Heng Li

Last updated
Heng Li
Known for Bioinformatics
Burrows–Wheeler transform
Samtools
TreeFam
Awards Benjamin Franklin Award (Bioinformatics) (2012) [1]
Scientific career
Institutions Wellcome Trust Sanger Institute
Broad Institute
Beijing Genomics Institute
Thesis Constructing the TreeFam database  (2006)
Doctoral advisor Wei-Mou Zheng [2]
Website hlilab.github.io

Heng Li is a Chinese bioinformatics scientist. He is an associate professor at the department of Biomedical Informatics of Harvard Medical School and the department of Data Science of Dana-Farber Cancer Institute. [3] [4] [5] He was previously a research scientist working at the Broad Institute in Cambridge, Massachusetts with David Reich and David Altshuler. [6] Li's work has made several important contributions in the field of next generation sequencing.

Contents

Education

Li majored in physics at Nanjing University from 1997 to 2001. [7] He received his PhD from the Institute of Theoretical Physics at the Chinese Academy of Sciences in 2006. His thesis, titled "Constructing the TreeFam database", was supervised by Wei-Mou Zheng. [2]

Research

Li was involved in a number of projects while working at the Beijing Genomics Institute from 2002 to 2006. These included studying rice finishing, [8] silkworm sequencing, [9] and genetic variation in chickens. [10]

From 2006 to 2009, Li worked on a postdoctoral research fellowship with Richard M. Durbin at the Wellcome Trust Sanger Institute. [11] During this time, Li made several important contributions to the field of next generation sequencing (NGS) through the development of software such as the SAMtools NGS utilities, [12] the Burrows–Wheeler aligner (BWA), [13] MAQ, [14] TreeSoft and TreeFam. [15]

Li joined the Broad Institute in 2009, working in the core faculty lab of David Altshuler, [11] [16] which investigates the discovery and understanding of the genetic causes of disease.

As of December 2018, Li's papers on SAMtools [12] and BWA [13] (sequence alignment using the Burrows–Wheeler transform) have both been cited over 16,000 times. [17]

Awards

In 2012, Li won the Benjamin Franklin award [1] in bioinformatics. Li became the fourth former member of Richard Durbin's lab to win the award, following Sean Eddy, Ewan Birney and Alex Bateman. [18] . Li has been an ISCB Fellow since 2023.

Personal

Li lives in Boston with his wife, daughter, and two cats. [6]

References

  1. 1 2 "Broad's Heng Li Wins 2012 Benjamin Franklin Award - Bio-IT World". Archived from the original on 2012-04-01.
  2. 1 2 Li, Heng (2006). Constructing the TreeFam database (PDF) (PhD thesis). Chinese Academy of Sciences.
  3. ↑ "Heng Li | Department of Biomedical Informatics". dbmi.hms.harvard.edu. Retrieved 2018-10-30.
  4. ↑ "Noted computational biologist Heng Li joins faculty". harvard.edu. Retrieved 2018-10-30.
  5. ↑ "HLi Lab - Home". hlilab.github.io. Retrieved 2018-10-30.
  6. 1 2 "Heng Li's Homepage". sourceforge.net. Archived from the original on 2012-04-19.
  7. ↑ https://www.linkedin.com/in/lh3lh3 [ self-published source ]
  8. ↑ Yu, Jun; et al. (2005). "The Genomes of Oryza sativa: A History of Duplications". PLOS Biology. 3 (2): e38. doi: 10.1371/journal.pbio.0030038 . PMC   546038 . PMID   15685292.
  9. ↑ Xia, Q; et al. (Dec 10, 2004). "A draft sequence for the genome of the domesticated silkworm (Bombyx mori)". Science. 306 (5703): 1937–40. Bibcode:2004Sci...306.1937X. doi:10.1126/science.1102210. PMID   15591204. S2CID   7227719.{{cite journal}}: |first94= has generic name (help)
  10. ↑ Ka-Shu Wong, Gane; et al. (9 December 2004). "A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms". Nature. 432 (7018): 717–722. Bibcode:2004Natur.432..717B. doi:10.1038/nature03156. PMC   2263125 . PMID   15592405.
  11. 1 2 "ResearcherID: Heng Li". researcherid.com. Retrieved 11 September 2014.
  12. 1 2 Li, H.; Handsaker, B.; Wysoker, A.; Fennell, T.; Ruan, J.; Homer, N.; Marth, G.; Abecasis, G.; Durbin, R.; 1000 Genome Project Data Processing Subgroup (2009). "The Sequence Alignment/Map format and SAMtools". Bioinformatics. 25 (16): 2078–2079. doi:10.1093/bioinformatics/btp352. PMC   2723002 . PMID   19505943.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  13. 1 2 Li, H.; Durbin, R. (2009). "Fast and accurate short read alignment with Burrows–Wheeler transform". Bioinformatics. 25 (14): 1754–1760. doi:10.1093/bioinformatics/btp324. PMC   2705234 . PMID   19451168.
  14. ↑ Li, H.; Ruan, J.; Durbin, R. (2008). "Mapping short DNA sequencing reads and calling variants using mapping quality scores". Genome Research. 18 (11): 1851–1858. doi:10.1101/gr.078212.108. PMC   2577856 . PMID   18714091.
  15. ↑ Li, H.; Coghlan, A.; Ruan, J.; Coin, L. J.; Hériché, J. K.; Osmotherly, L.; Li, R.; Liu, T.; Zhang, Z.; Bolund, L.; Wong, G. K.; Zheng, W.; Dehal, P.; Wang, J.; Durbin, R. (2006). "TreeFam: A curated database of phylogenetic trees of animal gene families". Nucleic Acids Research. 34 (90001): D572 –D580. doi:10.1093/nar/gkj118. PMC   1347480 . PMID   16381935.
  16. ↑ "Current Lab Members - Altshuler Lab". broadinstitute.org. 2010-05-25. Retrieved 11 September 2014.
  17. ↑ "Heng Li - Google Scholar Citations". scholar.google.co.uk. Retrieved 16 April 2015.
  18. ↑ "Heng Li Credits Durbin Pedigree in Accepting Franklin Award". bio-itworld.com. Retrieved 11 September 2014.
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