Publications

Group highlights

At the end of this page, you can find the full list of publications. See also Google Scholar.

(† for corresponding authors; bold font for lab members)

  • Cheng H†, Qu H, McKenzie S, Lawrence KR, Windsor R, Vella M, Park PJ and Li H† (2025) Efficient near telomere-to-telomere assembly of Nanopore Simplex reads. bioRxiv. [PMID: pending]
  • Cheng H, Asri M, Lucas J, Koren S, Li H† (2024) Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nat Methods. [PMID: 38730258]
  • Cheng H, Jarvis ED, Fedrigo O, Koepfli K-P, Urban L, Gemmell NJ, Li H† (2022) Haplotype-resolved assembly of diploid individuals without parental data. Nat Biotechnol. [PMID: 35332338]
  • Cheng H, Concepcion GT, Feng X, Zhang H, Li H† (2021) Haplotype-resolved de novo assembly with phased assembly graphs with hifiasm. Nat Methods. [PMID: 33526886]

Full List of publications

  • Cheng H†, Qu H, McKenzie S, Lawrence KR, Windsor R, Vella M, Park PJ and Li H† (2025) Efficient near telomere-to-telomere assembly of Nanopore Simplex reads. bioRxiv. [PMID: pending]
  • Gamaarachchi H, Stevanovski I, Hammond JM, Reis AL, ..., Cheng H, ..., Deveson IW† (2025) Adaptively integrated sequencing and assembly of near-complete genomes. bioRxiv. [PMID: pending]
  • Logsdon GA, Ebert P, ..., Cheng H, ..., Konkel MK†, Korbel JO†, Lee C†, Beck CR†, Eichler EE†, Marschall T† (2024) Complex genetic variation in nearly complete human genomes. bioRxiv. [PMID: 39372794]
  • Cheng H, Asri M, Lucas J, Koren S, Li H† (2024) Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nat Methods. [PMID: 38730258]
  • Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, ..., Cheng H, ..., Jarvis ED†, Schatz MC†, Nekrutenko A†, Formenti G† (2024) Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nat Biotechnol. [PMID: 38278971]
  • Zhang Y, Chu J, Cheng H, Li H† (2023) De novo reconstruction of satellite repeat units from sequence data. Genome Res. [PMID: 37918962]
  • Liao WW, Asri M, Ebler J, Doerr D, ..., Cheng H, ..., Garrison E†, Marschall T†, Hall IM†, Li H†, Paten B† (2023) A draft human pangenome reference. Nature. [PMID: 37165242]
  • Jarvis ED†, Formenti G†, Rhie A, ..., Cheng H, ...,Paten B, Howe K†, Miga KH† (2022) Semi-automated assembly of high-quality diploid human reference genomes. Nature. [PMID: 36261518]
  • Cheng H, Jarvis ED, Fedrigo O, Koepfli K-P, Urban L, Gemmell NJ, Li H† (2022) Haplotype-resolved assembly of diploid individuals without parental data. Nat Biotechnol. [PMID: 35332338]
  • Feng X, Cheng H, Portik D, Li H† (2022) Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nat Methods. [PMID: 35534630]
  • Wagner J, Olson ND, Harris L, McDaniel J, Cheng H, ..., Chin CS†, Zook JM†, Sedlazeck FJ† (2022) Curated variation benchmarks for challenging medically relevant autosomal genes. Nat Biotechnol. [PMID: 35132260]
  • Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, ..., Cheng H, ..., Eichler EE†, Miga KH†, Phillippy AM† (2022) The complete sequence of a human genome. Science. [PMID: 35357919]
  • Zhang H, Song L, Wang X, Cheng H, Wang C, Meyer C. A, Liu T, Tang M, Aluru S, Yue F, Liu XS†, Li H† (2021) Fast alignment and preprocessing of chromatin profiles with Chromap. Nat Commun. [PMID: 34772935]
  • Zhang H, Li H, Jain C, Cheng H, Au KF†, Li H†, Aluru S† (2021) Real-time mapping of nanopore raw signals. Bioinformatics. [PMID: 34252938]
  • Garg S†, Fungtammasan A, Carroll A, ..., Cheng H, Heller D, Zook JM, Moemke T, Marschall T, Sedlazeck FJ, Aach J, Chin CS†, Church GM†, Li H† (2021) Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol. [PMID: 33288905]
  • Cheng H, Concepcion GT, Feng X, Zhang H, Li H† (2021) Haplotype-resolved de novo assembly with phased assembly graphs with hifiasm. Nat Methods. [PMID: 33526886]
  • Cheng H, Zhang Y, Xu Y† (2018) BitMapper2: a GPU-accelerated all-mapper based on the sparse q-gram index. IEEE/ACM Trans Comput Biol Bioinform. [PMID: 29993660]
  • Cheng H, J, Wu M, Xu Y† (2018) FMtree: a fast locating algorithm of FM-indexes for genomic data. Bioinformatics. [PMID: 28968761]
  • Cheng H, Jiang H, Yang J, Xu Y†, Shang Y† (2015) BitMapper: an efficient all-mapper based on bit-vector computing. BMC Bioinformatics. [PMID: 26063651]