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 Programs
Minimap2: pairwise alignment for nucleotide sequences.
Authors: Li H.
Bioinformatics
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Three-dimensional genome structures of single diploid human cells.
Authors: Tan L, Xing D, Chang CH, Li H, Xie XS.
Science
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A synthetic-diploid benchmark for accurate variant-calling evaluation.
Authors: Li H, Bloom JM, Farjoun Y, Fleharty M, Gauthier L, Neale B, MacArthur D.
Nat Methods
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Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
Authors: Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM.
Genome Res
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Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI).
Authors: Chen C, Xing D, Tan L, Li H, Zhou G, Huang L, Xie XS.
Science
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The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.
Authors: Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G, Erlich Y, Willems T, Gallo C, Spence JP, Song YS, Poletti G, Balloux F, van Driem G, de Knijff P, Romero IG, Jha AR, Behar DM, Bravi CM, Capelli C, Hervig T, Moreno-Estrada A, Posukh OL, Balanovska E, Balanovsky O, Karachanak-Yankova S, Sahakyan H, Toncheva D, Yepiskoposyan L, Tyler-Smith C, Xue Y, Abdullah MS, Ruiz-Linares A, Beall CM, Di Rienzo A, Jeong C, Starikovskaya EB, Metspalu E, Parik J, Villems R, Henn BM, Hodoglugil U, Mahley R, Sajantila A, Stamatoyannopoulos G, Wee JT, Khusainova R, Khusnutdinova E, Litvinov S, Ayodo G, Comas D, Hammer MF, Kivisild T, Klitz W, Winkler CA, Labuda D, Bamshad M, Jorde LB, Tishkoff SA, Watkins WS, Metspalu M, Dryomov S, Sukernik R, Singh L, Thangaraj K, Pääbo S, Kelso J, Patterson N, Reich D.
Nature
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Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
Authors: Li H.
Bioinformatics
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BGT: efficient and flexible genotype query across many samples.
Authors: Li H.
Bioinformatics
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The contribution of rare variation to prostate cancer heritability.
Authors: Mancuso N, Rohland N, Rand KA, Tandon A, Allen A, Quinque D, Mallick S, Li H, Stram A, Sheng X, Kote-Jarai Z, Easton DF, Eeles RA, Le Marchand L, Lubwama A, Stram D, Watya S, Conti DV, Henderson B, Haiman CA, Pasaniuc B, Reich D.
Nat Genet
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FermiKit: assembly-based variant calling for Illumina resequencing data.
Authors: Li H.
Bioinformatics
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