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.


Wang J, Chen L, Zhou C, et al. Prospective chromosome analysis of 3429 amniocentesis samples in China using copy number variation sequencing. Am J Obstet Gynecol. 2018. doi:10.1016/j.ajog.2018.05.030.

Retshabile G, Mlotshwa BC, Williams L, et al. Whole-Exome Sequencing Reveals Uncaptured Variation and Distinct Ancestry in the Southern African Population of Botswana. Am J Hum Genet. 2018;102(5):731-743. doi:10.1016/j.ajhg.2018.03.010.

Morrison AC, Huang Z, Yu B, et al. Practical Approaches for Whole-Genome Sequence Analysis of Heart- and Blood-Related Traits. Am J Hum Genet. 2017;100(2):205-215. doi:10.1016/j.ajhg.2016.12.009.

Rustagi N, Zhou A, W Watkins S, et al. Extremely low-coverage whole genome sequencing in South Asians captures population genomics information. BMC Genomics. 2017;18(1):396. doi:10.1186/s12864-017-3767-6.

Campbell IM, Gambin T, Jhangiani SN, et al. Multiallelic Positions in the Human Genome: Challenges for Genetic Analyses. Hum Mutat. 2016;37(3):231-4. doi:10.1002/humu.22944.

Xue C, Raveendran M, R Harris A, et al. The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences. Genome Res. 2016;26(12):1651-1662. doi:10.1101/gr.204255.116.

Song J, Xue C, Preisser JS, et al. Association of Single Nucleotide Polymorphisms in the ST3GAL4 Gene with VWF Antigen and Factor VIII Activity. PLoS One. 2016;11(9):e0160757. doi:10.1371/journal.pone.0160757.

Huang Z, Rustagi N, Veeraraghavan N, et al. A hybrid computational strategy to address WGS variant analysis in >5000 samples. BMC Bioinformatics. 2016;17(1):361. doi:10.1186/s12859-016-1211-6.

Xue C, Chen H, Yu F. Base-Biased Evolution of Disease-Associated Mutations in the Human Genome. Hum Mutat. 2016;37(11):1209-1214. doi:10.1002/humu.23065.