Heng Li, Ph.D.

Heng Li, PhD

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

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 survey of sequence alignment algorithms for next-generation sequencing.
Authors: Li H, Homer N.
Brief Bioinform
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A draft sequence of the Neandertal genome.
Authors: Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S.
Science
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Fast and accurate long-read alignment with Burrows-Wheeler transform.
Authors: Li H, Durbin R.
Bioinformatics
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The sequence and de novo assembly of the giant panda genome.
Authors: Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Zheng H, Li Y, Steiner CC, Lam TT, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford MW, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam TW, Yiu SM, Liu S, Zhang H, Li D, Huang Y, Wang X, Yang G, Jiang Z, Wang J, Qin N, Li L, Li J, Bolund L, Kristiansen K, Wong GK, Olson M, Zhang X, Li S, Yang H, Wang J, Wang J.
Nature
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The Sequence Alignment/Map format and SAMtools.
Authors: Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R.
Bioinformatics
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Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.
Authors: Holt KE, Teo YY, Li H, Nair S, Dougan G, Wain J, Parkhill J.
Bioinformatics
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Fast and accurate short read alignment with Burrows-Wheeler transform.
Authors: Li H, Durbin R.
Bioinformatics
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Haplotype frequencies in a sub-region of chromosome 19q13.3, related to risk and prognosis of cancer, differ dramatically between ethnic groups.
Authors: Schierup MH, Mailund T, Li H, Wang J, Tjønneland A, Vogel U, Bolund L, Nexø BA.
BMC Med Genet
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EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
Authors: Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E.
Genome Res
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Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels.
Authors: Sudbery I, Stalker J, Simpson JT, Keane T, Rust AG, Hurles ME, Walter K, Lynch D, Teboul L, Brown SD, Li H, Ning Z, Nadeau JH, Croniger CM, Durbin R, Adams DJ.
Genome Biol
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