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    Jieming Chen, PhD

    TitlePostdoctoral Scholar
    SchoolUCSF School of Medicine
    DepartmentComputational Health Scienc
    Address550 16th. Street
    San Francisco CA 94158
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      Collapse Biography 
      Collapse Education and Training
      National University of SingaporeB Sc. (Hons)Computational Biology2008
      Yale UniversityPh.DComputational Biology and Bioinformatics2015

      Collapse Overview 
      Collapse Overview
      Prior to UCSF, Jieming completed his undergraduate degree at the National University of Singapore and worked at the Genome Institute of Singapore as a bioinformatics specialist on population genetics, with a focus on population structure. In 2015, he graduated from Yale University with a Ph.D in Computational Biology and Bioinformatics, from the laboratories of Professors Mark Gerstein and Lynne Regan. His thesis centered on large-scale computational annotation and interpretation of personal genomes/exomes, using protein science, network biology and functional genomics. He has extensive experience in molecular data, in DNA sequencing (microarray, whole exome and whole genome), RNA-seq, ChIP-seq and protein sequence and structure analyses.

      Jieming's current interest lies at the intersection of personalized and translational medicine and big data analytics. He presently works in the fields of organ transplant and asthma, leveraging bioinformatic and machine-learning methods in clinical data - clinical trials, electronic health records and drug repositioning - to bring more direct impact to patients.

      Collapse Interests
      genomics, protein science, organ transplantation, asthma, population genetics, population structure, pharmacogenomics, synthetic biology, systems biology, networks, electronic health records, drug repositioning, biotechnology, data science, machine learning, deep learning, bioinformatics, clinical and translational informatics, open data, data privacy, gender, ethnic groups, squash

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      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Chen J, Rozowsky J, Galeev TR, Harmanci A, Kitchen R, Bedford J, Abyzov A, Kong Y, Regan L, Gerstein M. A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals. Nat Commun. 2016; 7:11101. PMID: 27089393.
        View in: PubMed
      2. Clarke D, Sethi A, Li S, Kumar S, Chang RW, Chen J, Gerstein M. Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation. Structure. 2016 May 3; 24(5):826-37. PMID: 27066750.
        View in: PubMed
      3. Sethi A, Clarke D, Chen J, Kumar S, Galeev TR, Regan L, Gerstein M. Reads meet rotamers: structural biology in the age of deep sequencing. Curr Opin Struct Biol. 2015 Dec; 35:125-34. PMID: 26658741.
        View in: PubMed
      4. Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 1; 526(7571):75-81. PMID: 26432246; PMCID: PMC4617611 [Available on 04/01/16].
      5. Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. A global reference for human genetic variation. Nature. 2015 Oct 1; 526(7571):68-74. PMID: 26432245.
        View in: PubMed
      6. Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science. 2013 Oct 4; 342(6154):1235587. PMID: 24092746; PMCID: PMC3947637.
      7. Khurana E, Fu Y, Chen J, Gerstein M. Interpretation of genomic variants using a unified biological network approach. PLoS Comput Biol. 2013; 9(3):e1002886. PMID: 23505346; PMCID: PMC3591262.
      8. Chen J, Sawyer N, Regan L. Protein-protein interactions: general trends in the relationship between binding affinity and interfacial buried surface area. Protein Sci. 2013 Apr; 22(4):510-5. PMID: 23389845; PMCID: PMC3610057.
      9. Sawyer N, Chen J, Regan L. All repeats are not equal: a module-based approach to guide repeat protein design. J Mol Biol. 2013 May 27; 425(10):1826-38. PMID: 23434848; PMCID: PMC3928981.
      10. Zilberman-Schapira G, Chen J, Gerstein M. On sports and genes. Recent Pat DNA Gene Seq. 2012 Dec; 6(3):180-8. PMID: 22762737.
        View in: PubMed
      11. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1; 491(7422):56-65. PMID: 23128226; PMCID: PMC3498066.
      12. Amps K, Andrews PW, Anyfantis G, Armstrong L, Avery S, Baharvand H, Baker J, Baker D, Munoz MB, Beil S, Benvenisty N, Ben-Yosef D, Biancotti JC, Bosman A, Brena RM, Brison D, Caisander G, Camarasa MV, Chen J, Chiao E, Choi YM, Choo AB, Collins D, Colman A, Crook JM, Daley GQ, Dalton A, De Sousa PA, Denning C, Downie J, Dvorak P, Montgomery KD, Feki A, Ford A, Fox V, Fraga AM, Frumkin T, Ge L, Gokhale PJ, Golan-Lev T, Gourabi H, Gropp M, Lu G, Hampl A, Harron K, Healy L, Herath W, Holm F, Hovatta O, Hyllner J, Inamdar MS, Irwanto AK, Ishii T, Jaconi M, Jin Y, Kimber S, Kiselev S, Knowles BB, Kopper O, Kukharenko V, Kuliev A, Lagarkova MA, Laird PW, Lako M, Laslett AL, Lavon N, Lee DR, Lee JE, Li C, Lim LS, Ludwig TE, Ma Y, Maltby E, Mateizel I, Mayshar Y, Mileikovsky M, Minger SL, Miyazaki T, Moon SY, Moore H, Mummery C, Nagy A, Nakatsuji N, Narwani K, Oh SK, Oh SK, Olson C, Otonkoski T, Pan F, Park IH, Pells S, Pera MF, Pereira LV, Qi O, Raj GS, Reubinoff B, Robins A, Robson P, Rossant J, Salekdeh GH, Schulz TC, Sermon K, Sheik Mohamed J, Shen H, Sherrer E, Sidhu K, Sivarajah S, Skottman H, Spits C, Stacey GN, Strehl R, Strelchenko N, Suemori H, Sun B, Suuronen R, Takahashi K, Tuuri T, Venu P, Verlinsky Y, Ward-van Oostwaard D, Weisenberger DJ, Wu Y, Yamanaka S, Young L, Zhou Q. Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol. 2011 Dec; 29(12):1132-44. PMID: 22119741; PMCID: PMC3454460.
      13. Suo C, Xu H, Khor CC, Ong RT, Sim X, Chen J, Tay WT, Sim KS, Zeng YX, Zhang X, Liu J, Tai ES, Wong TY, Chia KS, Teo YY. Natural positive selection and north-south genetic diversity in East Asia. Eur J Hum Genet. 2012 Jan; 20(1):102-10. PMID: 21792231; PMCID: PMC3234507.
      14. Chen J. Systems biology: new institute and applications. Yale J Biol Med. 2011 Mar; 84(1):59-61. PMID: 21451788; PMCID: PMC3064249.
      15. Chen J, Teo YY, Toh DS, Sung C. Interethnic comparisons of important pharmacology genes using SNP databases: potential application to drug regulatory assessments. Pharmacogenomics. 2010 Aug; 11(8):1077-94. PMID: 20712526.
        View in: PubMed
      16. Chen J, Zheng H, Bei JX, Sun L, Jia WH, Li T, Zhang F, Seielstad M, Zeng YX, Zhang X, Liu J. Genetic structure of the Han Chinese population revealed by genome-wide SNP variation. Am J Hum Genet. 2009 Dec; 85(6):775-85. PMID: 19944401; PMCID: PMC2790583.
      17. Teo YY, Sim X, Ong RT, Tan AK, Chen J, Tantoso E, Small KS, Ku CS, Lee EJ, Seielstad M, Chia KS. Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations. Genome Res. 2009 Nov; 19(11):2154-62. PMID: 19700652; PMCID: PMC2775604.
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