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 |
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.
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]
Personal
Li lives in Boston with his wife, daughter, and fish. [6]
References
- ^ a b "Broad's Heng Li Wins 2012 Benjamin Franklin Award - Bio-IT World". Archived from the original on 2012-04-01.
- ^ a b Li, Heng (2006). Constructing the TreeFam database (PDF) (PhD thesis). Chinese Academy of Sciences.
- ^ "Heng Li | Department of Biomedical Informatics". dbmi.hms.harvard.edu. Retrieved 2018-10-30.
- ^ "Noted computational biologist Heng Li joins faculty". harvard.edu. Retrieved 2018-10-30.
- ^ "HLi Lab - Home". hlilab.github.io. Retrieved 2018-10-30.
- ^ a b "Heng Li's Homepage". sourceforge.net. Archived from the original on 2012-04-19.
- ^ https://www.linkedin.com/in/lh3lh3 [ self-published source]
- ^ 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.
- ^ 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.
- ^ 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.
- ^ a b "ResearcherID: Heng Li". researcherid.com. Retrieved 11 September 2014.
- ^
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.
doi:
10.1093/bioinformatics/btp352.
PMC
2723002.
PMID
19505943.
{{ cite journal}}: CS1 maint: numeric names: authors list ( link) - ^ a b 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.
- ^ 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.
- ^ 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.
- ^ "Current Lab Members - Altshuler Lab". broadinstitute.org. 2010-05-25. Retrieved 11 September 2014.
- ^ "Heng Li - Google Scholar Citations". scholar.google.co.uk. Retrieved 16 April 2015.
- ^ "Heng Li Credits Durbin Pedigree in Accepting Franklin Award". bio-itworld.com. Retrieved 11 September 2014.
| Authority control databases: Academics |
|---|
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 |
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.
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]
Personal
Li lives in Boston with his wife, daughter, and fish. [6]
References
- ^ a b "Broad's Heng Li Wins 2012 Benjamin Franklin Award - Bio-IT World". Archived from the original on 2012-04-01.
- ^ a b Li, Heng (2006). Constructing the TreeFam database (PDF) (PhD thesis). Chinese Academy of Sciences.
- ^ "Heng Li | Department of Biomedical Informatics". dbmi.hms.harvard.edu. Retrieved 2018-10-30.
- ^ "Noted computational biologist Heng Li joins faculty". harvard.edu. Retrieved 2018-10-30.
- ^ "HLi Lab - Home". hlilab.github.io. Retrieved 2018-10-30.
- ^ a b "Heng Li's Homepage". sourceforge.net. Archived from the original on 2012-04-19.
- ^ https://www.linkedin.com/in/lh3lh3 [ self-published source]
- ^ 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.
- ^ 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.
- ^ 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.
- ^ a b "ResearcherID: Heng Li". researcherid.com. Retrieved 11 September 2014.
- ^
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.
doi:
10.1093/bioinformatics/btp352.
PMC
2723002.
PMID
19505943.
{{ cite journal}}: CS1 maint: numeric names: authors list ( link) - ^ a b 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.
- ^ 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.
- ^ 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.
- ^ "Current Lab Members - Altshuler Lab". broadinstitute.org. 2010-05-25. Retrieved 11 September 2014.
- ^ "Heng Li - Google Scholar Citations". scholar.google.co.uk. Retrieved 16 April 2015.
- ^ "Heng Li Credits Durbin Pedigree in Accepting Franklin Award". bio-itworld.com. Retrieved 11 September 2014.
| Authority control databases: Academics |
|---|