist Wins 2009 Benjamin Franklin Award". Bio-itworld.com. Retrieved 2011-02-27.
  31. ↑ OFL | Philip Bourne | Travel Blog
Preceded by President of the
International Society for Computational Biology
2002 – 2003		Succeeded by
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