Lior Pachter

Lior Pachter
Lior Pachter in 2013
Born
Lior Samuel Pachter

(1973-05-03) May 3, 1973 (age 51)
Ramat Gan, Israel
Alma materCalifornia Institute of Technology (BS)
Massachusetts Institute of Technology (PhD)
AwardsISCB Fellow (2017)
Scientific career
FieldsComputational biology
Bioinformatics
Genomics
Computer science
Mathematics[1]
InstitutionsUniversity of California, Berkeley
ThesisDomino Tiling, Gene Recognition and Mice (1999)
Doctoral advisorBonnie Berger[2]
Doctoral studentsCole Trapnell[2][3]
Websiteliorpachter.wordpress.com

Lior Samuel Pachter is a computational biologist. He works at the California Institute of Technology, where he is the Bren Professor of Computational Biology. He has widely varied research interests including genomics, combinatorics, computational geometry, machine learning, scientific computing, and statistics.[1][4][5]

Early life and education

Pachter was born in Israel and grew up in South Africa.[6] He earned a bachelor's degree in mathematics from the California Institute of Technology in 1994.[4] He completed his doctorate in mathematics from the Massachusetts Institute of Technology in 1999, supervised by Bonnie Berger,[2] with Eric Lander and Daniel Kleitman as co-advisors.[4]

Career and research

Pachter was with the University of California, Berkeley faculty from 1999 to 2018[7] and was given the Sackler Chair in 2012.[4]

As well as for his technical contributions, Pachter is known for using new media to promote open science[8] and for a thought experiment he posted on his blog according to which 'the nearest neighbor to the "perfect human"' is from Puerto Rico.[9] This received considerable media attention,[10] and a response was published in Scientific American.[11] He is also known for criticisms of the All-of-us project's use of UMAP to visualize and interpret population genetics data.[12]

Awards and honors

In 2017, Pachter was elected a Fellow of the International Society for Computational Biology (ISCB).[13]

See also

References

  1. ^ a b Lior Pachter publications indexed by Google Scholar Edit this at Wikidata
  2. ^ a b c Lior Pachter at the Mathematics Genealogy Project
  3. ^ Trapnell, Cole; Pachter, Lior; Salzberg, Steven L. (2009). "TopHat: discovering splice junctions with RNA-Seq". Bioinformatics. 25 (9): 1105–1111. doi:10.1093/bioinformatics/btp120. ISSN 1460-2059. PMC 2672628. PMID 19289445.
  4. ^ a b c d Curriculum vitae: Lior Pachter (PDF), 2017, retrieved 2017-05-16.
  5. ^ Trapnell, Cole; Williams, Brian A; Pertea, Geo; Mortazavi, Ali; Kwan, Gordon; van Baren, Marijke J; Salzberg, Steven L; Wold, Barbara J; Pachter, Lior (2010). "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation". Nature Biotechnology. 28 (5): 511–515. doi:10.1038/nbt.1621. ISSN 1087-0156. PMC 3146043. PMID 20436464.
  6. ^ Eskenazi, Joe (June 14, 2002), "U.C. divestment petition troubles pro-Israel activists", Jweekly.
  7. ^ "UC Berkeley, Mathematics Department Faculty, Lior Pachter". Retrieved 2019-06-08.
  8. ^ Lesen, Amy E. (2015), "A new paradigm for science communication? Social media, twitter, science, and public engagement: a literature review", in Lesen, Amy E. (ed.), Scientists, Experts, and Civic Engagement: Walking a Fine Line, Ashgate Studies in Environmental Policy and Practice, Ashgate Publishing, Ltd., pp. 111–136, ISBN 9781472415240. See in particular pp. 119–120.
  9. ^ Pachter, Lior (December 2, 2014). "The perfect human is Puerto Rican". Bits of DNA – Reviews and commentary on computational biology by Lior Pachter. Retrieved 2016-12-11.
  10. ^ Valdez, Maria G. (December 4, 2014), "New Study Reveals The Perfect Human Genetically Speaking Is From This Caribbean Island!", Latin Times
  11. ^ Oleksyk, Taras K.; Martinez-Cruzado, Juan Carlos (February 5, 2015). "Why There Is No Perfect Human In Puerto Rico or Anywhere Else". Scientific American..
  12. ^ pachter, lior (February 26, 2024). "all of us failed". wordpress. Retrieved 2024-03-08. all of us failed
  13. ^ "February 13, 2017: The International Society for Computational Biology Names Seven Members as the ISCB Fellows Class of 2017". www.iscb.org. Retrieved 2017-02-13.