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Chih-Hao Hsu F PhD.

Chih-Hao Hsu

Chih-Hao Hsu, PhD
Chih-Hao Hsu PhD.

Division of Animal and Food Microbiology


Dr. Hsu got his PhD in computer science and engineering from the Pennsylvania State University in 2009. Since graduation, Dr. Hsu has worked as a Visiting Fellow in the National Center for Biotechnology Information (NCBI) and as a Research Fellow in the National Cancer Institute (NCI). Dr. Hsu joined the FDA in 2015 and has provided his bioinformatics expertise in support of the study of antimicrobial resistance for the National Antimicrobial Resistance Monitoring System (NARMS) project.


  • Provides bioinformatics expertise in support of next-generation sequencing and metagenomics data analyses.
  • Initiates and performs studies in accordance with Center priorities in collaboration with microbiologists in the Division of Food and Animal Microbiology and other scientists within the Center for Veterinary Medicine’s Office of Research
  • Works with principal investigators to understand their bioinformatics analysis needs and turns ideas into practical design and implementation, optimizes non-production code, constructs pipelines from building blocks, and conducts advanced data analysis and modeling
  • Leads experiments in which experimental theories and new analysis methods are developed and applied to problems whose analyses are not supported by usual data analysis methods

Select Publications

Hill, S.M., Heiser, L.M., Cokelaer, T., Unger, M., Nesser, N.K., Carlin, D.E., Zhang, Y., Sokolov, A., Paull, E.O., Wong, C.K., Graim, K., The HPN-DREAM Consortium, et al., 2016. Inferring causal molecular networks: empirical assessment through a community-based effort. Nature methods, 13(4), pp.310–318.

Hsu, C.H., Nguyen, C., Yan, C., Ries, R.E., Chen, Q.R., Hu, Y., Ostronoff, F., Stirewalt, D.L., Komatsoulis, G., Levy, S. and Meerzaman, D., 2015. Transcriptome profiling of pediatric core binding factor AML. PloS one, 10(9), p.e0138782.

Ewing, A.D., Houlahan, K.E., Hu, Y., Ellrott, K., Caloian, C., Yamaguchi, T.N., Bare, J.C., P'ng, C., Waggott, D., Sabelnykova, V.Y. and ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, 2015. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nature methods, 12(7), pp.623–630.

Perlman, E.J., Gadd, S., Arold, S.T., Radhakrishnan, A., Gerhard, D.S., Jennings, L., Huff, V., JM, G.A., Davidsen, T.M., Dome, J.S., Meerzaman, D., Hsu, C.H., et al., 2014. MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours. Nature communications, 6, pp.10013–10013.

Hsu, C.H. and Ovcharenko, I., 2013. Effects of gene regulatory reprogramming on gene expression in human and mouse developing hearts. Phil. Trans. R. Soc. B, 368(1620), p.20120366.

Contact Information
Chih-Hao Hsu