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INFORMATION FOR

Haoyu Cheng, PhD

Assistant Professor of Biomedical Informatics and Data Science
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Appointments

Biomedical Informatics & Data Science
Primary

Additional Titles

Affiliated Faculty, Yale Center for Genomic Health

About

Titles

Assistant Professor of Biomedical Informatics and Data Science

Affiliated Faculty, Yale Center for Genomic Health

Biography

Haoyu Cheng is a tenure-track Assistant Professor at the Department of Biomedical Informatics and Data Science (BIDS) at Yale University. His research is dedicated to creating highly efficient computational methodologies for genomic applications, such as genome assembly, read alignment, variant calling, and string indexing. He has developed a series of de novo genome assembly algorithms (e.g. hifiasm) that have been extensively utilized across a variety of large-scale sequencing projects, including the Human Pangenome Reference Consortium, the Vertebrate Genomes Project, and the Darwin Tree of Life project. Within these projects, he also works closely with collaborators to explore the applications of genome assemblies. Haoyu was a Postdoctoral Scholar working with Dr. Heng Li at Dana-Farber Cancer Institute and Harvard Medical School. He obtained his Ph.D. degree in Computer Science from the University of Science and Technology of China, under the supervision of Dr. Yun Xu.

Selected publications

1. 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).

2. 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).

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

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

Appointments

  • Biomedical Informatics & Data Science

    Assistant Professor
    Primary

Other Departments & Organizations

  • Biomedical Informatics & Data Science
  • Computational Biology and Biomedical Informatics
  • Janeway Society
  • Yale Center for Genomic Health
  • Yale Combined Program in the Biological and Biomedical Sciences (BBS)

Education & Training

Postdoctoral Fellow
Dana-Farber Cancer Institute and Harvard Medical School (2024)
PhD
University of Science and Technology of China, Computer Science (2019)

Research

Overview

Public Health Interests

Bioinformatics; Genetics, Genomics, Epigenetics

Research at a Glance

Yale Co-Authors

Frequent collaborators of Haoyu Cheng's published research.

Publications

Featured Publications

2024

  • Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy.
    Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Antunes A, Balacco JR, Chaisson MJP, Cheng H, Collins J, Couture M, Denisova A, Fedrigo O, Gallo GR, Giani AM, Gooder GM, Horan K, Jain N, Johnson C, Kim H, Lee C, Marques-Bonet T, O'Toole B, Rhie A, Secomandi S, Sozzoni M, Tilley T, Uliano-Silva M, van den Beek M, Williams RW, Waterhouse RM, Phillippy AM, Jarvis ED, Schatz MC, Nekrutenko A, Formenti G. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nat Biotechnol 2024, 42: 367-370. PMID: 38278971, DOI: 10.1038/s41587-023-02100-3.
    Peer-Reviewed Original Research

2023

  • Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome
    Lee H, Greer S, Pavlichin D, Zhou B, Urban A, Weissman T, Consortium H, Liao W, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas J, Monlong J, Abel H, Buonaiuto S, Chang X, Cheng H, Chu J, Colonna V, Eizenga J, Feng X, Fischer C, Fulton R, Garg S, Groza C, Guarracino A, Harvey W, Heumos S, Howe K, Jain M, Lu T, Markello C, Martin F, Mitchell M, Munson K, Mwaniki M, Novak A, Olsen H, Pesout T, Porubsky D, Prins P, Sibbesen J, Tomlinson C, Villani F, Vollger M, Antonacci-Fulton L, Baid G, Baker C, Belyaeva A, Billis K, Carroll A, Chang P, Cody S, Cook D, Cornejo O, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld A, Formenti G, Frankish A, Gao Y, Giron C, Green R, Haggerty L, Hoekzema K, Hourlier T, Ji H, Kolesnikov A, Korbel J, Kordosky J, Lee H, Lewis A, Magalhães H, Marco-Sola S, Marijon P, McDaniel J, Mountcastle J, Nattestad M, Olson N, Puiu D, Regier A, Rhie A, Sacco S, Sanders A, Schneider V, Schultz B, Shafin K, Sirén J, Smith M, Sofia H, Tayoun A, Thibaud-Nissen F, Tricomi F, Wagner J, Wood J, Zimin A, Popejoy A, Bourque G, Chaisson M, Flicek P, Phillippy A, Zook J, Eichler E, Haussler D, Jarvis E, Miga K, Wang T, Garrison E, Marschall T, Hall I, Li H, Paten B, Ji H. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome. Cell Reports Methods 2023, 3: 100543. PMID: 37671027, PMCID: PMC10475782, DOI: 10.1016/j.crmeth.2023.100543.
    Peer-Reviewed Original Research
  • A draft human pangenome reference
    Liao W, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas J, Monlong J, Abel H, Buonaiuto S, Chang X, Cheng H, Chu J, Colonna V, Eizenga J, Feng X, Fischer C, Fulton R, Garg S, Groza C, Guarracino A, Harvey W, Heumos S, Howe K, Jain M, Lu T, Markello C, Martin F, Mitchell M, Munson K, Mwaniki M, Novak A, Olsen H, Pesout T, Porubsky D, Prins P, Sibbesen J, Sirén J, Tomlinson C, Villani F, Vollger M, Antonacci-Fulton L, Baid G, Baker C, Belyaeva A, Billis K, Carroll A, Chang P, Cody S, Cook D, Cook-Deegan R, Cornejo O, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld A, Formenti G, Frankish A, Gao Y, Garrison N, Giron C, Green R, Haggerty L, Hoekzema K, Hourlier T, Ji H, Kenny E, Koenig B, Kolesnikov A, Korbel J, Kordosky J, Koren S, Lee H, Lewis A, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson N, Popejoy A, Puiu D, Rautiainen M, Regier A, Rhie A, Sacco S, Sanders A, Schneider V, Schultz B, Shafin K, Smith M, Sofia H, Abou Tayoun A, Thibaud-Nissen F, Tricomi F, Wagner J, Walenz B, Wood J, Zimin A, Bourque G, Chaisson M, Flicek P, Phillippy A, Zook J, Eichler E, Haussler D, Wang T, Jarvis E, Miga K, Garrison E, Marschall T, Hall I, Li H, Paten B. A draft human pangenome reference. Nature 2023, 617: 312-324. PMID: 37165242, PMCID: PMC10172123, DOI: 10.1038/s41586-023-05896-x.
    Peer-Reviewed Original Research
  • Gaps and complex structurally variant loci in phased genome assemblies
    Porubsky D, Vollger M, Harvey W, Rozanski A, Ebert P, Hickey G, Hasenfeld P, Sanders A, Stober C, Consortium H, Korbel J, Paten B, Marschall T, Eichler E, Abel H, Antonacci-Fulton L, Asri M, Baid G, Baker C, Belyaeva A, Billis K, Bourque G, Buonaiuto S, Carroll A, Chaisson M, Chang P, Chang X, Cheng H, Chu J, Cody S, Colonna V, Cook D, Cook-Deegan R, Cornejo O, Diekhans M, Doerr D, Ebert P, Ebler J, Eichler E, Eizenga J, Fairley S, Fedrigo O, Felsenfeld A, Feng X, Fischer C, Flicek P, Formenti G, Frankish A, Fulton R, Gao Y, Garg S, Garrison E, Garrison N, Giron C, Green R, Groza C, Guarracino A, Haggerty L, Hall I, Harvey W, Haukness M, Haussler D, Heumos S, Hickey G, Hoekzema K, Hourlier T, Howe K, Jain M, Jarvis E, Ji H, Kenny E, Koenig B, Kolesnikov A, Korbel J, Kordosky J, Koren S, Lee H, Lewis A, Li H, Liao W, Lu S, Lu T, Lucas J, Magalhães H, Marco-Sola S, Marijon P, Markello C, Marschall T, Martin F, McCartney A, McDaniel J, Miga K, Mitchell M, Monlong J, Mountcastle J, Munson K, Mwaniki M, Nattestad M, Novak A, Nurk S, Olsen H, Olson N, Paten B, Pesout T, Phillippy A, Popejoy A, Porubsky D, Prins P, Puiu D, Rautiainen M, Regier A, Rhie A, Sacco S, Sanders A, Schneider V, Schultz B, Shafin K, Sibbesen J, Sirén J, Smith M, Sofia H, Tayoun A, Thibaud-Nissen F, Tomlinson C, Tricomi F, Villani F, Vollger M, Wagner J, Walenz B, Wang T, Wood J, Zimin A, Zook J. Gaps and complex structurally variant loci in phased genome assemblies. Genome Research 2023, 33: 496-510. PMID: 37164484, PMCID: PMC10234299, DOI: 10.1101/gr.277334.122.
    Peer-Reviewed Original Research

2022

See All Publications

Academic Achievements & Community Involvement

  • honor

    K99/R00 Pathway to Independence Award

    National AwardNational Human Genome Research Institute
  • honor

    Essential Open Source Software for Science

    Other AwardChan Zuckerberg Initiative (CZI)

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