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Yale University: New Haven, US

2024-07-01 to present | Assistant Professor (Biomedical Informatics & Data Science)
Employment
Source: Self-asserted source
Haoyu Cheng

Works (19)

Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph.

Nature methods
2024-05-10 | Journal article | Author
DOI: 10.1038/s41592-024-02269-8
PMID: 38730258
Contributors: Haoyu Cheng; Asri M; Lucas J; Sergey Koren; Heng Li
Source: Self-asserted source
Haoyu Cheng

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

Nature Biotechnology
2024-03 | Journal article
DOI: 10.1038/s41587-023-02100-3
Part of ISSN: 1087-0156
Part of ISSN: 1546-1696
Contributors: Delphine Lariviere; Linelle Abueg; Nadolina Brajuka; Cristóbal Gallardo-Alba; Björn Grüning; Byung June Ko; Alex Ostrovsky; Marc Palmada-Flores; Brandon Pickett; Keon Rabbani et al.
Source: Self-asserted source
Haoyu Cheng

De novo reconstruction of satellite repeat units from sequence data

Genome Research
2023-11 | Journal article
DOI: 10.1101/gr.278005.123
Part of ISSN: 1088-9051
Part of ISSN: 1549-5469
Contributors: Yujie Zhang; Justin Chu; Haoyu Cheng; Heng Li
Source: Self-asserted source
Haoyu Cheng

Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Cell Reports Methods
2023-08 | Journal article
DOI: 10.1016/j.crmeth.2023.100543
Part of ISSN: 2667-2375
Contributors: HoJoon Lee; Stephanie U. Greer; Dmitri S. Pavlichin; Bo Zhou; Alexander E. Urban; Tsachy Weissman; Hanlee Ji; Wen-Wei Liao; Mobin Asri; Jana Ebler et al.
Source: Self-asserted source
Haoyu Cheng

A draft human pangenome reference

Nature
2023-05-11 | Journal article
DOI: 10.1038/s41586-023-05896-x
Part of ISSN: 0028-0836
Part of ISSN: 1476-4687
Contributors: Wen-Wei Liao; Mobin Asri; Jana Ebler; Daniel Doerr; Marina Haukness; Glenn Hickey; Shuangjia Lu; Julian K. Lucas; Jean Monlong; Haley J. Abel et al.
Source: Self-asserted source
Haoyu Cheng

Gaps and complex structurally variant loci in phased genome assemblies

Genome Research
2023-04 | Journal article
DOI: 10.1101/gr.277334.122
Part of ISSN: 1088-9051
Part of ISSN: 1549-5469
Contributors: David Porubsky; Mitchell R. Vollger; William T. Harvey; Allison Rozanski; Peter Ebert; Glenn Hickey; Patrick Hasenfeld; Ashley D Sanders; Catherine Stober Brasseur; Human Pangenome Reference Consortium et al.
Source: Self-asserted source
Haoyu Cheng

Semi-automated assembly of high-quality diploid human reference genomes

Nature
2022-11-17 | Journal article
DOI: 10.1038/s41586-022-05325-5
Part of ISSN: 0028-0836
Part of ISSN: 1476-4687
Contributors: Erich Jarvis; Giulio Formenti; Arang Rhie; Andrea Guarracino; Chentao Yang; Jonathan Wood; Alan Tracey; Françoise Thibaud-Nissen; Mitchell R. Vollger; David Porubsky et al.
Source: Self-asserted source
Haoyu Cheng

Haplotype-resolved assembly of diploid genomes without parental data

Nature Biotechnology
2022-09 | Journal article | Author
DOI: 10.1038/s41587-022-01261-x
Part of ISSN: 1087-0156
Part of ISSN: 1546-1696
Contributors: Haoyu Cheng; Erich Jarvis; Olivier Fedrigo; Klaus-Peter Koepfli; Lara Urban; Neil J. Gemmell; Heng Li
Source: Self-asserted source
Haoyu Cheng

Metagenome assembly of high-fidelity long reads with hifiasm-meta

Nature Methods
2022-06 | Journal article
DOI: 10.1038/s41592-022-01478-3
Part of ISSN: 1548-7091
Part of ISSN: 1548-7105
Contributors: Xiaowen Feng; Haoyu Cheng; Daniel Portik; Heng Li
Source: Self-asserted source
Haoyu Cheng

The complete sequence of a human genome

Science
2022-04 | Journal article | Author
DOI: 10.1126/science.abj6987
Part of ISSN: 0036-8075
Part of ISSN: 1095-9203
Contributors: Sergey Nurk; Sergey Koren; Arang Rhie; Mikko Rautiainen; Andrey Bzikadze; Alla Mikheenko; Mitchell R. Vollger; Nicolas Altemose; Lev Uralsky; Ariel R. Gershman et al.
Source: Self-asserted source
Haoyu Cheng

Curated variation benchmarks for challenging medically relevant autosomal genes

Nature Biotechnology
2022-02-07 | Journal article
DOI: 10.1038/s41587-021-01158-1
Part of ISSN: 1087-0156
Part of ISSN: 1546-1696
Source: Self-asserted source
Haoyu Cheng

Fast alignment and preprocessing of chromatin profiles with Chromap

Nature Communications
2021-12 | Journal article
DOI: 10.1038/s41467-021-26865-w
Part of ISSN: 2041-1723
Source: Self-asserted source
Haoyu Cheng

Real-time mapping of nanopore raw signals

Bioinformatics
2021-08-04 | Journal article
DOI: 10.1093/bioinformatics/btab264
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
Haoyu Cheng

Chromosome-scale, haplotype-resolved assembly of human genomes

Nature Biotechnology
2021-03 | Journal article
DOI: 10.1038/s41587-020-0711-0
Part of ISSN: 1087-0156
Part of ISSN: 1546-1696
Source: Self-asserted source
Haoyu Cheng

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

Nature Methods
2021-02 | Journal article
DOI: 10.1038/s41592-020-01056-5
Part of ISSN: 1548-7091
Part of ISSN: 1548-7105
Source: Self-asserted source
Haoyu Cheng

BitMapper2: A GPU-Accelerated All-Mapper Based on the Sparse q-Gram Index

IEEE/ACM Transactions on Computational Biology and Bioinformatics
2019-05-01 | Journal article
DOI: 10.1109/tcbb.2018.2822687
Part of ISSN: 1545-5963
Part of ISSN: 1557-9964
Part of ISSN: 2374-0043
Source: Self-asserted source
Haoyu Cheng

BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing

[]
2018-10-14 | Preprint
DOI: 10.1101/442798
Source: Self-asserted source
Haoyu Cheng

FMtree: a fast locating algorithm of FM-indexes for genomic data

Bioinformatics
2018-02-01 | Journal article
DOI: 10.1093/bioinformatics/btx596
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
Haoyu Cheng

BitMapper: an efficient all-mapper based on bit-vector computing

BMC Bioinformatics
2015-12 | Journal article
DOI: 10.1186/s12859-015-0626-9
Part of ISSN: 1471-2105
Source: Self-asserted source
Haoyu Cheng

Peer review (7 reviews for 6 publications/grants)

Review activity for Communications biology. (1)
Review activity for Genomics, Proteomics & Bioinformatics. (1)
Review activity for Journal of Molecular Biology. (1)
Review activity for Nature communications (2)
Review activity for Nature methods. (1)
Review activity for Nature plants. (1)
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