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Yi-Hsiang Hsu

Scientific Director
Genome Analysis Unit

Dr. Hsu is a physician scientist. He has led multiple large-scale whole genome sequencing (WGS), genome-wide association study (GWAS) and Multi-OMICS projects on metabolic-relevant disorders, cardiovascular disorders, musculoskeletal disorders and neuropsychiatric disorders. He has published 120 papers about human genetics and statistical genetics and is regarded as one of the leading experts in the field of using sophisticated statistical genetics and AI deep-learning machine-learning to conduct advanced statistical analysis. His research focus is: (1) Precision medicine in immuno-oncology utilizing AI deep-learning algorithms to develop personalized tumor-specific neoantigen prediction pipelines for potential use in cancer vaccine therapies; (2) AI machine learning approaches to identify novel therapeutic targets and to understand mechanisms of action (MOA); (3) Statistical methodology development for GWAS approaches; (4) Identifying genetic determinants of common aging relevant disorders via population-based whole genome sequencing approaches; (5) Building cell-specific gene regulatory circuits/landscapes via 3D genomics structure, chromatin accessibility and functional genomics approaches to identify disease-risk causal genetic variants and targeted genes.

Dr. Hsu leads a group of computational biologists at Amgen and has contributed to 13 INDs and 4 product teams across therapeutic areas. As a human-genetics expert, he has contributed to 14 target discovery efforts in cardiometabolic disorders, immuno-oncology and neurology. He has been the computational biology lead for patient stratification and treatment response as well as a subject matter expert for multiple development and clinical projects including the evaluation of AI deep learning, machine learning and quantum computing in clinical research organizations.

Featured Publications

Pei B & Hsu YH. "IConMHC": A Deep Learning Convolutional Neural Network Model to Predict Peptide and MHC-I Binding Affinity. Immunogenetics. 2020 Jul;72(5):295-304. DOI: 10.1007/s00251-020-01163-9 https://link.springer.com/article/10.1007/s00251-020-01163-9

Targan SR, Feagan B, Vermeire S, Panaccione R, Melmed GY, Landers C, Li D, Russell C, Newmark R, Zhang N, Chon Y, Hsu YH, Lin SL, Klekotka P. A Randomized, Double-Blind, Placebo-Controlled Phase 2 Study of Brodalumab in Patients with Moderate-to-Severe Crohn's Disease. Am J Gastroenterol. 2016 Nov;111(11):1599-1607.  DOI: 10.1038/ajg.2016.298. https://journals.lww.com/ajg/Abstract/2016/11000/A_Randomized,_Double_Blind,_Placebo_Controlled.25.aspx

Zheng H, Forgetta V, Hsu YH, et al. Whole-genome sequencing identifies non-coding variants near EN1 with large effects on bone mineral density. Nature. 2015 Oct 1;526(7571):112-7. DOI:  10.1038/nature14878. https://www.nature.com/articles/nature14878

Perry JR, Hsu YH, Chasman DI, et al. DNA mismatch repair gene MSH6 implicated in determining age at natural menopause. Hum Mol Genet. 2014 May 1;23(9):2490-7.  DOI: 10.1093/hmg/ddt620. https://academic.oup.com/hmg/article/23/9/2490/631965

Hsu YH, Liu Y, Hannan MT, et al. Genome-wide association meta-analyses to identify common genetic variants associated with hallux valgus in Caucasian and African Americans. J Med Genet. 2015 Nov;52(11):762-9.  DOI: 10.1136/jmedgenet-2015-103142. https://jmg.bmj.com/content/52/11/762

Education

M.D., Harvard Medical School
Harvard University