David J. Lipman

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David Lipman
Paul Ginsparg and David Lipman (cropped).jpg
David Lipman in June 2013
Born
David J. Lipman
Alma materBrown University
University at Buffalo, The State University of New York
Known forInfluence on development of BLAST (biotechnology)[1]
AwardsISCB Senior Scientist Award
Member of the U.S. National Academy of Sciences
ISCB Fellow[2]
Scientific career
FieldsBioinformatics
Computational biology
Sequence comparison methods
Comparative genomics
Molecular evolution
InstitutionsNational Center for Biotechnology Information
Brown University
University at Buffalo, The State University of New York
Notable studentsStephen Altschul[3]
Mark Boguski[citation needed]
Websitewww.ncbi.nlm.nih.gov/research/staff/lipman

David J. Lipman is an American biologist who from 1989[1] to 2017 was the director of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health.[4][5] NCBI is the home of GenBank,[6] the U.S. node of the International Sequence Database Consortium, and PubMed, one of the most heavily used sites in the world for the search and retrieval of biomedical information. Lipman is one of the original authors of the BLAST sequence alignment program, and a respected figure in bioinformatics.[7][8][9] In 2017, he left NCBI and became Chief Science Officer at Impossible Foods.[10]

Education[edit]

Lipman received his undergraduate degree from Brown University and his M.D. in 1980 from the University at Buffalo, The State University of New York[11]

Career[edit]

Lipman was the founding director of the National Center for Biotechnology Information, part of the National Library of Medicine at the U.S. National Institutes of Health. Under his leadership, NCBI grew from fewer than a dozen people to more than 500 scientific staff, and it now hosts hundreds of scientific and medical databases including GenBank, PubMed, PubMed Central, dbGaP, dbSNP, the Sequence Read Archive (SRA), RefSeq, PubChem, and many more. The internal research program at NCBI included groups led by Stephen Altschul (another BLAST co-author), David Landsman, Eugene Koonin[12] (a prolific author on comparative genomics), and L. Aravind.

Lipman is very well known for his seminal work on a series of sequence similarity algorithms, starting from the Wilbur-Lipman[13] algorithm in 1983, FASTA search[14][15] in 1985, BLAST[16] in 1990, and Gapped BLAST and PSI-BLAST[17] in 1997. BLAST eventually became the most widely-used and highly-cited (over 160,000 citations as of 2021) sequence alignment program in the field, and the NCBI BLAST server today is one of its most heavily used resources.

Lipman also worked for many years with Dennis A. Benson and others at NCBI on the maintenance and improvement of GenBank, one of the world's largest databases of genome and protein sequence data. GenBank along with the European Nucleotide Archive and the DNA Data Bank of Japan form the International Nucleotide Sequence Database Collaboration (INSDC), a fully open, unrestricted database of genome sequences that has been the world's repository of such data since 1990.[18][19][20]

He was one of the originators of the Influenza Genome Sequencing Project, a project to sequence and make available the genomes of thousands of influenza virus isolates.[citation needed]

He was one of the original signatories of the Bethesda Statement on Open Access Publishing.[citation needed]

He is also the editor-in-chief for an open-access, peer-reviewed online scientific journal called Biology Direct.[21]

In May 2017, Lipman left his role at the NCBI to join the plant-based meat company Impossible Foods as chief scientific officer.[22]

Awards and honors[edit]

Lipman received the Association of Biomolecular Resource Facilities Award for outstanding contributions to Biomolecular Technologies in 1996.

In 2000, he was elected to the National Academy of Medicine.[23]

In 2004, he was awarded the ISCB Senior Scientist Award and elected an ISCB Fellow in 2009 by the International Society for Computational Biology.[2][24]

In 2005, Dr. Lipman was elected to the US National Academy of Sciences.[citation needed]

In 2013, he received the award of a White House "Open Science" Champion of Change.[25][26]

References[edit]

  1. ^ a b "Research Institute Posts Gene Data on Internet". The New York Times. June 26, 1997.
  2. ^ a b Anon (2017). "ISCB Fellows". iscb.org. International Society for Computational Biology. Archived from the original on 2017-03-20.
  3. ^ "Sense from Sequences: Stephen F. Altschul on Bettering BLAST". 2000. Archived from the original on 2007-10-07.
  4. ^ "David J. Lipman, MD, Director, National Center for Biotechnology Information". Archived from the original on 2013-09-26.
  5. ^ "Open Access Now | Conversation with David Lipman". Biomedcentral.com. Archived from the original on 29 June 2011. Retrieved 2 July 2011.
  6. ^ Benson, D. A.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Wheeler, D. L. (2007). "GenBank". Nucleic Acids Research. 36 (Database issue): D25–D30. doi:10.1093/nar/gkm929. PMC 2238942. PMID 18073190.
  7. ^ "david lipman – Google Scholar". Scholar.google.com. Retrieved 2017-03-26.
  8. ^ David J. Lipman publications indexed by Microsoft Academic[dead link]
  9. ^ David J. Lipman at DBLP Bibliography Server Edit this at Wikidata
  10. ^ "National Library of Medicine Announces Departure of NCBI Director Dr. David Lipman". www.nlm.nih.gov. Retrieved 2017-05-05.
  11. ^ "David J. Lipman, M.D. Biography". nih.gov. Archived from the original on 2017-02-11. Retrieved 2017-02-09.
  12. ^ Tatusov, R. L.; Koonin, E. V.; Lipman, D. J. (1997). "A Genomic Perspective on Protein Families". Science. 278 (5338): 631–637. Bibcode:1997Sci...278..631T. doi:10.1126/science.278.5338.631. PMID 9381173.
  13. ^ Wilbur, W. J.; Lipman, D. J. (1983). "Rapid similarity searches of nucleic acid and protein data banks". Proceedings of the National Academy of Sciences of the United States of America. 80 (3): 726–730. Bibcode:1983PNAS...80..726W. doi:10.1073/pnas.80.3.726. PMC 393452. PMID 6572363.
  14. ^ Lipman, D.; Pearson, W. (1985). "Rapid and sensitive protein similarity searches". Science. 227 (4693): 1435–1441. Bibcode:1985Sci...227.1435L. doi:10.1126/science.2983426. PMID 2983426.
  15. ^ Pearson, W. R.; Lipman, D. J. (1988). "Improved tools for biological sequence comparison". Proceedings of the National Academy of Sciences of the United States of America. 85 (8): 2444–2448. Bibcode:1988PNAS...85.2444P. doi:10.1073/pnas.85.8.2444. PMC 280013. PMID 3162770.
  16. ^ Altschul, Stephen; Gish, Warren; Miller, Webb; Myers, Eugene; Lipman, David (1990). "Basic local alignment search tool". Journal of Molecular Biology. 215 (3): 403–410. doi:10.1016/S0022-2836(05)80360-2. PMID 2231712. S2CID 14441902.
  17. ^ Altschul, S.; Madden, T. L.; Schäffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. (1997). "Gapped BLAST and PSI-BLAST: A new generation of protein database search programs". Nucleic Acids Research. 25 (17): 3389–3402. doi:10.1093/nar/25.17.3389. PMC 146917. PMID 9254694.
  18. ^ Benson, D. A.; Cavanaugh, M.; Clark, K.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Sayers, E. W. (2012). "GenBank". Nucleic Acids Research. 41 (Database issue): D36–D42. doi:10.1093/nar/gks1195. PMC 3531190. PMID 23193287.
  19. ^ Benson, D. A.; Karsch-Mizrachi, I.; Clark, K.; Lipman, D. J.; Ostell, J.; Sayers, E. W. (2011). "GenBank". Nucleic Acids Research. 40 (Database issue): D48–D53. doi:10.1093/nar/gkr1202. PMC 3245039. PMID 22144687.
  20. ^ Benson, D. A.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Sayers, E. W. (2010). "GenBank". Nucleic Acids Research. 39 (Database issue): D32–D37. doi:10.1093/nar/gkq1079. PMC 3013681. PMID 21071399.
  21. ^ "Biology Direct | Editorial board". Archived from the original on 2011-09-30. Retrieved 2011-10-28.
  22. ^ "National Library of Medicine Announces Departure of NCBI Director Dr. David Lipman". www.nlm.nih.gov. Retrieved 2017-05-04.
  23. ^ "Institute of Medicine Elects New Members".
  24. ^ "ISCB Names 2004 Senior Scientist Accomplishment Award Winner, Dr. David Lipman ISCB Newsletter 7-3". Iscb.org. Retrieved 2 July 2011.
  25. ^ "Open Science | the White House". whitehouse.gov. Archived from the original on 2017-01-21. Retrieved 2016-04-02 – via National Archives.
  26. ^ "Dr. David Lipman Receives White House "Open Science" Champions of Change Award on Behalf of NCBI". Ncbi.nlm.nih.gov. Retrieved 2 April 2016.