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    David Jimenez-Morales, PhD

    SchoolUCSF School of Medicine
    DepartmentCellular Molecular Pharmacology
    Address1700 4th Street
    San Francisco CA 94158
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      University of Illinois, ChicagoPhD BioinformaticsBioengineering2013
      Universidad Complutense de MadridMSc Computational BiologyFac. Ciencias Quimicas2004

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      My research interest is understanding the set of components, interactions, and processes that govern the complexity of living organisms as a means to provide solutions to major biomedical challenges. My strategy is based on the development of innovative computational approaches for the integration and exploration of different datasets, within the experimental framework. I am determined to leverage my biology background and computational skills to create better links between the biology and informatics worlds. During my graduate work I studied a variety of physicochemical and functional constraints acting on the sequence and structure of proteins. For example, I characterized the evolutionary patterns in a membrane protein family and applied this information to successfully engineer altered versions of a protein of this family; I explored physicochemical properties of the functional cavities of enzymes, proposed new metrics, and characterized defining features of these important functional spaces; I evaluated the relationship between enzyme structures, enzyme functions, and metabolic fluxes in the central carbon metabolism of E. coli. Perhaps most significantly, I unveiled the distinctive nature of lysine carboxylation, a non-enzymatic posttranslational modification affecting active sites. The growing necessity of my research to better understand how biological data is collected, stored, and managed led me to dictyBase, where I had the opportunity to learn the methodology of professional software development and advance my computational skills. In my current research, I am developing computational methods to integrate high-throughput data and model host-pathogen interactions.

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      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. Basu S, Fey P, Jimenez-Morales D, Dodson RJ, Chisholm RL. dictyBase 2015: Expanding data and annotations in a new software environment. Genesis. 2015 Aug; 53(8):523-34. PMID: 26088819; PMCID: PMC4545684 [Available on 08/01/16].
      2. Jimenez-Morales D, Adamian L, Shi D, Liang J. Lysine carboxylation: unveiling a spontaneous post-translational modification. Acta Crystallogr D Biol Crystallogr. 2014 Jan; 70(Pt 1):48-57. PMID: 24419378; PMCID: PMC3919261.
      3. Jimenez-Morales D, Liang J, Eisenberg B. Ionizable side chains at catalytic active sites of enzymes. Eur Biophys J. 2012 May; 41(5):449-60. PMID: 22484856; PMCID: PMC3360948.
      4. Naveed H, Jimenez-Morales D, Tian J, Pasupuleti V, Kenney LJ, Liang J. Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding. J Mol Biol. 2012 May 25; 419(1-2):89-101. PMID: 22391420; PMCID: PMC3772668.
      5. Jimenez-Morales D, Liang J. Pattern of amino acid substitutions in transmembrane domains of ß-barrel membrane proteins for detecting remote homologs in bacteria and mitochondria. PLoS One. 2011; 6(11):e26400. PMID: 22069449; PMCID: PMC3206045.
      6. Liang J, Naveed H, Jimenez-Morales D, Adamian L, Lin M. Computational studies of membrane proteins: models and predictions for biological understanding. Biochim Biophys Acta. 2012 Apr; 1818(4):927-41. PMID: 22051023; PMCID: PMC3737997.
      7. Jimenez-Morales D, Adamian L, Liang J. Detecting remote homologues using scoring matrices calculated from the estimation of amino acid substitution rates of beta-barrel membrane proteins. Conf Proc IEEE Eng Med Biol Soc. 2008; 2008:1347-50. PMID: 19162917; PMCID: PMC2630510.
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