Heng Li

Heng Li, PhD

Associate Professor of Biomedical Informatics, Dana-Farber Cancer Institute and Harvard Medical School

Address: Clsb 11007 Department of Biostatistics and Computational Biology 3 Blackfan Circle Boston, MA 02115

HLi Lab

Research
Publications

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

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 2014-01-02
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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 2013-10-17
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The anatomy of successful computational biology software.

Authors: Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C.
Nat Biotechnol 2013-10-01
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Mapping the human reference genome's missing sequence by three-way admixture in Latino genomes.

Authors: Genovese G, Handsaker RE, Li H, Kenny EE, McCarroll SA.
Am J Hum Genet 2013-09-05
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Using population admixture to help complete maps of the human genome.

Authors: Genovese G, Handsaker RE, Li H, Altemose N, Lindgren AM, Chambert K, Pasaniuc B, Price AL, Reich D, Morton CC, Pollak MR, Wilson JG, McCarroll SA.
Nat Genet 2013-04-01
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SOAPindel: efficient identification of indels from short paired reads.

Authors: Li S, Li R, Li H, Lu J, Li Y, Bolund L, Schierup MH, Wang J.
Genome Res 2013-01-01
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An integrated map of genetic variation from 1,092 human genomes.

Authors: Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.
Nature 2012-11-01
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A high-coverage genome sequence from an archaic Denisovan individual.

Authors: Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S.
Science 2012-10-12
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A direct characterization of human mutation based on microsatellites.

Authors: Sun JX, Helgason A, Masson G, Ebenesersdóttir SS, Li H, Mallick S, Gnerre S, Patterson N, Kong A, Reich D, Stefansson K.
Nat Genet 2012-10-01
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Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly.

Authors: Li H.
Bioinformatics 2012-07-15
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