(See also Google Scholar; # for corresponding authors; bold font for lab members)

Computational methodologies for genome assembly

  • Cheng H, Asri M, Lucas J, Koren S, Li H#. “Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph.” Nat Methods (2024).

  • Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, …, Cheng H, …, Formenti G#. “Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy.” Nat Biotechnol (2024).

  • Cheng H, Jarvis ED, Fedrigo O, Koepfli KP, Urban L, Gemmell NJ, Li H#. “Haplotype-resolved assembly of diploid genomes without parental data.” Nat Biotechnol (2022).

  • Feng X, Cheng H, Portik D. and Li H#. “Metagenome assembly of high-fidelity long reads with hifiasm-meta.” Nat Methods (2022).

  • Cheng H, Concepcion GT, Feng X, Zhang H, Li H#. “Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.” Nat Methods (2021).

Large-scale genome analysis

  • Liao WW, Asri M, Ebler J, Doerr D, Haukness M, …, Cheng H, …, Paten B#. “A draft human pangenome reference.” Nature (2023).

  • Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, …, Cheng H, …, Miga KH#. “Semi-automated assembly of high-quality diploid human reference genomes.” Nature (2022).

  • Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, …, Cheng H, …, Phillippy AM#. “The complete sequence of a human genome.” Science (2022).

  • Wagner J, Olson ND, Harris L, McDaniel J, Cheng H, …, Sedlazeck FJ#. “Curated variation benchmarks for challenging medically relevant autosomal genes.” Nat Biotechnol (2022).

String algorithms for sequence analysis

  • Zhang Y, Chu J, Cheng H, Li H#. “De novo reconstruction of satellite repeat units from sequence data.” Genome Res (2023).

  • Zhang H, Song L, Wang X, Cheng H, Wang C, …, Li H#. “Fast alignment and preprocessing of chromatin profiles with Chromap.” Nat Commun (2021).

  • Zhang H, Li H, Jain C, Cheng H, Au KF, Li H, Aluru S#. “Real-time mapping of nanopore raw signals.” Bioinformatics (2021).

  • Cheng H, Zhang Y, Xu Y#. “BitMapper2: A GPU-Accelerated All-Mapper Based on the Sparse q-Gram Index.” IEEE/ACM Trans Comput Biol Bioinform (2018).

  • Cheng H, Wu M, Xu Y#. “FMtree: a fast locating algorithm of FM-indexes for genomic data.” Bioinformatics (2018).

  • Cheng H, Jiang H, Yang J, Xu Y, Shang Y#. “BitMapper: an efficient all-mapper based on bit-vector computing.” BMC Bioinformatics (2015).