Haoyu Cheng

Haoyu Cheng is a tenure-track Assistant Professor at the Department of Biomedical Informatics and Data Science (BIDS) at Yale University. His research focuses on developing computational methodologies for genomic applications, including genome assembly, read alignment, variant calling, and string indexing. He leads the Cheng Lab, which collaborates with initiatives like the Human Pangenome Reference Consortium and the Darwin Tree of Life project. He holds a Ph.D. in Computer Science from the University of Science and Technology of China and completed a postdoctoral fellowship at Dana-Farber Cancer Institute and Harvard Medical School under Dr. Heng Li.

Key research interests include telomere-to-telomere assembly, haplotype-resolved genome analysis, and scalable genomic tools. Notable contributions include the hifiasm assembly algorithm, widely used in large-scale sequencing projects. His work bridges computational efficiency and genomic innovation, addressing challenges in diploid/polyploid genomes and structural variation analysis.

Awards include the K99/R00 Pathway to Independence Award and recognition for Essential Open Source Software for Science (CZI). Collaborations span Yale’s Center for Genomic Health and global consortia like the Vertebrate Genomes Project.

Publications highlight advancements in genome assembly techniques, including scalable methods for complex genomes and haplotype-resolved approaches. His lab actively engages in pangenome research and translational genomics, driving reproducible genomic analysis through platforms like Galaxy.