Heng Li, Ph.D.
Heng Li, Ph.D.
Assistant Professor of Biomedical Informatics
Address: Clsb 11007 Department of Biostatistics and Computational Biology 3 Blackfan Circle Boston, MA 02115

Heng Li studies advanced computational algorithms to solve practical biological problems, currently with a focus on sequence alignment, variant calling, de novo assembly, data storage, and information query. He developed and maintains several widely used software packages, such as BWA, samtools, minimap2, and seqtk, for analyzing high-throughput sequencing data. He has also collaborated with multiple research groups and published work on the analysis of single-cell sequence data, chromosome conformation, cancer genomics, population genetics and species evolution.


DBMI Research Areas
A global reference for human genetic variation.
Authors: Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR.
Nature
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BFC: correcting Illumina sequencing errors.
Authors: Li H.
Bioinformatics
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Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth.
Authors: Palkopoulou E, Mallick S, Skoglund P, Enk J, Rohland N, Li H, Omrak A, Vartanyan S, Poinar H, Götherström A, Reich D, Dalén L.
Curr Biol
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No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans.
Authors: Do R, Balick D, Li H, Adzhubei I, Sunyaev S, Reich D.
Nat Genet
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Fast construction of FM-index for long sequence reads.
Authors: Li H.
Bioinformatics
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Genome sequence of a 45,000-year-old modern human from western Siberia.
Authors: Fu Q, Li H, Moorjani P, Jay F, Slepchenko SM, Bondarev AA, Johnson PL, Aximu-Petri A, Prüfer K, de Filippo C, Meyer M, Zwyns N, Salazar-García DC, Kuzmin YV, Keates SG, Kosintsev PA, Razhev DI, Richards MP, Peristov NV, Lachmann M, Douka K, Higham TF, Slatkin M, Hublin JJ, Reich D, Kelso J, Viola TB, Pääbo S.
Nature
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Toward better understanding of artifacts in variant calling from high-coverage samples.
Authors: Li H.
Bioinformatics
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Ancient human genomes suggest three ancestral populations for present-day Europeans.
Authors: Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, Berger B, Economou C, Bollongino R, Fu Q, Bos KI, Nordenfelt S, Li H, de Filippo C, Prüfer K, Sawyer S, Posth C, Haak W, Hallgren F, Fornander E, Rohland N, Delsate D, Francken M, Guinet JM, Wahl J, Ayodo G, Babiker HA, Bailliet G, Balanovska E, Balanovsky O, Barrantes R, Bedoya G, Ben-Ami H, Bene J, Berrada F, Bravi CM, Brisighelli F, Busby GB, Cali F, Churnosov M, Cole DE, Corach D, Damba L, van Driem G, Dryomov S, Dugoujon JM, Fedorova SA, Gallego Romero I, Gubina M, Hammer M, Henn BM, Hervig T, Hodoglugil U, Jha AR, Karachanak-Yankova S, Khusainova R, Khusnutdinova E, Kittles R, Kivisild T, Klitz W, Kucinskas V, Kushniarevich A, Laredj L, Litvinov S, Loukidis T, Mahley RW, Melegh B, Metspalu E, Molina J, Mountain J, Näkkäläjärvi K, Nesheva D, Nyambo T, Osipova L, Parik J, Platonov F, Posukh O, Romano V, Rothhammer F, Rudan I, Ruizbakiev R, Sahakyan H, Sajantila A, Salas A, Starikovskaya EB, Tarekegn A, Toncheva D, Turdikulova S, Uktveryte I, Utevska O, Vasquez R, Villena M, Voevoda M, Winkler CA, Yepiskoposyan L, Zalloua P, Zemunik T, Cooper A, Capelli C, Thomas MG, Ruiz-Linares A, Tishkoff SA, Singh L, Thangaraj K, Villems R, Comas D, Sukernik R, Metspalu M, Meyer M, Eichler EE, Burger J, Slatkin M, Pääbo S, Kelso J, Reich D, Krause J.
Nature
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The complete genome sequence of a Neanderthal from the Altai Mountains.
Authors: Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S.
Nature
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Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology.
Authors: Ruan J, Jiang L, Chong Z, Gong Q, Li H, Li C, Tao Y, Zheng C, Zhai W, Turissini D, Cannon CH, Lu X, Wu CI.
BMC Genomics
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