Fuli Yu, Ph.D.

Assistant Professor of Molecular and Human Genetics

Fuli Yu, Ph.D.Other Positions

Assistant Professor, Computational and Integrative Biomedical Research Center and Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC)


Ph.D., Baylor College of Medicine, 2005

Postdoc, Harvard Medical School, 2008

Contact Information


Research Interests

My research program is centered around high throughput DNA technologies. One major area that I focus on is computational tool development for next-generation sequencing (NGS) data analysis. We have developed two software packages (Atlas2 and SNPTools) for variation analysis in both personal genomic data and population sequencing data. They have been applied in a number of large-scale projects, including the 1000 Genomes Project, The Cancer Genome Atlas Project, CHARGE-S, and Autism. Atlas2 also powers the backend of the BCM Whole Genome Laboratory (WGL) pipeline.

My close affiliation with the BCM-HGSC allows me to stay updated on technologies in both the bench side and the computational side. My group interacts with others in our center to drive the development and dissemination of the technologies. For example, we are in the process of developing an AWS Cloud based environment to address the genomic BIG DATA challenge.

I am also interested in both population genetics and human genetics. They are very active fields because of the abundance of datasets and technological revolution in the sequencing arena. I have a number of ongoing collaborative projects in these areas.


Li JN, Carrero IG, Dong JF, Yu F. Complexity and diversity of F8 genetic variations in the 1000 genomes. J Thromb Haemost. 2015;13(11):2031-40. doi:10.1111/jth.13144.

Challis D, Antunes L, Garrison E, et al. The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes. BMC Genomics. 2015;16:143. doi:10.1186/s12864-015-1333-7.

Reid JG, Carroll A, Veeraraghavan N, et al. Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline. BMC Bioinformatics. 2014;15:30. doi:10.1186/1471-2105-15-30.

Morrison AC, Voorman A, Johnson AD, et al. Whole-genome sequence-based analysis of high-density lipoprotein cholesterol. Nat Genet. 2013;45(8):899-901. doi:10.1038/ng.2671.

Wang Y, Lu J, Yu J, Gibbs RA, Yu F. An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data. Genome Res. 2013;23(5):833-42. doi:10.1101/gr.146084.112.

Wang QY, Song J, Gibbs RA, Boerwinkle E, Dong JF, Yu F. Characterizing polymorphisms and allelic diversity of von Willebrand factor gene in the 1000 Genomes. J Thromb Haemost. 2013;11(2):261-9. doi:10.1111/jth.12093.

Evani US, Challis D, Yu J, et al. Atlas2 Cloud: a framework for personal genome analysis in the cloud. BMC Genomics. 2012;13 Suppl 6:S19. doi:10.1186/1471-2164-13-S6-S19.