Heng Li

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
Samtools
TreeFam
Notable awards Benjamin Franklin Award (Bioinformatics) (2012) [2]
Website
lh3lh3.users.sourceforge.net

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.

Education

Li 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]

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,[4] silkworm sequencing,[5] and genetic variation in chickens.[6]

From 2006 to 2009, Li worked on a postdoctoral research fellowship with Richard M. Durbin at the Wellcome Trust Sanger Institute.[7] 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,[8] the Burrows–Wheeler aligner (BWA),[9] MAQ,[10] TreeSoft and TreeFam.[11]

Li joined the Broad Institute in 2009, working in the core faculty lab of David Altshuler,[7][12] which investigates the discovery and understanding of the genetic causes of disease.

As of April 2015, Li's papers on SAMtools[8] and BWA[9] (sequence alignment using the Burrows-Wheeler transform) have both been cited over 5,000 times.[13]

Awards

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.[14]

Personal

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

References

  1. ↑ 1.0 1.1 Li, Heng (2006). Constructing the TreeFam database (PhD thesis). Chinese Academy of Sciences.
  2. ↑ 2.0 2.1 "Broad's Heng Li Wins 2012 Benjamin Franklin Award - Bio-IT World". Archived from the original on 2012-03-14.
  3. ↑ 3.0 3.1 "Heng Li's Homepage". Archived from the original on 2012-03-14.
  4. ↑ Yu, Jun et al. "The Genomes of Oryza sativa: A History of Duplications". PLoS Biology 3 (2): e38. doi:10.1371/journal.pbio.0030038. PMC 546038. PMID 15685292.
  5. ↑ Xia, Q et al. (Dec 10, 2004). "A draft sequence for the genome of the domesticated silkworm (Bombyx mori).". Science 306 (5703): 1937–40. doi:10.1126/science.1102210. PMID 15591204.
  6. ↑ 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. doi:10.1038/nature03156. PMC 2263125. PMID 15592405.
  7. ↑ 7.0 7.1 "ResearcherID: Heng Li". http://www.researcherid.com''. Retrieved 11 September 2014.
  8. ↑ 8.0 8.1 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.
  9. ↑ 9.0 9.1 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.
  10. ↑ 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.
  11. ↑ 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.
  12. ↑ "Current Lab Members - Altshuler Lab". https://www.broadinstitute.org''. Retrieved 11 September 2014.
  13. ↑ "Heng Li - Google Scholar Citations". http://scholar.google.co.uk''. Retrieved 16 April 2015.
  14. ↑ "Heng Li Credits Durbin Pedigree in Accepting Franklin Award". http://www.bio-itworld.com''. Retrieved 11 September 2014.