Photo of Heng Li,  PhD

Heng Li, PhD

Dana-Farber Cancer Institute

Dana-Farber Cancer Institute


hli@jimmy.harvard.edu

Heng Li, PhD

Dana-Farber Cancer Institute

EDUCATIONAL TITLES

  • Assistant Professor, Biomedical Informatics, Harvard Medical School
  • Assistant professor, Biostatistics and Computational Biology, Dana-Farber Cancer Institute

DF/HCC PROGRAM AFFILIATION

Research Abstract

My lab develops advanced computational algorithms to perform sequence alignment, sequence assembly and mutation discovery. We have extended expertises in the analysis of whole-genome sequencing, Hi-C and single-cell data. We are interested in applying these computational skills to cancer genomics data to improve the accuracy of point and structural mutation calling and to study the mosaic of cancer cells.

Publications

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  • 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. Haplotype-resolved germline and somatic alterations in renal medullary carcinomas. Genome Med 2021; 13:114. PubMed
  • Xing D, Tan L, Chang CH, Li H, Xie XS. Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands. Proc Natl Acad Sci U S A 2021. PubMed
  • Bonfield JK, Marshall J, Danecek P, Li H, Ohan V, Whitwham A, Keane T, Davies RM. HTSlib: C library for reading/writing high-throughput sequencing data. Gigascience 2021. PubMed
  • Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience 2021. PubMed
  • Chu C, Borges-Monroy R, Viswanadham VV, Lee S, Li H, Lee EA, Park PJ. Comprehensive identification of transposable element insertions using multiple sequencing technologies. Nat Commun 2021; 12:3836. PubMed
  • 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. Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol 2020. PubMed
  • Garg S, Aach J, Li H, Durbin R, Church G. A haplotype-aware de novo assembly of related individuals using pedigree sequence graph. Bioinformatics 2019. PubMed
  • Li H. Identifying centromeric satellites with dna-brnn. Bioinformatics 2019. PubMed
  • Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 2018; 34:3094-3100. PubMed
  • Li H, Bloom JM, Farjoun Y, Fleharty M, Gauthier L, Neale B, MacArthur D. A synthetic-diploid benchmark for accurate variant-calling evaluation. Nat Methods 2018; 15:595-597. PubMed
  • Tan L, Xing D, Chang CH, Li H, Xie XS. Three-dimensional genome structures of single diploid human cells. Science 2018; 361:924-928. PubMed
  • Chen C, Xing D, Tan L, Li H, Zhou G, Huang L, Xie XS. Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI). Science 2017; 356:189-194. PubMed
  • 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. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 2017; 538:201-206. PubMed
  • Li H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 2018; 32:2103-10. PubMed
  • Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 2016; 27:2987-93. PubMed
  • Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature 2018; 475:493-6. PubMed
  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, . The Sequence Alignment/Map format and SAMtools. Bioinformatics 2016; 25:2078-9. PubMed
  • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2016; 25:1754-60. PubMed
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