David Jimenez-Morales, PhD

InstitutionUniversity of California San Francisco
DepartmentCellular Molecular Pharmacology
Address1700 4th St
San Francisco CA 94158
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    University of Illinois, ChicagoPhD Bioinformatics2013Bioengineering
    Universidad Complutense de MadridMSc Computational Biology2004Fac. Ciencias Quimicas

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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. Paulo E, Wu D, Wang Y, Zhang Y, Wu Y, Swaney DL, Soucheray M, Jimenez-Morales D, Chawla A, Krogan NJ, Wang B. Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis. Sci Rep. 2018 Jul 20; 8(1):11001. PMID: 30030465.
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    2. Masand R, Paulo E, Wu D, Wang Y, Swaney DL, Jimenez-Morales D, Krogan NJ, Wang B. Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits. Cell Metab. 2018 Mar 06; 27(3):616-629.e4. PMID: 29514069.
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    3. Rialdi A, Hultquist J, Jimenez-Morales D, Peralta Z, Campisi L, Fenouil R, Moshkina N, Wang ZZ, Laffleur B, Kaake RM, McGregor MJ, Haas K, Pefanis E, Albrecht RA, Pache L, Chanda S, Jen J, Ochando J, Byun M, Basu U, García-Sastre A, Krogan N, van Bakel H, Marazzi I. The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity. Cell. 2017 May 04; 169(4):679-692.e14. PMID: 28475896.
      View in: PubMed
    4. 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):523-534. PMID: 26088819; PMCID: PMC4545684.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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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