| Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm H Cheng, GT Concepcion, X Feng, H Zhang, H Li Nature methods 18 (2), 170-175, 2021 | 3050 | 2021 |
| The complete sequence of a human genome S Nurk, S Koren, A Rhie, M Rautiainen, AV Bzikadze, A Mikheenko, ... Science 376 (6588), 44-53, 2022 | 2389 | 2022 |
| A draft human pangenome reference WW Liao, M Asri, J Ebler, D Doerr, M Haukness, G Hickey, S Lu, JK Lucas, ... Nature 617 (7960), 312-324, 2023 | 534 | 2023 |
| Haplotype-resolved assembly of diploid genomes without parental data H Cheng, ED Jarvis, O Fedrigo, KP Koepfli, L Urban, NJ Gemmell, H Li Nature Biotechnology 40 (9), 1332-1335, 2022 | 284 | 2022 |
| Chromosome-scale, haplotype-resolved assembly of human genomes S Garg, A Fungtammasan, A Carroll, M Chou, A Schmitt, X Zhou, S Mac, ... Nature biotechnology 39 (3), 309-312, 2021 | 179 | 2021 |
| Curated variation benchmarks for challenging medically relevant autosomal genes J Wagner, ND Olson, L Harris, J McDaniel, H Cheng, A Fungtammasan, ... Nature biotechnology 40 (5), 672-680, 2022 | 158 | 2022 |
| Semi-automated assembly of high-quality diploid human reference genomes ED Jarvis, G Formenti, A Rhie, A Guarracino, C Yang, J Wood, A Tracey, ... Nature 611 (7936), 519-531, 2022 | 148 | 2022 |
| Metagenome assembly of high-fidelity long reads with hifiasm-meta X Feng, H Cheng, D Portik, H Li Nature methods 19 (6), 671-674, 2022 | 114 | 2022 |
| Fast alignment and preprocessing of chromatin profiles with Chromap H Zhang, L Song, X Wang, H Cheng, C Wang, CA Meyer, T Liu, M Tang, ... Nature communications 12 (1), 6566, 2021 | 87 | 2021 |
| Real-time mapping of nanopore raw signals H Zhang, H Li, C Jain, H Cheng, KF Au, H Li, S Aluru Bioinformatics 37 (Supplement_1), i477-i483, 2021 | 60 | 2021 |
| BitMapper: an efficient all-mapper based on bit-vector computing H Cheng, H Jiang, J Yang, Y Xu, Y Shang BMC bioinformatics 16, 1-16, 2015 | 39 | 2015 |
| Lvmapper: A large-variance clone detector using sequencing alignment approach M Wu, P Wang, K Yin, H Cheng, Y Xu, CK Roy IEEE access 8, 27986-27997, 2020 | 38 | 2020 |
| Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph H Cheng, M Asri, J Lucas, S Koren, H Li Nature Methods, 1-4, 2024 | 33 | 2024 |
| Gaps and complex structurally variant loci in phased genome assemblies D Porubsky, MR Vollger, WT Harvey, AN Rozanski, P Ebert, G Hickey, ... Genome research 33 (4), 496-510, 2023 | 27 | 2023 |
| De novo reconstruction of satellite repeat units from sequence data Y Zhang, J Chu, H Cheng, H Li Genome Research 33 (11), 1994-2001, 2023 | 16 | 2023 |
| Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy D Larivière, L Abueg, N Brajuka, C Gallardo-Alba, B Grüning, BJ Ko, ... Nature biotechnology 42 (3), 367-370, 2024 | 15 | 2024 |
| BitMapper2: A GPU-Accelerated All-Mapper Based on the Sparse q-Gram Index H Cheng, Y Zhang, Y Xu IEEE/ACM Transactions on Computational Biology and Bioinformatics 16 (3 …, 2018 | 14 | 2018 |
| BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing H Cheng, Y Xu BioRxiv, 442798, 2018 | 11 | 2018 |
| FMtree: a fast locating algorithm of FM-indexes for genomic data H Cheng, M Wu, Y Xu Bioinformatics 34 (3), 416-424, 2018 | 11 | 2018 |
| Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome HJ Lee, SU Greer, DS Pavlichin, B Zhou, AE Urban, T Weissman, ... Cell Reports Methods 3 (8), 2023 | 5 | 2023 |
