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    Chu, Ken

    TitleComputer Systems Group Lead
    SchoolLawrence Berkeley National Lab
    DepartmentComputational Research
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone925/296-5691
    vCardDownload vCard

      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.
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      1. Hadjithomas M, Chen IA, Chu K, Huang J, Ratner A, Palaniappan K, Andersen E, Markowitz V, Kyrpides NC, Ivanova NN. IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes. Nucleic Acids Res. 2017 Jan 04; 45(D1):D560-D565. PMID: 27903896.
        View in: PubMed
      2. Chen IA, Markowitz VM, Chu K, Palaniappan K, Szeto E, Pillay M, Ratner A, Huang J, Andersen E, Huntemann M, Varghese N, Hadjithomas M, Tennessen K, Nielsen T, Ivanova NN, Kyrpides NC. IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res. 2017 Jan 04; 45(D1):D507-D516. PMID: 27738135.
        View in: PubMed
      3. Chen IM, Markowitz VM, Palaniappan K, Szeto E, Chu K, Huang J, Ratner A, Pillay M, Hadjithomas M, Huntemann M, Mikhailova N, Ovchinnikova G, Ivanova NN, Kyrpides NC. Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. BMC Genomics. 2016 Apr 26; 17:307. PMID: 27118214; PMCID: PMC4847265.
      4. Markowitz VM, Chen IM, Chu K, Pati A, Ivanova NN, Kyrpides NC. Ten years of maintaining and expanding a microbial genome and metagenome analysis system. Trends Microbiol. 2015 Nov; 23(11):730-41. PMID: 26439299.
        View in: PubMed
      5. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M, Anderson I, Billis K, Varghese N, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 2014 Jan; 42(Database issue):D560-7. PMID: 24165883; PMCID: PMC3965111.
      6. Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Pillay M, Ratner A, Huang J, Pagani I, Tringe S, Huntemann M, Billis K, Varghese N, Tennessen K, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC. IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res. 2014 Jan; 42(Database issue):D568-73. PMID: 24136997; PMCID: PMC3964948.
      7. Chen IM, Markowitz VM, Chu K, Anderson I, Mavromatis K, Kyrpides NC, Ivanova NN. Improving microbial genome annotations in an integrated database context. PLoS One. 2013; 8(2):e54859. PMID: 23424620; PMCID: PMC3570495.
      8. Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Jacob B, Ratner A, Liolios K, Pagani I, Huntemann M, Mavromatis K, Ivanova NN, Kyrpides NC. IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. PLoS One. 2012; 7(7):e40151. PMID: 22792232; PMCID: PMC3390314.
      9. Fan B, Dachrut S, Coral H, Yuen ST, Chu K, Law S, Zhang L, Ji J, Leung SY, Chen X. Integration of DNA copy number alterations and transcriptional expression analysis in human gastric cancer. PLoS One. 2012; 7(4):e29824. PMID: 22539939; PMCID: PMC3335165.
      10. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC. IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res. 2012 Jan; 40(Database issue):D115-22. PMID: 22194640; PMCID: PMC3245086.
      11. Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, Ratner A, Jacob B, Pati A, Huntemann M, Liolios K, Pagani I, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 2012 Jan; 40(Database issue):D123-9. PMID: 22086953; PMCID: PMC3245048.
      12. Mavromatis K, Chu K, Ivanova N, Hooper SD, Markowitz VM, Kyrpides NC. Gene context analysis in the Integrated Microbial Genomes (IMG) data management system. PLoS One. 2009 Nov 24; 4(11):e7979. PMID: 19956731; PMCID: PMC2776528.
      13. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC. The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res. 2010 Jan; 38(Database issue):D382-90. PMID: 19864254; PMCID: PMC2808961.
      14. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009 Sep 01; 25(17):2271-8. PMID: 19561336.
        View in: PubMed
      15. Miller BA, Chu K, Hankey BF, Ries LA. Cancer incidence and mortality patterns among specific Asian and Pacific Islander populations in the U.S. Cancer Causes Control. 2008 Apr; 19(3):227-56. PMID: 18066673; PMCID: PMC2268721.
      16. Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC. The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res. 2008 Jan; 36(Database issue):D528-33. PMID: 17933782; PMCID: PMC2238897.
      17. Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 2008 Jan; 36(Database issue):D534-8. PMID: 17932063; PMCID: PMC2238950.
      18. Kem R, Chu K. Cambodian cancer incidence rates in California and Washington, 1998-2002. Cancer. 2007 Sep 15; 110(6):1370-5. PMID: 17654663.
        View in: PubMed

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