Heng Li

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Heng Li
Institutions Wellcome Trust Sanger Institute
Broad Institute
Beijing Genomics Institute
Thesis Constructing the TreeFam database (2006)
Doctoral advisor Wei-Mou Zheng[1]
Known for Bioinformatics
Burrows–Wheeler transform
Notable awards Benjamin Franklin Award (Bioinformatics) (2012) [2]

Heng Li is a Chinese bioinformatics research scientist currently working at the Broad Institute in Cambridge, Massachusetts with David Reich and David Altshuler.[3] Li's work has made several important contributions in the field of next generation sequencing.


Li majored in physics at Nanjing University during 1997-2001.[4] 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.[1]


Li was involved in a number of projects while working at the Beijing Genomics Institute from 2002 to 2006. These included studying rice finishing,[5] silkworm sequencing,[6] and genetic variation in chickens.[7]

From 2006 to 2009, Li worked on a postdoctoral research fellowship with Richard M. Durbin at the Wellcome Trust Sanger Institute.[8] 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,[9] the Burrows–Wheeler aligner (BWA),[10] MAQ,[11] TreeSoft and TreeFam.[12]

Li joined the Broad Institute in 2009, working in the core faculty lab of David Altshuler,[8][13] which investigates the discovery and understanding of the genetic causes of disease.

As of April 2015, Li's papers on SAMtools[9] and BWA[10] (sequence alignment using the Burrows-Wheeler transform) have both been cited over 5,000 times.[14]


In 2012, Li won the Benjamin Franklin award[2] 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.[15]


Li lives in Boston with his wife and daughter.[3]


  1. ^ a b Li, Heng (2006). Constructing the TreeFam database (PDF) (PhD thesis). Chinese Academy of Sciences. 
  2. ^ a b "Broad's Heng Li Wins 2012 Benjamin Franklin Award - Bio-IT World". Archived from the original on 2012-03-14. 
  3. ^ a b "Heng Li's Homepage". Archived from the original on 2012-03-14. 
  4. ^ https://www.linkedin.com/in/lh3lh3
  5. ^ Yu, Jun; et al. "The Genomes of Oryza sativa: A History of Duplications". PLoS Biology. 3 (2): e38. PMC 546038Freely accessible. PMID 15685292. doi:10.1371/journal.pbio.0030038. 
  6. ^ Xia, Q; et al. (Dec 10, 2004). "A draft sequence for the genome of the domesticated silkworm (Bombyx mori).". Science. 306 (5703): 1937–40. PMID 15591204. doi:10.1126/science.1102210. 
  7. ^ 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. PMC 2263125Freely accessible. PMID 15592405. doi:10.1038/nature03156. 
  8. ^ a b "ResearcherID: Heng Li". http://www.researcherid.com. Retrieved 11 September 2014.  External link in |website= (help)
  9. ^ a b 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. PMC 2723002Freely accessible. PMID 19505943. doi:10.1093/bioinformatics/btp352. 
  10. ^ a b Li, H.; Durbin, R. (2009). "Fast and accurate short read alignment with Burrows-Wheeler transform". Bioinformatics. 25 (14): 1754–1760. PMC 2705234Freely accessible. PMID 19451168. doi:10.1093/bioinformatics/btp324. 
  11. ^ 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. PMC 2577856Freely accessible. PMID 18714091. doi:10.1101/gr.078212.108. 
  12. ^ 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. PMC 1347480Freely accessible. PMID 16381935. doi:10.1093/nar/gkj118. 
  13. ^ "Current Lab Members - Altshuler Lab". https://www.broadinstitute.org. Retrieved 11 September 2014.  External link in |website= (help)
  14. ^ "Heng Li - Google Scholar Citations". http://scholar.google.co.uk. Retrieved 16 April 2015.  External link in |website= (help)
  15. ^ "Heng Li Credits Durbin Pedigree in Accepting Franklin Award". http://www.bio-itworld.com. Retrieved 11 September 2014.  External link in |website= (help)