BIMSA > Yongtao Guan
Associate Professor Yongtao Guan

Yongtao Guan

Associate Professor
Affiliation: BIMSA
Research Field: Statistical Genetics
Office: A11-105
Email: ytguan@bimsa.cn
Webpage: https://haplotype.org/

Biography

I am an Associate Professor at BIMSA. I joined BIMSA in the summer of 2025. My Research area is statistical genetics, where I develop statistical and computational methods, mainly from Bayesian perspective, with targeted applications in genomic studies and genetic diagnosis. Currently I am working on studying haplotype variation using deep learning models. I am also interested in studying genetic determinants of autism, and early cancer screening.

Research Interest

  • Statistical and computational methods for genetic association studies
  • Haplotype variation, local ancestry, and admixture analysis
  • Parent-of-origin effects in gene expression and complex traits

Education Experience

  • 2002 - 2006 | University of Idaho | Mathematics | Ph.D
  • 2000 - 2002 | University of Minnesota, Duluth | Mathematics | M.Sc.
  • 1992 - -- | Southeast University | Biomedical Engineering | B.Sc.

Work Experience

  • 2025 - -- | BIMSA | Associate Professor
  • 2022 - 2025 | Framingham Heart Study, National Heart, Lung, and Blood Institute | Staff Scientist
  • 2018 - 2022 | Dept. of Biostatistics and Bioinformatics, Duke University | Assistant Professor
  • 2010 - 2018 | Dept.’s of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine | Assistant Professor
  • 2010 - 2018 | USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine | Faculty
  • 2006 - 2010 | Dept.’s of Statistic and Human Genetics, U of Chicago | Postdoc

Publication

  • [1] Y Guan, D Levy, Bayes factor for linear mixed model in genetic association studies, Quantitative Biology, 14(2), e70036 (2026)
  • [2] Y Guan, T Huan, D Levy, Abundant Parent-of-origin Effect eQTL in Humans: The Framingham Heart Study, eLife (2025)
  • [3] Y Guan, D Levy, Reflection Knockoffs via Householder Reflection: Applications in Proteomics and Genetic Fine Mapping, Genetics , 231(3), iyaf178 (2025)
  • [4] Y Guan, D Levy, Asymptotically exact fit for linear mixed model in genetic association studies, Genetics, 228(2), iyae143 (2024)
  • [5] Y Guan, D Levy, Estimation of inbreeding and kinship coefficients via latent identity-by-descent states, Bioinformatics, 40(2), btae082 (2024)
  • [6] A Jajoo, O Hirschi, K Schulze, Y Guan, NA Hanchard, A first-generation genome-wide map of correlated DNA methylation demonstrates highly coordinated and tissue-independent clustering across regulatory regions, Research Square, 3 (2023)
  • [7] H Qi, H Zhang, Y Zhao, C Chen, JJ Long, WK Chung, Y Guan, Y Shen, MVP predicts the pathogenicity of missense variants by deep learning, Nature communications, 12(1), 510 (2021)
  • [8] M Dang, H Xu, J Zhang, W Wang, L Bai, N Fang, L Liang, J Zhang, F Liu, ..., Inferring fetal fractions from read heterozygosity empowers the noninvasive prenatal screening, Genetics in medicine, 22(2), 301-308 (2020)
  • [9] H Dai, Y Guan, The Nubeam reference-free approach to analyze metagenomic sequencing reads, Genome research, 30(9), 1364-1375 (2020)
  • [10] H Dai, Y Guan, : a fast and RAM-efficient tool to de-duplicate sequencing reads without mapping, Bioinformatics, 36(10), 3254-3256 (2020)
  • [11] KV Schulze, S Swaminathan, S Howell, A Jajoo, NC Lie, O Brown, ..., Edematous severe acute malnutrition is characterized by hypomethylation of DNA, Nature communications, 10(1), 5791 (2019)
  • [12] Q Zhou, Y Guan, On the null distribution of Bayes factors in linear regression, Journal of the American Statistical Association, 113(523), 1362-1371 (2018)
  • [13] Z Qi, S Xie, R Chen, HA Aisa, GC Hon, Y Guan, Tissue-specific gene expression prediction associates vitiligo with SUOX through an active enhancer, bioRxiv (2018)
  • [14] Q Zhou, Y Guan, Fast model-fitting of Bayesian variable selection regression using the iterative complex factorization algorithm, Bayesian analysis, 14(2), 573 (2018)
  • [15] H Xu, S Wang, LL Ma, S Huang, L Liang, Q Liu, YY Liu, KD Liu, ZM Tan, ..., Informative priors on fetal fraction increase power of the noninvasive prenatal screen, Genetics in Medicine, 20(8), 817-824 (2018)
  • [16] LM Williams, Z Qi, K Batai, S Hooker, NJ Hall, RF Machado, A Chen, ..., A locus on chromosome 5 shows African ancestry–limited association with alloimmunization in sickle cell disease, Blood advances, 2(24), 3637-3647 (2018)
  • [17] D He, Q Zhu, Q Zhou, Q Qi, H Sun, LM Zachariah, G Wang, JD Reveille, ..., Correlation of serum MMP3 and other biomarkers with clinical outcomes in patients with ankylosing spondylitis: a pilot study, Clinical rheumatology, 36, 1819-1826 (2017)
  • [18] Q Zhou, L Zhao, Y Guan, Strong selection at MHC in Mexicans since admixture, PLoS genetics, 12(2), e1005847 (2016)
  • [19] L Shi, Y Guo, C Dong, J Huddleston, H Yang, X Han, A Fu, Q Li, N Li, ..., Long-read sequencing andassembly of a Chinese genome, Nature communications, 7(1), 12065 (2016)
  • [20] DH Yu, M Gadkari, Q Zhou, S Yu, N Gao, Y Guan, D Schady, TN Roshan, ..., Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome, Genome biology, 16, 1-16 (2015)
  • [21] P Dominguez-Salas, SE Moore, MS Baker, AW Bergen, SE Cox, RA Dyer, ..., Maternal nutrition at conception modulates DNA methylation of human metastable epialleles, Nature communications, 5(1), 3746 (2014)
  • [22] H Xu, Y Guan, Detecting local haplotype sharing and haplotype association, Genetics, 197(3), 823-838 (2014)
  • [23] DH Yu, RA Waterland, P Zhang, D Schady, MH Chen, Y Guan, M Gadkari, ..., Targetedepimutation causes tumorigenesis and reduces survival in mice, The Journal of clinical investigation, 124(9), 3708-3712 (2014)
  • [24] Y Guan, Detecting structure of haplotypes and local ancestry, Genetics, 196(3), 625-642 (2014)
  • [25] A Fledel-Alon, EM Leffler, Y Guan, M Stephens, G Coop, M Przeworski, Variation in human recombination rates and its genetic determinants, PloS one, 6(6), e20321 (2011)
  • [26] Y Guan, M Stephens, Bayesian variable selection regression for genome-wide association studies and other large-scale problems, Annals of Applied Statistics, 5(3), 1780-1815 (2011)
  • [27] AP Reiner, MJ Barber, Y Guan, PM Ridker, LA Lange, DI Chasman, ..., Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1α are associated with C-reactive protein, The American Journal of Human Genetics, 82(5), 1193-1201 (2008)
  • [28] Y Guan, M Stephens, Practical issues in imputation-based association mapping, PLoS genetics, 4(12), e1000279 (2008)
  • [29] Y Guan, SM Krone, Small-world MCMC and convergence to multi-modal distributions: From slow mixing to fast mixing, Annals of Applied Probability, 17(1), 284-304 (2007)
  • [30] Y Guan, R Fleißner, P Joyce, SM Krone, Markov chain Monte Carlo in small worlds, Statistics and computing, 16, 193-202 (2006)
  • [31] SM Krone, Y Guan, Spatial self-organization in a cyclic resource–species model, Journal of theoretical biology, 241(1), 14-25 (2006)
Update Time: 2026-06-19 18:00:09