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Haoyu Cheng
Haoyu Cheng
Dana-Farber Cancer Institute & Harvard Medical School
Verificeret mail på ds.dfci.harvard.edu
Titel
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Citeret af
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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
23802021
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
20172022
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
3812023
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
2092022
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
1622021
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
1342022
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
1172022
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
862022
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
572021
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
562021
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
372020
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
372015
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
202023
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
162024
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
142018
BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing
H Cheng, Y Xu
BioRxiv, 442798, 2018
112018
FMtree: a fast locating algorithm of FM-indexes for genomic data
H Cheng, M Wu, Y Xu
Bioinformatics 34 (3), 416-424, 2018
112018
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
82023
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
72024
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
22023
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