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Warren Cheung, PhD

TitleSr. Computational Biologist
InstitutionChildren's Mercy Kansas City
DepartmentPediatrics
Address2401 Gillham Rd
Kansas City MO 64108
ORCID ORCID Icon0000-0003-0267-7464 Additional info
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    Collapse Biography 
    Collapse education and training
    University of British Columbia, British Columbia CanadaPh.D.2012Bioinformatics
    Wasserman Laboratory, Centre for Molecular Medicine and Therapeutics, British Columbia CanadaFellowship2013Bioinformatics
    McGill University and Génome Québec Innovation Centre, Epigenetics Mapping Center, Quebec CanadaFellowship2016Genetics
    McGill University Health Centre, Quebec Canada Fellowship2017Genetics

    Collapse Overview 

    Collapse Research 
    Collapse research overview
    Dr. Cheung’s research interests involve exploring the elegance of computational algorithms, focused in the myriad of diverse application domains of bioinformatics. His current ongoing projects involve high-throughput epigenomics datasets and associated data, interrogating the interplay between the genome, methylome, transcriptome, chromatin histone mark deposition and accessibility. Dr. Cheung previously worked on the epigenomics of pediatric glioblastomas, and his interests have also ranged as far as the inference of novel associations from medical subject annotations in the PubMed biomedical database, privacy in epigenomics and medical image analysis. He is currently focusing on simultaneous aggregate analysis of multiple single-cell transcriptomics from the 10X platforms, and bridging this with methylation and other datasets in human blood immune cell types.

    Collapse Bibliography 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Madore AM, Pain L, Boucher-Lafleur AM, Morin A, Meloche J, Simon MM, Ge B, Kwan T, Cheung WA, Pastinen T, Laprise C. Asthma-associated polymorphisms in 17q12-21 locus modulate methylation and gene expression of GSDMA in naïve CD4+ T cells. J Genet Genomics. 2020 Mar 25. PMID: 32312674.
      View in: PubMed
    2. Vijay J, Gauthier MF, Biswell RL, Louiselle DA, Johnston JJ, Cheung WA, Belden B, Pramatarova A, Biertho L, Gibson M, Simon MM, Djambazian H, Staffa A, Bourque G, Laitinen A, Nystedt J, Vohl MC, Fraser JD, Pastinen T, Tchernof A, Grundberg E. Single-cell analysis of human adipose tissue identifies depot and disease specific cell types. Nat Metab. 2020 Jan; 2(1):97-109. PMID: 32066997.
      View in: PubMed
    3. Cheung WA, Shao X, Morin A, Siroux V, Kwan T, Ge B, Aïssi D, Chen L, Vasquez L, Allum F, Guénard F, Bouzigon E, Simon MM, Boulier E, Redensek A, Watt S, Datta A, Clarke L, Flicek P, Mead D, Paul DS, Beck S, Bourque G, Lathrop M, Tchernof A, Vohl MC, Demenais F, Pin I, Downes K, Stunnenberg HG, Soranzo N, Pastinen T, Grundberg E. Correction to: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome. Genome Biol. 2019 05 07; 20(1):89. PMID: 31064398.
      View in: PubMed
    4. Harutyunyan AS, Krug B, Chen H, Papillon-Cavanagh S, Zeinieh M, De Jay N, Deshmukh S, Chen CCL, Belle J, Mikael LG, Marchione DM, Li R, Nikbakht H, Hu B, Cagnone G, Cheung WA, Mohammadnia A, Bechet D, Faury D, McConechy MK, Pathania M, Jain SU, Ellezam B, Weil AG, Montpetit A, Salomoni P, Pastinen T, Lu C, Lewis PW, Garcia BA, Kleinman CL, Jabado N, Majewski J. H3K27M induces defective chromatin spread of PRC2-mediated repressive H3K27me2/me3 and is essential for glioma tumorigenesis. Nat Commun. 2019 03 19; 10(1):1262. PMID: 30890717.
      View in: PubMed
    5. Allum F, Hedman ÅK, Shao X, Cheung WA, Vijay J, Guénard F, Kwan T, Simon MM, Ge B, Moura C, Boulier E, Rönnblom L, Bernatsky S, Lathrop M, McCarthy MI, Deloukas P, Tchernof A, Pastinen T, Vohl MC, Grundberg E. Dissecting features of epigenetic variants underlying cardiometabolic risk using full-resolution epigenome profiling in regulatory elements. Nat Commun. 2019 03 14; 10(1):1209. PMID: 30872577.
      View in: PubMed
    6. Quintana AM, Yu HC, Brebner A, Pupavac M, Geiger EA, Watson A, Castro VL, Cheung W, Chen SH, Watkins D, Pastinen T, Skovby F, Appel B, Rosenblatt DS, Shaikh TH. Mutations in THAP11 cause an inborn error of cobalamin metabolism and developmental abnormalities. Hum Mol Genet. 2017 08 01; 26(15):2838-2849. PMID: 28449119.
      View in: PubMed
    7. Cheung WA, Shao X, Morin A, Siroux V, Kwan T, Ge B, Aïssi D, Chen L, Vasquez L, Allum F, Guénard F, Bouzigon E, Simon MM, Boulier E, Redensek A, Watt S, Datta A, Clarke L, Flicek P, Mead D, Paul DS, Beck S, Bourque G, Lathrop M, Tchernof A, Vohl MC, Demenais F, Pin I, Downes K, Stunnenberg HG, Soranzo N, Pastinen T, Grundberg E. Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome. Genome Biol. 2017 03 10; 18(1):50. PMID: 28283040.
      View in: PubMed
    8. Paul DS, Teschendorff AE, Dang MA, Lowe R, Hawa MI, Ecker S, Beyan H, Cunningham S, Fouts AR, Ramelius A, Burden F, Farrow S, Rowlston S, Rehnstrom K, Frontini M, Downes K, Busche S, Cheung WA, Ge B, Simon MM, Bujold D, Kwan T, Bourque G, Datta A, Lowy E, Clarke L, Flicek P, Libertini E, Heath S, Gut M, Gut IG, Ouwehand WH, Pastinen T, Soranzo N, Hofer SE, Karges B, Meissner T, Boehm BO, Cilio C, Elding Larsson H, Lernmark Å, Steck AK, Rakyan VK, Beck S, Leslie RD. Increased DNA methylation variability in type 1 diabetes across three immune effector cell types. Nat Commun. 2016 11 29; 7:13555. PMID: 27898055.
      View in: PubMed
    9. Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells. Cell. 2016 11 17; 167(5):1398-1414.e24. PMID: 27863251.
      View in: PubMed
    10. Pupavac M, Watkins D, Petrella F, Fahiminiya S, Janer A, Cheung W, Gingras AC, Pastinen T, Muenzer J, Majewski J, Shoubridge EA, Rosenblatt DS. Inborn Error of Cobalamin Metabolism Associated with the Intracellular Accumulation of Transcobalamin-Bound Cobalamin and Mutations in ZNF143, Which Codes for a Transcriptional Activator. Hum Mutat. 2016 09; 37(9):976-82. PMID: 27349184.
      View in: PubMed
    11. Busche S, Shao X, Caron M, Kwan T, Allum F, Cheung WA, Ge B, Westfall S, Simon MM, Barrett A, Bell JT, McCarthy MI, Deloukas P, Blanchette M, Bourque G, Spector TD, Lathrop M, Pastinen T, Grundberg E. Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation. Genome Biol. 2015 Dec 23; 16:290. PMID: 26699896.
      View in: PubMed
    12. Zheng HF, Forgetta V, Hsu YH, Estrada K, Rosello-Diez A, Leo PJ, Dahia CL, Park-Min KH, Tobias JH, Kooperberg C, Kleinman A, Styrkarsdottir U, Liu CT, Uggla C, Evans DS, Nielson CM, Walter K, Pettersson-Kymmer U, McCarthy S, Eriksson J, Kwan T, Jhamai M, Trajanoska K, Memari Y, Min J, Huang J, Danecek P, Wilmot B, Li R, Chou WC, Mokry LE, Moayyeri A, Claussnitzer M, Cheng CH, Cheung W, Medina-Gómez C, Ge B, Chen SH, Choi K, Oei L, Fraser J, Kraaij R, Hibbs MA, Gregson CL, Paquette D, Hofman A, Wibom C, Tranah GJ, Marshall M, Gardiner BB, Cremin K, Auer P, Hsu L, Ring S, Tung JY, Thorleifsson G, Enneman AW, van Schoor NM, de Groot LC, van der Velde N, Melin B, Kemp JP, Christiansen C, Sayers A, Zhou Y, Calderari S, van Rooij J, Carlson C, Peters U, Berlivet S, Dostie J, Uitterlinden AG, Williams SR, Farber C, Grinberg D, LaCroix AZ, Haessler J, Chasman DI, Giulianini F, Rose LM, Ridker PM, Eisman JA, Nguyen TV, Center JR, Nogues X, Garcia-Giralt N, Launer LL, Gudnason V, Mellström D, Vandenput L, Amin N, van Duijn CM, Karlsson MK, Ljunggren Ö, Svensson O, Hallmans G, Rousseau F, Giroux S, Bussière J, Arp PP, Koromani F, Prince RL, Lewis JR, Langdahl BL, Hermann AP, Jensen JE, Kaptoge S, Khaw KT, Reeve J, Formosa MM, Xuereb-Anastasi A, Åkesson K, McGuigan FE, Garg G, Olmos JM, Zarrabeitia MT, Riancho JA, Ralston SH, Alonso N, Jiang X, Goltzman D, Pastinen T, Grundberg E, Gauguier D, Orwoll ES, Karasik D, Davey-Smith G, Smith AV, Siggeirsdottir K, Harris TB, Zillikens MC, van Meurs JB, Thorsteinsdottir U, Maurano MT, Timpson NJ, Soranzo N, Durbin R, Wilson SG, Ntzani EE, Brown MA, Stefansson K, Hinds DA, Spector T, Cupples LA, Ohlsson C, Greenwood CM, Jackson RD, Rowe DW, Loomis CA, Evans DM, Ackert-Bicknell CL, Joyner AL, Duncan EL, Kiel DP, Rivadeneira F, Richards JB. Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture. Nature. 2015 Oct 01; 526(7571):112-7. PMID: 26367794.
      View in: PubMed
    13. Dyke SO, Cheung WA, Joly Y, Ammerpohl O, Lutsik P, Rothstein MA, Caron M, Busche S, Bourque G, Rönnblom L, Flicek P, Beck S, Hirst M, Stunnenberg H, Siebert R, Walter J, Pastinen T. Epigenome data release: a participant-centered approach to privacy protection. Genome Biol. 2015 Jul 17; 16:142. PMID: 26185018.
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    14. Joly Y, Dyke SO, Cheung WA, Rothstein MA, Pastinen T. Risk of re-identification of epigenetic methylation data: a more nuanced response is needed. Clin Epigenetics. 2015; 7:45. PMID: 25904991.
      View in: PubMed
    15. Cheung WA, Ouellette BF, Wasserman WW. Compensating for literature annotation bias when predicting novel drug-disease relationships through Medical Subject Heading Over-representation Profile (MeSHOP) similarity. BMC Med Genomics. 2013; 6 Suppl 2:S3. PMID: 23819887.
      View in: PubMed
    16. Cheung WA, Ouellette BF, Wasserman WW. Inferring novel gene-disease associations using Medical Subject Heading Over-representation Profiles. Genome Med. 2012; 4(9):75. PMID: 23021552.
      View in: PubMed
    17. Cheung WA, Ouellette BF, Wasserman WW. Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs). BMC Bioinformatics. 2012 Sep 27; 13:249. PMID: 23017167.
      View in: PubMed
    18. Yusuf D, Butland SL, Swanson MI, Bolotin E, Ticoll A, Cheung WA, Zhang XY, Dickman CT, Fulton DL, Lim JS, Schnabl JM, Ramos OH, Vasseur-Cognet M, de Leeuw CN, Simpson EM, Ryffel GU, Lam EW, Kist R, Wilson MS, Marco-Ferreres R, Brosens JJ, Beccari LL, Bovolenta P, Benayoun BA, Monteiro LJ, Schwenen HD, Grontved L, Wederell E, Mandrup S, Veitia RA, Chakravarthy H, Hoodless PA, Mancarelli MM, Torbett BE, Banham AH, Reddy SP, Cullum RL, Liedtke M, Tschan MP, Vaz M, Rizzino A, Zannini M, Frietze S, Farnham PJ, Eijkelenboom A, Brown PJ, Laperrière D, Leprince D, de Cristofaro T, Prince KL, Putker M, del Peso L, Camenisch G, Wenger RH, Mikula M, Rozendaal M, Mader S, Ostrowski J, Rhodes SJ, Van Rechem C, Boulay G, Olechnowicz SW, Breslin MB, Lan MS, Nanan KK, Wegner M, Hou J, Mullen RD, Colvin SC, Noy PJ, Webb CF, Witek ME, Ferrell S, Daniel JM, Park J, Waldman SA, Peet DJ, Taggart M, Jayaraman PS, Karrich JJ, Blom B, Vesuna F, O'Geen H, Sun Y, Gronostajski RM, Woodcroft MW, Hough MR, Chen E, Europe-Finner GN, Karolczak-Bayatti M, Bailey J, Hankinson O, Raman V, LeBrun DP, Biswal S, Harvey CJ, DeBruyne JP, Hogenesch JB, Hevner RF, Héligon C, Luo XM, Blank MC, Millen KJ, Sharlin DS, Forrest D, Dahlman-Wright K, Zhao C, Mishima Y, Sinha S, Chakrabarti R, Portales-Casamar E, Sladek FM, Bradley PH, Wasserman WW. The transcription factor encyclopedia. Genome Biol. 2012; 13(3):R24. PMID: 22458515.
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    19. Fjell CD, Jenssen H, Cheung WA, Hancock RE, Cherkasov A. Optimization of antibacterial peptides by genetic algorithms and cheminformatics. Chem Biol Drug Des. 2011 Jan; 77(1):48-56. PMID: 20942839.
      View in: PubMed
    20. Cheung W, Hamarneh G. n-SIFT: n-dimensional scale invariant feature transform. IEEE Trans Image Process. 2009 Sep; 18(9):2012-21. PMID: 19502129.
      View in: PubMed
    21. Fjell CD, Jenssen H, Hilpert K, Cheung WA, Panté N, Hancock RE, Cherkasov A. Identification of novel antibacterial peptides by chemoinformatics and machine learning. J Med Chem. 2009 Apr 09; 52(7):2006-15. PMID: 19296598.
      View in: PubMed
    22. Kemmer D, Podowski RM, Yusuf D, Brumm J, Cheung W, Wahlestedt C, Lenhard B, Wasserman WW. Gene characterization index: assessing the depth of gene annotation. PLoS One. 2008 Jan 23; 3(1):e1440. PMID: 18213364.
      View in: PubMed
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