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Heng Li
open-in-new
<h2 id="education">Education</h2> <p>Li majored in physics at Nanjing University from 1997 to 2001.<a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a> He received his <a href="/facts/PhD/paJumdN8">PhD</a> from the Institute of Theoretical Physics at the <a href="/facts/Chinese_Academy_of_Sciences/zzHb3yVm">Chinese Academy of Sciences</a> in 2006. His thesis, titled "Constructing the <a href="/facts/TreeFam/U2sPDCLt">TreeFam</a> database", was supervised by Wei-Mou Zheng.<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> </p> <h2 id="research">Research</h2> <p>Li was involved in a number of projects while working at the <a href="/facts/Beijing_Genomics_Institute/IEjfX8lm">Beijing Genomics Institute</a> from 2002 to 2006. These included studying rice finishing,<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> <a href="/facts/Silkworm/r4IJIUtk">silkworm</a> sequencing,<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a> and genetic variation in chickens.<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> </p><p>From 2006 to 2009, Li worked on a <a href="/facts/Postdoctoral_research/uGIGIC1X">postdoctoral research</a> fellowship with <a href="/facts/Richard_M._Durbin/8lkj3NNj">Richard M. Durbin</a> at the <a href="/facts/Wellcome_Trust_Sanger_Institute/uQchlx8p">Wellcome Trust Sanger Institute</a>.<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> During this time, Li made several important contributions to the field of <a href="/facts/Next_generation_sequencing/hsPsNCQW">next generation sequencing</a> (NGS) through the development of software such as the <a href="/facts/SAMtools/WFzNmNVs">SAMtools</a> NGS utilities,<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a> the Burrows–Wheeler aligner (BWA),<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a> MAQ,<a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a> TreeSoft and TreeFam.<a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a> </p><p>Li joined the <a href="/facts/Broad_Institute/RchJRWLN">Broad Institute</a> in 2009, working in the core faculty lab of <a href="/facts/David_Altshuler_(physician)/wXyCMJDl">David Altshuler</a>,<a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a><a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a> which investigates the discovery and understanding of the genetic causes of disease. </p><p>As of December 2018, Li's papers on <a href="/facts/SAMtools/WFzNmNVs">SAMtools</a><a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a> and BWA<a class="footnote-ref" id="fnref:18" href="#fn:18"><sup>18</sup></a> (sequence alignment using the <a href="/facts/Burrows%25E2%2580%2593Wheeler_transform/yxIc9E94">Burrows–Wheeler transform</a>) have both been cited over 16,000 times.<a class="footnote-ref" id="fnref:19" href="#fn:19"><sup>19</sup></a> </p> <h2 id="awards">Awards</h2> <p>In 2012, Li won the <a href="/facts/Benjamin_Franklin_Award_(Bioinformatics)/9Tsan1Ke">Benjamin Franklin award</a><a class="footnote-ref" id="fnref:20" href="#fn:20"><sup>20</sup></a> in <a href="/facts/Bioinformatics/D5x2L8ee">bioinformatics</a>. Li became the fourth former member of Richard Durbin's lab to win the award, following <a href="/facts/Sean_Eddy/JyGtLTKl">Sean Eddy</a>, <a href="/facts/Ewan_Birney/0rQu4F60">Ewan Birney</a> and <a href="/facts/Alex_Bateman/X8K4LDNx">Alex Bateman</a>.<a class="footnote-ref" id="fnref:21" href="#fn:21"><sup>21</sup></a> </p> <h2 id="personal">Personal</h2> <p>Li lives in <a href="/facts/Boston/exjfn6xf">Boston</a> with his wife, daughter, and fish.<a class="footnote-ref" id="fnref:22" href="#fn:22"><sup>22</sup></a> </p> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>"Heng Li | Department of Biomedical Informatics". dbmi.hms.harvard.edu. Retrieved 2018-10-30. <a href="http://dbmi.hms.harvard.edu/person/faculty/heng-li" target="_blank">http://dbmi.hms.harvard.edu/person/faculty/heng-li</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>"Noted computational biologist Heng Li joins faculty". harvard.edu. Retrieved 2018-10-30. <a href="http://bcb.dfci.harvard.edu/index.php/posts/126-hengli18" target="_blank">http://bcb.dfci.harvard.edu/index.php/posts/126-hengli18</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>"HLi Lab - Home". hlilab.github.io. Retrieved 2018-10-30. <a href="https://hlilab.github.io" target="_blank">https://hlilab.github.io</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>"Heng Li's Homepage". sourceforge.net. Archived from the original on 2012-04-19. <a href="https://web.archive.org/web/20120419031958/http://lh3lh3.users.sourceforge.net/" target="_blank">https://web.archive.org/web/20120419031958/http://lh3lh3.users.sourceforge.net/</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>https://www.linkedin.com/in/lh3lh3 [self-published source] <a href="https://www.linkedin.com/in/lh3lh3" target="_blank">https://www.linkedin.com/in/lh3lh3</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Li, Heng (2006). Constructing the TreeFam database (PDF) (PhD thesis). Chinese Academy of Sciences. <a href="http://lh3lh3.users.sourceforge.net/download/PhD-thesis-liheng-2006-English.pdf" target="_blank">http://lh3lh3.users.sourceforge.net/download/PhD-thesis-liheng-2006-English.pdf</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546038" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546038</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>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) <a href="/wiki/Bibcode_(identifier)" target="_blank">/wiki/Bibcode_(identifier)</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>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 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2263125" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2263125</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>"ResearcherID: Heng Li". researcherid.com. Retrieved 11 September 2014. <a href="http://www.researcherid.com/rid/D-9344-2011" target="_blank">http://www.researcherid.com/rid/D-9344-2011</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>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 href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>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. <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>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. <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>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. <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>"ResearcherID: Heng Li". researcherid.com. Retrieved 11 September 2014. <a href="http://www.researcherid.com/rid/D-9344-2011" target="_blank">http://www.researcherid.com/rid/D-9344-2011</a> <a href="#fnref:15" class="footnote-back-ref">↩</a></p></li> <li id="fn:16"><p>"Current Lab Members - Altshuler Lab". broadinstitute.org. 2010-05-25. Retrieved 11 September 2014. <a href="https://www.broadinstitute.org/scientific-community/science/core-faculty-labs/altshuler-lab/current-lab-members" target="_blank">https://www.broadinstitute.org/scientific-community/science/core-faculty-labs/altshuler-lab/current-lab-members</a> <a href="#fnref:16" class="footnote-back-ref">↩</a></p></li> <li id="fn:17"><p>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 href="#fnref:17" class="footnote-back-ref">↩</a></p></li> <li id="fn:18"><p>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. <a href="#fnref:18" class="footnote-back-ref">↩</a></p></li> <li id="fn:19"><p>"Heng Li - Google Scholar Citations". scholar.google.co.uk. Retrieved 16 April 2015. <a href="https://scholar.google.co.uk/citations?user=HQv0p0kAAAAJ&hl=en" target="_blank">https://scholar.google.co.uk/citations?user=HQv0p0kAAAAJ&hl=en</a> <a href="#fnref:19" class="footnote-back-ref">↩</a></p></li> <li id="fn:20"><p>"Broad's Heng Li Wins 2012 Benjamin Franklin Award - Bio-IT World". Archived from the original on 2012-04-01. <a href="https://web.archive.org/web/20120401213327/http://www.bio-itworld.com/2012/03/14/broads-heng-li-wins-2012-benjamin-franklin-award.html" target="_blank">https://web.archive.org/web/20120401213327/http://www.bio-itworld.com/2012/03/14/broads-heng-li-wins-2012-benjamin-franklin-award.html</a> <a href="#fnref:20" class="footnote-back-ref">↩</a></p></li> <li id="fn:21"><p>"Heng Li Credits Durbin Pedigree in Accepting Franklin Award". bio-itworld.com. Retrieved 11 September 2014. <a href="http://www.bio-itworld.com/news/04/26/12/Heng-Li-credits-Durbin-pedigree-Franklin-Award.html" target="_blank">http://www.bio-itworld.com/news/04/26/12/Heng-Li-credits-Durbin-pedigree-Franklin-Award.html</a> <a href="#fnref:21" class="footnote-back-ref">↩</a></p></li> <li id="fn:22"><p>"Heng Li's Homepage". sourceforge.net. Archived from the original on 2012-04-19. <a href="https://web.archive.org/web/20120419031958/http://lh3lh3.users.sourceforge.net/" target="_blank">https://web.archive.org/web/20120419031958/http://lh3lh3.users.sourceforge.net/</a> <a href="#fnref:22" class="footnote-back-ref">↩</a></p></li> </ol>