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Molecular and Human Genetics

Houston, Texas

Department of Molecular and Human Genetics
Department of Molecular and Human Genetics
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Fuli Yu, Ph.D,

Fuli Yu, Ph.D,Assistant Professor of Molecular and Human Genetics

Other Positions

Assistant Professor, Computational and Integrative Biomedical Research Center and Human Genome Sequencing Center


Ph.D., Baylor College of Medicine, 2005
Postdoc, Harvard Medical School, 2008

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 Autisms. Atlas2 also powers the backend of the BCM Whole Genome Laboratory (WGL) pipeline.

My close affiliation with the BCM Human Genome Sequencing Center allows me to stay updated on technologies in both the bench side and the computational side. My group interacts with others in the 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.

Selected Publications

  1. Lu JT, Wang Y, Gibbs RA, Yu F (2012). Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms. Genome Biol. 13(2): R15. PubMed PMID: 22377349
  2. Campos M, Buchanan A, Yu F, Barbalic M, Xiao Y, Chambless LE, Wu KK, Folsom AR, Boerwinkle E, Dong JF (2012). Influence of single nucleotide polymorphisms in factor VIII and von Willebrand factor genes on plasma factor VIII activity: the ARIC Study. Blood 119(8): 1929-34. PubMed PMID: 22219226
  3. Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, Milosavljevic A, Gibbs RA, Yu F (2012). An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics 13: 8. PubMed PMID: 22239737
  4. Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R; 1000 Genomes Project (2011). The functional spectrum of low-frequency coding variation. Genome Biol. 12(9): R84. PubMed PMID: 21917140
  5. 1000 Genomes Project Consortium (2010). A map of human genome variation from population-scale sequencing. Nature 467(7319): 1061-73. PubMed PMID: 20981092
  6. International HapMap 3 Consortium, Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA, de Bakker PI, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Yu F, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Gibbs RA, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, Nemesh J, Dermitzakis E, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Bonnen PE, Gibbs RA, Gonzaga-Jauregui C, Keinan A, Price AL, Yu F, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Schaffner SF, Zhang Q, Ghori MJ, McGinnis R, McLaren W, Pollack S, Price AL, Schaffner SF, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C, Brooks LD, McEwen JE (2010). Integrating common and rare genetic variation in diverse human populations. Nature 467(7311): 52-8. PubMed PMID: 20811451
  7. Xing J, Watkins WS, Hu Y, Huff CD, Sabo A, Muzny DM, Bamshad MJ, Gibbs RA, Jorde LB, Yu F (2010). Genetic diversity in India and the inference of Eurasian population expansion. Genome Biol. 11(11): R113. PubMed PMID: 21106085
  8. Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F (2010). A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res. 20(2): 273-80. PubMed PMID: 20019143
  9. Yu F, Hill RS, Schaffner SF, Sabeti PC, Wang ET, Mignault AA, Ferland RJ, Moyzis RK, Walsh CA, Reich D (2007). Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens". Science 316(5823): 370. PubMed PMID: 17446375
  10. International HapMap Consortium (2005). A haplotype map of the human genome. Nature 437(7063): 1299-320. PubMed PMID: 16255080

Contact Information

Fuli Yu, Ph.D.
Department of Molecular and Human Genetics
Baylor College of Medicine
One Baylor Plaza
Mail Stop: BCM225
Houston, TX, 77030, U.S.A.

Phone: 713-798-7676

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