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
Curated variation benchmarks for challenging medically relevant autosomal genes.
Authors: Wagner J, Olson ND, Harris L, McDaniel J, Cheng H, Fungtammasan A, Hwang YC, Gupta R, Wenger AM, Rowell WJ, Khan ZM, Farek J, Zhu Y, Pisupati A, Mahmoud M, Xiao C, Yoo B, Sahraeian SME, Miller DE, Jáspez D, Lorenzo-Salazar JM, Muñoz-Barrera A, Rubio-Rodríguez LA, Flores C, Narzisi G, Evani US, Clarke WE, Lee J, Mason CE, Lincoln SE, Miga KH, Ebbert MTW, Shumate A, Li H, Chin CS, Zook JM, Sedlazeck FJ.
Nat Biotechnol
View full abstract on Pubmed
The Human Pangenome Project: a global resource to map genomic diversity.
Authors: Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, Garrison NA, Graves-Lindsay TA, Ji H, Kenny EE, Koenig BA, Li D, Marschall T, McMichael JF, Novak AM, Purushotham D, Schneider VA, Schultz BI, Smith MW, Sofia HJ, Weissman T, Flicek P, Li H, Miga KH, Paten B, Jarvis ED, Hall IM, Eichler EE, Haussler D.
Nature
View full abstract on Pubmed
The complete sequence of a human genome.
Authors: Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sovic I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM.
Science
View full abstract on Pubmed
CoLoRd: compressing long reads.
Authors: Kokot M, Gudys A, Li H, Deorowicz S.
Nat Methods
View full abstract on Pubmed
New strategies to improve minimap2 alignment accuracy.
Authors: Li H.
Bioinformatics
View full abstract on Pubmed
Fast alignment and preprocessing of chromatin profiles with Chromap.
Authors: Zhang H, Song L, Wang X, Cheng H, Wang C, Meyer CA, Liu T, Tang M, Aluru S, Yue F, Liu XS, Li H.
Nat Commun
View full abstract on Pubmed
Haplotype-resolved germline and somatic alterations in renal medullary carcinomas.
Authors: Tan KT, Kim H, Carrot-Zhang J, Zhang Y, Kim WJ, Kugener G, Wala JA, Howard TP, Chi YY, Beroukhim R, Li H, Ha G, Alper SL, Perlman EJ, Mullen EA, Hahn WC, Meyerson M, Hong AL.
Genome Med
View full abstract on Pubmed
Real-time mapping of nanopore raw signals.
Authors: Zhang H, Li H, Jain C, Cheng H, Au KF, Li H, Aluru S.
Bioinformatics
View full abstract on Pubmed
Higher Rates of Processed Pseudogene Acquisition in Humans and Three Great Apes Revealed by Long-Read Assemblies.
Authors: Feng X, Li H.
Mol Biol Evol
View full abstract on Pubmed
Comprehensive identification of transposable element insertions using multiple sequencing technologies.
Authors: Chu C, Borges-Monroy R, Viswanadham VV, Lee S, Li H, Lee EA, Park PJ.
Nat Commun
View full abstract on Pubmed