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Haoyu Cheng, PhD

Assistant Professor of Biomedical Informatics and Data Science

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Haoyu Cheng, PhD

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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).

        Education & Training

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

        Honors & Recognition

        AwardAwarding OrganizationDate
        K99/R00 Pathway to Independence AwardNational Human Genome Research Institute2023
        Essential Open Source Software for ScienceChan Zuckerberg Initiative (CZI)2021

        Departments & Organizations