Dr. He Zhang

Dr. He Zhang

Computational Biologist III at UT Southwestern Medical Center

Curriculum Vitae

Academic Experience

  • University of Texas Southwestern Medical Center, Dallas, TX, 01/2016 - present
    • Computational Biologist III
  • University of Michigan, Ann Arbor, MI, 04/2012 – 01/2016
  • Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China, 07/2011 – 04/2012
  • Peking University, Beijing, China, 08/2006 – 07/2011

Education

  • Peking University, Beijing, China, 08/2006 – 07/2011
    • Ph.D. in Bioinformatics
    • Advisor: Dr. Jingchu Luo and Dr. Ge Gao
  • Ocean University of China, Qingdao, China, 08/2002 – 07/2006
    • B.S. in Biology
    • B.S. in Computer Science, 08/2003 – 07/2006

Teaching

  • Instructor, UTSW nanocourse – R Beginer, UTSW, 2017
  • Instructor, nanocourse – Genome-Wide Association Study, UTSW, 2017
  • Instructor, nanocourse – Genome-Wide Association Study, UTSW, 2016
  • Teaching Assistant, Computational Evolution Biology for graduates, Peking University, 2010
  • Teaching Assistant, Biostatistics for undergraduates, Peking University, 2008
  • Teaching Assistant, Method in Bioinformatics course for graduates, Peking University, 2007
  • Teaching Assistant, Applied Bioinformatics course for graduates, Peking University, 2007

Publications

First and co-first author papers

  1. Zhang H, Xie Y: Novel start codons introduce novel coding sequences in the human genomes. Sci Rep 2023, 13(1):8141. [PMID:37208378]
  2. Zhang H, Zhan X, Brugarolas J, Xie Y: DEFOR: depth- and frequency-based somatic copy number alteration detector. Bioinformatics 2019, 35(19):3824-3825. [PMID:30860569]
  3. Tang CS*, Zhang H*, Cheung CY, Xu M, Ho JC, Zhou W, Cherny SS, Zhang Y, Holmen O, Au K-W, et al: Exome-wide association analysis reveals novel coding sequence variants associated with lipid traits in Chinese. Nature communications 2015, 6. [PMID:26690388]
  4. Lange LA*, Hu Y*, Zhang H*, Xue C, Schmidt EM, Tang Z-Z, Bizon C, Lange EM, Smith JD, Turner EH: Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. The American Journal of Human Genetics 2014, 94(2):233-245 [PMID:24507775]
  5. Holmen OL*, Zhang H*, Zhou W*, Schmidt E, Hovelson DH, Langhammer A, Løchen M-L, Ganesh SK, Mathiesen EB, Vatten L: No large-effect low-frequency coding variation found for myocardial infarction. Human molecular genetics 2014, 23(17):4721-4728. [PMID:24728188]
  6. Holmen OL*, Zhang H*, Fan Y*, Hovelson DH, Schmidt EM, Zhou W, Guo Y, Zhang J, Langhammer A, Løchen M-L: Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk. Nature genetics 2014, 46(4):345-351. [PMID:24633158]
  7. Zhang H, Jin J, Tang L, Zhao Y, Gu X, et al: PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Research 2011, 39: D1114-D1117. [PMID:21097470]

Other papers

  1. Brumpton BM, Graham S, Surakka I, Skogholt AH, Loset M, Fritsche LG, Wolford B, Zhou W, Nielsen JB, Holmen OL et al: The HUNT study: A population-based cohort for genetic research. Cell Genom 2022, 2(10):100193.
  2. Thomas A, Rehfeld F, Zhang H, Chang TC, Goodarzi M, Gillet F, Mendell JT: RBM33 directs the nuclear export of transcripts containing GC-rich elements. Genes Dev 2022, 36(9-10):550-565.
  3. Aguilar M, Zhang H, Zhang M, Cantarell B, Sahoo SS, Li HD, Cuevas IC, Lea J, Miller DS, Chen H et al: Serial genomic analysis of endometrium supports the existence of histologically indistinct endometrial cancer precursors. J Pathol 2021, 254(1):20-30.
  4. Nielsen JB, Rom O, Surakka I, Graham SE, Zhou W, Roychowdhury T, Fritsche LG, Gagliano Taliun SA, Sidore C, Liu Y et al: Loss-of-function genomic variants highlight potential therapeutic targets for cardiovascular disease. Nat Commun 2020, 11(1):6417.
  5. Han J, LaVigne CA, Jones BT, Zhang H, Gillett F, Mendell JT: A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming. Science 2020, 370(6523).
  6. Surendran P, Feofanova EV, Lahrouchi N, Ntalla I, Karthikeyan S, Cook J, Chen L, Mifsud B, Yao C, Kraja AT et al: Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals. Nat Genet 2020, 52(12):1314-1332.
  7. Li HD, Cuevas I, Zhang M, Lu C, Alam MM, Fu YX, You MJ, Akbay EA, Zhang H, Castrillon DH: Polymerase-mediated ultramutagenesis in mice produces diverse cancers with high mutational load. J Clin Invest 2018. [PMID:30124468]2. Hunter RW, Liu Y, Manjunath H, Acharya A, Jones BT, Zhang H, Chen B, Ramalingam H, Hammer RE, Xie Y et al: Loss of Dis3l2 partially phenocopies Perlman syndrome in mice and results in up-regulation of Igf2 in nephron progenitor cells. Genes Dev 2018, 32(13-14):903-908. [PMID:29950491]
  8. Lu X, Peloso GM, Liu DJ, Wu Y, Zhang H, Zhou W, Li J, Tang CS, Dorajoo R, Li H et al: Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants that contribute to lipid levels and coronary artery disease. Nat Genet 2017, 49(12):1722-1730. [PMID:29083407]
  9. Liu DJ, Peloso GM, Yu H, Butterworth AS, Wang X, Mahajan A, Saleheen D, Emdin C, Alam D, Alves AC, …, Zhang H, …, et al: Exome-wide association study of plasma lipids in >300,000 individuals. Nat Genet 2017, 49(12):1758-1766. [PMID:29083408]
  10. Kraja AT, Cook JP, Warren HR, Surendran P, Liu C, Evangelou E, Manning AK, Grarup N, Drenos F, Sim X, …, Zhang H, …, et al: New Blood Pressure-Associated Loci Identified in Meta-Analyses of 475 000 Individuals. Circ Cardiovasc Genet 2017, 10(5). [PMID:29030403]
  11. Webb TR, Erdmann J, Stirrups KE, Stitziel NO, Masca NG, Jansen H, Kanoni S, Nelson CP, Ferrario PG, Konig IR …, Zhang H, et al: Systematic Evaluation of Pleiotropy Identifies 6 Further Loci Associated With Coronary Artery Disease. J Am Coll Cardiol 2017, 69(7):823-836. [PMID:28209224]
  12. Zhou W, Fritsche LG, Das S, Zhang H, Nielsen JB, Holmen OL, Chen J, Lin M, Elvestad MB, Hveem K et al: Improving power of association tests using multiple sets of imputed genotypes from distributed reference panels. Genet Epidemiol 2017, 41(8):744-755. [PMID:28861891]
  13. Chen W, Hill H, Christie A, Kim MS, Holloman E, Pavia-Jimenez A, Homayoun F, Ma Y, Patel N, Yell P, …, Zhang H, …, et al: Targeting renal cell carcinoma with a HIF-2 antagonist. Nature 2016, 539(7627):112-117. [PMID:27595394]
  14. McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A, Kang HM, Fuchsberger C, Danecek P, Sharp K et al: A reference panel of 64,976 haplotypes for genotype imputation. Nat Genet 2016, 48(10):1279-1283. [PMID:27548312]
  15. Stitziel NO, Stirrups KE, Masca NG, Erdmann J, Ferrario PG, König IR, Weeke PE, Webb TR, Auer PL, Schick UM: Coding variation in ANGPTL4, LPL, and SVEP1 and the risk of coronary disease. New England Journal of Medicine 2016, 374(12):1134-1144. [PMID:26934567]
  16. Feng S, Pistis G, Zhang H, Zawistowski M, Mulas A, Zoledziewska M, Holmen OL, Busonero F, Sanna S, Hveem K: Methods for Association Analysis and Meta‐Analysis of Rare Variants in Families. Genetic epidemiology 2015, 39(4):227-238. [PMID:25740221]
  17. Hu B, Jin J, Guo A-Y, Zhang H, Luo J, Gao G: GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 2014. [PMID:27595394]
  18. Crosby J, Peloso GM, Auer PL, Crosslin DR, Stitziel NO, Lange LA, Lu Y, Tang ZZ, Zhang H, Hindy G, et al. (2014) Loss-of-function mutations in APOC3, triglycerides, and coronary disease. The New England Journal of Medicine 371: 22-31. [PMID:24941081]
  19. Ganesh SK, Chasman DI, Larson MG, Guo X, Verwoert G, Bis JC, Gu X, Smith AV, Yang M-L, Zhang Y: Effects of long-term averaging of quantitative blood pressure traits on the detection of genetic associations. The American Journal of Human Genetics 2014, 95(1):49-65. [PMID:24975945]
  20. Liu DJ, Peloso GM, Zhan X, Holmen OL, Zawistowski M, Feng S, Nikpay M, Auer PL, Goel A, Zhang H: Meta-analysis of gene-level tests for rare variant association. Nature genetics 2014, 46(2):200-204. [PMID:24336170]
  21. Jin J, Zhang H, Kong L, Gao G, Luo J: PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Research 2013, 42:D1182-1187. [PMID:24174544]
  22. Wang J, Kong L, Zhao S, Zhang H, Tang L, et al: Rice-Map: a new-generation rice genome browser. BMC genomics 2011, 12: 165. [PMID:21450055]
  23. He Q-L, Cui S-J, Gu J-L, Zhang H, Wang M-X, et al: Analysis of floral transcription factors from Lycoris longituba. Genomics 2010, 96:119-127. [PMID:20406677]
  24. Shen L, Gao G, Zhang Y, Zhang H, Ye Z, et al. A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA. Nucleic Acids Research 2010, 38:6054-6064. [PMID:20507910]
  25. Li Z, Zhang H, Ge S, Gu X, Gao G, et al: Expression pattern divergence of duplicated genes in rice. BMC Bioinformatics 2009, 10:S8. [PMID:19534757]
  26. Guo A-Y, Chen X, Gao G, Zhang H, Zhu Q-H, et al: PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Research 2008, 36: D966-D969. [PMID:17933783]

Book Chapter

  • He K, Guo A, Gao G, Zhu Q, Liu X, Zhang H, Chen X, Gu X, Luo J. (2010) Computational identification of plant transcription factors and the construction of the PlantTFDB database. Computational Biology of Transcription Factor Binding: Springer. pp. 351-368.

Talks

  1. HUNT myocardial infarction study. Department of Human Genetics, University of Michigan, Ann Arbor, MI. 03/2013
  2. HUNT lipid study. Department of Human Genetics, University of Michigan, Ann Arbor, MI. 10/2013
  3. Identification of plant transcription factors. Chinese Academy of Agricultural Sciences, Beijing, China. 10/2010

Conference Poster Presentations

  1. He Zhang, Ming Xu, Wei Zhou, Yan Zhang, Oddgeir Holmen, Haiyi Yu, et al. Novel Asian-specific variants associated with blood lipid levels and myocardial infarction. ASHG Annual Meeting, San Diego, CA. 10/2014
  2. He Zhang, Oddgeir Lingaas Holmen, Daniel H. Hovelson, Ellen Schmidt, Goncalo Abecasis, Michael Boehnke, Inger Njølstad, Kristian Hveem, Cristen Willer. Exome-wide Coding Variation and Myocardial Infarction. ASHG Annual Meeting, Boston, MA. 10/2013
  3. He Zhang, Oddgeir Lingaas Holmen, Jin Chen, Ellen Schmidt, Goncalo Abecasis, Michael Boehnke, Kristian Hveem, Cristen Willer. Rare and Low Frequency Variants Are Associated With Myocardial Infarction and Lipid Levels. Third Annual Joint Institute Symposium, Ann Arbor, MI. 11/2012

Professional Service

  • Membership -The American Society of Human Genetics (ASHG) 2012 – 2017
  • Peviewers for journals
    • Plos Computational Biology
    • Bioinformatics
    • Genomics
    • Journal of Bioinformatics and Computational Biology
    • Computational Biology and Chemistry
    • BMC Bioinformatics
    • BMC Genomics and Plos One

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