Heng Li

Heng Li, PhD

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

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

Bedtk: finding interval overlap with implicit interval tree.

Authors: Li H, Rong J.
Bioinformatics 2021-06-09
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Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands.

Authors: Xing D, Tan L, Chang CH, Li H, Xie XS.
Proc Natl Acad Sci U S A 2021-03-23
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Twelve years of SAMtools and BCFtools.

Authors: Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H.
Gigascience 2021-03-16
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HTSlib: C library for reading/writing high-throughput sequencing data.

Authors: Bonfield JK, Marshall J, Danecek P, Li H, Ohan V, Whitwham A, Keane T, Davies RM.
Gigascience 2021-03-16
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Targeting a cytokine checkpoint enhances the fitness of armored cord blood CAR-NK cells.

Authors: Daher M, Basar R, Gokdemir E, Baran N, Uprety N, Nunez Cortes AK, Mendt M, Kerbauy LN, Banerjee PP, Shanley M, Imahashi N, Li L, Lim FLWI, Fathi M, Rezvan A, Mohanty V, Shen Y, Shaim H, Lu J, Ozcan G, Ensley E, Kaplan M, Nandivada V, Bdiwi M, Acharya S, Xi Y, Wan X, Mak D, Liu E, Jiang XR, Ang S, Muniz-Feliciano L, Li Y, Wang J, Kordasti S, Petrov N, Varadarajan N, Marin D, Brunetti L, Skinner RJ, Lyu S, Silva L, Turk R, Schubert MS, Rettig GR, McNeill MS, Kurgan G, Behlke MA, Li H, Fowlkes NW, Chen K, Konopleva M, Champlin RE, Shpall EJ, Rezvani K.
Blood 2021-03-04
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Chromosome-scale, haplotype-resolved assembly of human genomes.

Authors: Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook JM, Moemke T, Marschall T, Sedlazeck FJ, Aach J, Chin CS, Church GM, Li H.
Nat Biotechnol 2021-03-01
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Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.

Authors: Cheng H, Concepcion GT, Feng X, Zhang H, Li H.
Nat Methods 2021-02-01
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The design and construction of reference pangenome graphs with minigraph.

Authors: Li H, Feng X, Chu C.
Genome Biol 2020-10-16
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A haplotype-aware de novo assembly of related individuals using pedigree sequence graph.

Authors: Garg S, Aach J, Li H, Sebenius I, Durbin R, Church G.
Bioinformatics 2020-04-15
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Differential DNA methylation of vocal and facial anatomy genes in modern humans.

Authors: Gokhman D, Nissim-Rafinia M, Agranat-Tamir L, Housman G, García-Pérez R, Lizano E, Cheronet O, Mallick S, Nieves-Colón MA, Li H, Alpaslan-Roodenberg S, Novak M, Gu H, Osinski JM, Ferrando-Bernal M, Gelabert P, Lipende I, Mjungu D, Kondova I, Bontrop R, Kullmer O, Weber G, Shahar T, Dvir-Ginzberg M, Faerman M, Quillen EE, Meissner A, Lahav Y, Kandel L, Liebergall M, Prada ME, Vidal JM, Gronostajski RM, Stone AC, Yakir B, Lalueza-Fox C, Pinhasi R, Reich D, Marques-Bonet T, Meshorer E, Carmel L.
Nat Commun 2020-03-04
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