Director

Pui-Yan Kwok, M.D., Ph.D.

Distinguished Research Fellow
Academician, Academia Sinica
Specialty:
  1. Human Genetics
  2. Genomics
  3. DNA sequence Variation
  4. Complex Trait Analysis
  5. Pharmacogenetics
  6. Biotechnology

  • University of Chicago, Chicago, IL (1974-1975)
  • B.A.(1977-1979), M.S.(1979-1981), Ph.D.(1979-1985), University of Chicago, Chicago, IL
  • M.D., Pritzker School of Medicine, University of Chicago (1979-1987)
  • Intern, Rush Medical Center, Chicago, IL (1987-1988)
  • Resident (1988-1990), Chief Resident (1990-1991), Fellow (1990-1992), Washington University Medical Ctr., St. Louis, MO
  • Visiting Scientist, University of Washington, Seattle, WA (1992-1993)
  • Assistant Professor (1993-1999), Associate Professor (1999-2002), Washington University School of Medicine
  • Henry Bachrach Distinguished Professor (2002-present), University of California, San Francisco
  • Distinguished Research Fellow and Director (2017-present), Institute of Biomedical Sciences, Academia Sinica

  • University of Chicago, Chicago, IL (1974-1975)
  • B.A.(1977-1979), M.S.(1979-1981), Ph.D.(1979-1985), University of Chicago, Chicago, IL
  • M.D., Pritzker School of Medicine, University of Chicago (1979-1987)
  • Intern, Rush Medical Center, Chicago, IL (1987-1988)
  • Resident (1988-1990), Chief Resident (1990-1991), Fellow (1990-1992), Washington University Medical Ctr., St. Louis, MO
  • Visiting Scientist, University of Washington, Seattle, WA (1992-1993)
  • Assistant Professor (1993-1999), Associate Professor (1999-2002), Washington University School of Medicine
  • Henry Bachrach Distinguished Professor (2002-present), University of California, San Francisco
  • Distinguished Research Fellow and Director (2017-present), Institute of Biomedical Sciences, Academia Sinica

  1. Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, Deshpande P, Cao H, Nagarajan N, Xiao M, and Kwok PY. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol. 2012; 30:771-6.
  2. Mak AC, Pullinger CR, Tang LF, Wong JS, Deo RC, Schwarz JM, Gugliucci A, Movsesyan I, Ishida BY, Chu C, Poon A, Kim P, Stock EO, Schaefer EJ, Asztalos BF, Castellano JM, Wyss-Coray T, Duncan JL, Miller BL, Kane JP, Kwok PY, Malloy MJ. Effects of the absence of apolipoprotein e on lipoproteins, neurocognitive function, and retinal function. JAMA Neurol. 2014 Oct 1; 71(10):1228-36. PMID: 25111166.
  3. Watkin LB, Jessen B, Wiszniewski W, Vece TJ, Jan M, Sha Y, Thamsen M, Santos-Cortez RL, Lee K, Gambin T, Forbes LR, Law CS, Stray-Pedersen A, Cheng MH, Mace EM, Anderson MS, Liu D, Tang LF, Nicholas SK, Nahmod K, Makedonas G, Canter DL, Kwok PY, Hicks J, Jones KD, Penney S, Jhangiani SN, Rosenblum MD, Dell SD, Waterfield MR, Papa FR, Muzny DM, Zaitlen N, Leal SM, Gonzaga-Jauregui C. COPA mutations impair ER-Golgi transport and cause hereditary autoimmune-mediated lung disease and arthritis. Nat Genet. 2015 Jun; 47(6):654-60. PMID: 25894502.
  4. Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods. 2015 Aug; 12(8):780-6. PMID: 26121404.
  5. Kvale MN, Hesselson S, Hoffmann TJ, Cao Y, Chan D, Connell S, Croen LA, Dispensa BP, Eshragh J, Finn A, Gollub J, Iribarren C, Jorgenson E, Kushi LH, Lao R, Lu Y, Ludwig D, Mathauda GK, McGuire WB, Mei G, Miles S, Mittman M, Patil M, Quesenberry CP, Ranatunga D, Rowell S, Sadler M, Sakoda LC, Shapero M, Shen L, Shenoy T, Smethurst D, Somkin CP, Van Den Eeden SK, Walter L, Wan E, Webster T, Whitmer RA, Wong S, Zau C, Zhan Y, Schaefer C, Kwok PY, Risch N. Genotyping Informatics and Quality Control for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort. Genetics. 2015 Aug; 200(4):1051-60. PMID: 26092718.
  6. Mostovoy Y, Levy-Sakin M, Lam J, Lam ET, Hastie AR, Marks P, Lee J, Chu C, Lin C, Dzakula Z, Cao H, Schlebusch SA, Giorda K, Schnall-Levin M, Wall JD, Kwok PY. A hybrid approach for de novo human genome sequence assembly and phasing. Nat Methods. 2016 Jul; 13(7):587-90. PMID: 27159086.
  7. Mak AC, Lai YY, Lam ET, Kwok TP, Leung AK, Poon A, Mostovoy Y, Hastie AR, Stedman W, Anantharaman T, Andrews W, Zhou X, Pang AW, Dai H, Chu C, Lin C, Wu JJ, Li CM, Li JW, Yim AK, Chan S, Sibert J, Dzakula Z, Cao H, Yiu SM, Chan TF, Yip KY, Xiao M, Kwok PY. Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays. Genetics. 2016 Jan; 202(1):351-62. PMID: 26510793.
  8. HoffmannTJ, Ehret GB, Nandakumar P, Ranatunga D, Schaefer C, Kwok PY, Iribarren C, Chakravarti A, Risch N. Genome-wide association analyses using electronic health records identify new loci influencing blood pressure variation. Nat Genet. 2017 Jan; 49(1):54-64. PMID: 27841878
  9. Hoffmann TJ, Passarelli MN, Graff RE, Emami NC, Sakoda LC, Jorgenson E, Habel LA, Shan J, Ranatunga DK, Quesenberry CP, Chao CR, Ghai NR, Aaronson D, Presti J, Nordström T, Wang Z, Berndt SI, Chanock SJ, Mosley JD, Klein RJ, Middha M, Lilja H, Melander O, Kvale MN, Kwok PY, Schaefer C, Risch N, Van Den Eeden SK, Witte JS. Genome-wide association study of prostate-specific antigen levels identifies novel loci independent of prostate cancer. Nat Commun. 2017 Jan 31;8:14248. PMID: 28139693
  10. Hoffmann TJ, Theusch E, Haldar T, Ranatunga DK, Jorgenson E, Medina MW, Kvale MN, Kwok PY, Schaefer C, Krauss RM, Iribarren C, Risch N. A large electronic-health-record-based genome-wide study of serum lipids. Nat Genet. 2018 Mar; 50(3):401-413.
  11. Wong KHY, Levy-Sakin M, Kwok PY. De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations. Nat Commun. 2018 08 02; 9(1):3040.
  12. Levy-Sakin M, Pastor S, Mostovoy Y, Li L, Leung AKY, McCaffrey J, Young E, Lam ET, Hastie AR, Wong KHY, Chung CYL, Ma W, Sibert J, Rajagopalan R, Jin N, Chow EYC, Chu C, Poon A, Lin C, Naguib A, Wang WP, Cao H, Chan TF, Yip KY, Xiao M, Kwok PY. Genome maps across 26 human populations reveal population-specific patterns of structural variation. Nat Commun. 2019 03 04; 10(1):1025.
  13. Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun. 2019 04 16; 10(1):1784.
  14. Lind AL, Lai YYY, Mostovoy Y, Holloway AK, Iannucci A, Mak ACY, Fondi M, Orlandini V, Eckalbar WL, Milan M, Rovatsos M, Kichigin IG, Makunin AI, Johnson Pokorná M, Altmanová M, Trifonov VA, Schijlen E, Kratochvíl L, Fani R, Velenský P, Rehák I, Patarnello T, Jessop TS, Hicks JW, Ryder OA, Mendelson JR, Ciofi C, Kwok PY, Pollard KS, Bruneau BG. Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. Nat Ecol Evol. 2019 Aug; 3(8):1241-1252.
  15. Demaerel W, Mostovoy Y, Yilmaz F, Vervoort L, Pastor S, Hestand MS, Swillen A, Vergaelen E, Geiger EA, Coughlin CR, Chow SK, McDonald-McGinn D, Morrow B, Kwok PY, Xiao M, Emanuel BS, Shaikh TH, Vermeesch JR. The 22q11 low copy repeats are characterized by unprecedented size and structural variability. Genome Res. 2019 Sep;29(9):1389-1401.
  16. Kao HJ, Chiang HL, Chen HH, Fan PC, Tu YF, Chou YY, Hwu WL, Lin CL, Kwok PY, Lee NC. De novo mutation and skewed X-inactivation in girl with BCAP31-related syndrome. Hum Mutat. 2020 (Epub Jul 11).
  17. Adhikari AN, Gallagher RC, Wang YQ, Currier RJ, Amatuni G, Bassaganyas L, Chen F, Kundu K, Kvale M, Mooney SD, Nussbaum RL, Randi SS, Sanford J, Shieh JT, Srinivasan R, Sunderam U, Tang H, Vaka D, Zou Y, Koenig BA, Kwok PY, Risch N, Puck JM, Brenner SE. The Role of Exome Sequencing in Newborn Screening for Inborn Errors of Metabolism. Nature Medicine. 2020 Sep;26(9):1392-1397.
  18. Wong KHY, Ma W, Wei CY, Yeh EC, Lin WJ, Wang EHF, Su JP, Hsieh FJ, Kao HJ, Chen HH, Chow SK, Young E, Chu C, Poon A, Yang CF, Lin DS, Hu YF, Wu JY, Lee NC, Hwu WL, Boffelli D, Martin D, Xiao M, Kwok PY. Towards a reference genome that captures global genetic diversity. Nat Commun. 2020 Oct 30;11(1):5482.
  19. Wei CY, Yang JH, Yeh EC, Tsai MF, Kao HJ, Lo CZ, Chang LP, Lin WJ, Hsieh FJ, Belsare S, Bhaskar A, Su MW, Lee TC, Lin YL, Liu FT, Shen CY, Li LH, Chen CH, Wall JD, Wu JY, Kwok PY. Genetic profiles of 103,106 individuals in the Taiwan Biobank provide insights into the health and history of Han Chinese. NPJ Genom Med. 2021 Feb 11;6(1):10.
  20. Mostovoy Y, Yilmaz F, Chow SK, Chu C, Lin C, Geiger EA, Meeks NJL, Chatfield KC, Coughlin CR, Surti U, Kwok PY, Shaikh TH. Genomic regions associated with microdeletion/ microduplication syndromes exhibit extreme diversity of structural variation. Genetics. 2021 Feb 9;217(2):iyaa038.
  21. Shieh JT, Penon-Portmann M, Wong KHY, Levy-Sakin M, Verghese M, Slavotinek A, Gallagher RC, Mendelsohn BA, Tenney J, Beleford D, Perry H, Chow SK, Sharo AG, Brenner SE, Qi Z, Yu J, Klein OD, Martin D, Kwok PY, Boffelli D. Application of Full Genome Analysis to Diagnose Rare Monogenic Disorders. NPJ Genom Med. 2021 Sep 23;6(1):77.