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Qinghu Ren, Ph.D.
Bioinformatics Scientist

____Contact Details_____________________
Dr. Qinghu Ren
9712 Medical Center Dr.
Rockville, MD 20850
U.S.A.

Email: qren@jcvi.org
Phone: 1-301-795-7521
Fax: 1-301-838-0208


____Research Interests_____________________

  • Whole genome analysis of membrane transport systems
  • Maintain a web-integrated bioinformatics database TransportDB (http://www.membranetransport.org/)
  • Global comparisons of membrane transport capabilities in prokaryotic and eukaryotic genomes.
  • Genomic sequencing and annotation of microbial and eukaryotic organisms.

    ____Education_____________________________
    Ph.D., Cell, Molecular and Developmental Biology, University of Rochester, Rochester, New York, USA, 2002
    Bachelor of Medicine, Basic Medical Science, Beijing Medical University (now as Peking University Health Science Center), Beijing, China, 1997

    ____Experience____________________________
    2007 - present: Staff Scientist II, J. Craig Venter Institute, Rockville, MD, USA
    2004 - 2007: Staff Scientist I, The Institute for Genomic Research, Rockville, MD, USA
    2002 - 2004: Post-Doctoral Fellow, The Institute for Genomic Research, Rockville, MD, USA

    ____Honors/Awards/Societies_______________________________
    2002 - 2004: Post Doctoral Fellowship, The Institute for Genomic Research
    1997 - 2002: Graduate Student Scholarship
    1994: Outstanding Undergraduate Student Award, Beijing Medical University
    1995: Liu Chen Award in Pathology, Beijing Medical University, 1995
    2004 - present: Member, American Society for Microbiology
    2004 - present: Member, American Association for the Advancement of Science

    ____Selected Publications (Out of a total of 35 papers)___________________
    1. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q. H., Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernandez E, Fukuzawa H, Gonzalez-Ballester D, Gonzalez-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riano-Pachon DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martinez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318:245-50.
    2. Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q. H., Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW (2007) Genome sequence of Aedes aegypti, a major arbovirus vector. Science316:1718-23.
    3. Myers, G. S, Parker, D., Al-Hasani, K., Kennan, R. M., Seemann, T., Ren, Q. H., Badger, J. H., Selengut, J. D., Deboy, R. T., Tettelin, H., Boyce, J. D., McCarl, V. P., Han, X., Nelson, W. C., Madupu, R., Mohamoud, Y., Holley, T., Fedorova, N., Khouri, H., Bottomley, S. P., Whittington, R. J., Adler, B., Songer, J. G., Rood, J. I, and Paulsen, I. T. (2007) Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. Nature Biotechnology 25:569-575.
    4. Ren, Q. H., and Paulsen, I. T. (2007) Large-scale comparative genomic analyses of cytoplasmic membrane transport systems in prokaryotes. Journal of Molecular Microbiology and Biotechnology 12:165-79
    5. Ren, Q. H., Song, X., Goneska, E., Taverna, S. D., Allis, C. D., and Gorovsky, M. A. (2007) Phosphorylation of the SQ H2A.X Motif is Required for Proper Meiosis and Mitosis in Tetrahymena thermophila. Molecular and Cellular Biology 27:2648-60
    6. Ren, Q. H., Chen, K., and Paulsen, I. T. (2007) TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Research D274-9.
    7. Ren, Q. H., and Saier, M. H. Jr. (2006) The bioinformatic study of transmembrane molecular transport. (Editorial) Journal of Molecular Microbiology and Biotechnology 11:289-90.
    8. Eisen, J. A., Coyne, R. S., Wu, M., Wu, D., Thiagarajan, M., Wortman, J. R., Badger, J. H., Ren, Q. H., Amedeo, P., Jones, K. M., Tallon, L. J., Delcher, A. L., Salzberg, S. L., Silva, J. C., Haas, B. J., Majoros, W. H., Farzad, M., Carlton, J. M., Smith, R. K. Jr., Garg, J., Pearlman, R. E., Karrer, K. M., Sun, L., Manning, G., Elde, N. C., Turkewitz, A. P., Asai, D. J., Wilkes, D. E., Wang, Y., Cai, H., Collins, K., Stewart, B. A., Lee, S. R., Wilamowska, K., Weinberg, Z., Ruzzo, W. L., Wloga, D., Gaertig, J., Frankel, J., Tsao, C. C., Gorovsky, M. A., Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson, S. C., Barbeau, R. A., Hamilton, E. P., Orias, E. (2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. Public Library of Science Biology 4(9):e286.
    9. Palenik, B., Ren, Q. H., Dupont, C. L., Myers G. S., Heidelberg J. F., Badger, J. H., Madupu, R., Nelson, W. C., Brinkac, L. M., Dodson R. J., Durkin A. S., Daugherty, S. C., Sullivan, S. A., Khouri, H., Mohamoud, Y., Halpin, R. and Paulsen, I. T. (2006) Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proceedings of the National Academy of Sciences, USA 103(36):13555-9.
    10. Saidijam M., Benedetti G., Ren Q. H., Xu Z., Hoyle C. J., Palmer S. L., Ward A., Bettaney K. E., Szakonyi G., Meuller J., Morrison S., Pos M. K., Butaye P., Walravens K., Langton K., Herbert R. B., Skurray R. A., Paulsen I. T., O'reilly J., Rutherford N. G., Brown M. H., Bill R. M., Henderson P. J. (2006) Microbial drug efflux proteins of the major facilitator superfamily. Current drug targets 7(7):793-811.
    11. Dunning Hotopp, J. C., Lin, M., Madupu R., Crabtree J, Angiuoli, S. V., Eisen J., Seshadri R., Ren, Q. H., Wu, M., Utterback, T. R., Smith, S., Lewis, M., Khouri, H., Zhang, C., Hua, N., Lin, Q., Ohashi, N., Zhi, N., Nelson, W., Brinkac, L. M., Dodson, R. J., Rosovitz, M. J., Sundaram, J., Daugherty, S. C., Davidsen, T., Durkin, A., Gwinn, M., Haft, D. H., Selengut, J. D., Sullivan, S. A., Zafar, N., Zhou, L., Benahmed, F., Forberger, H., Halpin, R., Mulligan, S., Robinson, J., Rikihisa, Y. and Tettelin, H. (2006) Comparative Genomics of Emerging Human Ehrlichiosis Agents. Public Library of Science Genetics 2(2):e21.
    12. Ren, Q. H. and Paulsen, I. T. (2005) Transporter protein families. (Specialist Review), In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Wiley Press.
    13. Wu, M., Ren Q. H., Durkin, A. S., Daugherty, S. C., Brinkac, L. M., Dodson, R. J., Madupu, R., Sullivan, S. A., Kolonay, J. F., Nelson, W., Tallon, L. J., Jones, K. M., Ulrich, L. E., Gonzalez, J. M., Zhulin, I. B., Robb, F. T. and Eisen, J. A. (2005) Life in Hot Carbon Monoxide: the Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901. Public Library of Science Genetics 1(5):e65.
    14. Ren, Q. H. and Paulsen, I. T. (2005) Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. Public Library of Science Computational Biology 1(3): 190-201.
    15. Gardner M. J., Bishop R., Shah T., de Villiers E. P., Carlton J. M., Hall N., Ren, Q. H., Paulsen I. T., Pain A., Berriman M., Wilson R. J., Sato S., Ralph S. A., Mann D. J., Xiong Z., Shallom S. J., Weidman J., Jiang L., Lynn J., Weaver B., Shoaibi A., Domingo A. R, Wasawo D., Crabtree J., Wortman J. R., Haas B., Angiuoli S. V., Creasy T. H., Lu C., Suh B., Silva J. C., Utterback T. R., Feldblyum T. V., Pertea M., Allen J., Nierman W. C., Taracha E. L., Salzberg S. L., White O. R., Fitzhugh H. A., Morzaria S., Venter J. C., Fraser C. M., Nene V. (2005) Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science 309(5731): 134-7.
    16. Paulsen I. T., Press C. M., Ravel J., Kobayashi D. Y., Myers G. S., Mavrodi D. V., DeBoy R. T., Seshadri R., Ren, Q. H., Madupu R., Dodson R. J., Durkin A. S., Brinkac L. M., Daugherty S. C., Sullivan S. A., Rosovitz M. J., Gwinn M. L., Zhou L., Schneider D. J., Cartinhour S. W., Nelson W. C., Weidman J., Watkins K., Tran K., Khouri H., Pierson E. A., Pierson L. S. 3rd, Thomashow L. S., Loper J. E. (2005) Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nature Biotechnology 23(7):873-8.
    17. Paulsen, I. T., Kang, K. H., Hance, M. and Ren, Q. H. (2004) Genome analysis of membrane transport. In Fraser, C. M. et al. (ed.), Microbial Genomes Humana Press, Totowa, NJ, pp. 113-126
    18. Ren, Q. H., Kang, K. H. and Paulsen, I. T. (2004) TransportDB: A Relational Database of Cellular Membrane Transport Systems. Nucleic Acids Research 32: D284-D288.
    19. Ren, Q. H., and Gorovsky, M. A. (2003). Acetylation of the N-terminal tail of major H2A is not essential but it can replace the essential acetylation of H2A.Z tail. Molecular and Cellular Biology 23, 2778-2789.
    20. Ren, Q. H., and Gorovsky, M. A. (2001). H2A.Z acetylation modulates an essential charge patch. Molecular Cell 7, 1329-1335.

  •  

      Professor
    Group Leader

      (JCVI)
    Bioinformatics Scientist
    Lead developer of TransportDB

      (JCVI)
    Research Assistant
    Curator of EcoCyc

      (Macquarie)
    Post-Doctoral Fellow

      (Macquarie)
    Post-Doctoral Fellow

      (Macquarie)
    Research Fellow

    Amanda Mackie
      (Macquarie)
    Curator of EcoCyc
    Lab Manager
    Research Assistant

      (Macquarie)
    PhD Student

    Daniel Farrugia
      (Macquarie)
    PhD Student

    Bhumika Shah
      (Macquarie)
    PhD Student

    Katy Breakwell
      (Macquarie)
    Honours Student

    Liping Li
      (Macquarie)
    Honours Student

      (Macquarie)
    PhD Student
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