* Research Interests | * Web Resources | *Selected Publications


Previous UCSC Location: office PSB 320
Previous Telephone:9x4833
Previous Email: gerloff@soe.ucsc.edu


Dr Dietlind L. Gerloff

I have left UCSC, my new contact information from April 2013 is:

dgerloff@ffame.org
Dietlind L Gerloff, PhD
Senior Fellow (eq. Assoc Prof)
Foundation for Applied Molecular Evolution (FfAME)
Gainesville, FL 32604

During Spring and Summer I will frequently visit UCSC to advise ongoing research students.

  • Gerloff Group Research Interests & Web/Software Resources


  • Photo
	    of
	    Dietlind
	    Gerloff

    C.V.

    Dr sc nat, Department of Chemistry, ETH Zurich 1994
    Swiss National Science Foundation and Leukemia Society of America Postdoctoral Fellow,
    Department of Cellular & Molecular Pharmacology, University of California San Francisco 1995-1998
    Lecturer in Bioinformatics, University of Edinburgh 1999-2006
    Asst Prof, Biomolecular Engineering Dept, University of California Santa Cruz 2006-2013

    UCSC Teaching 2009-2013 (main courses only)

    Fall 2009: BME110 (BIOL181) - Computational Biology Tools
    Spring 2010: Sabbatical (University of Edinburgh, School of Informatics)
    Spring 2011: BME128 - Protein Engineering
    Spring 2012: BME128 - Protein Engineering
    Winter 2013: BME110 (BIOL181) - Computational Biology Tools

    Research interests

    My bioinformatics/biocomputing group's primary interests are in the structural/evolutionary principles of interactions between proteins – but also in how an appreciation of these principles combined with computer science can help us make sense of the vast amounts of functional genomics data that are being produced at present. We are developing novel approaches to facilitate research in all areas of modern biology by working at the interface between information technology and engineering, structural biochemistry, evolutionary biology, and experimental molecular biology. (See below for selected publications.)

    A molecular understanding of biomolecular interactions, and our ability to predict them from sequence, is especially important for informing computational efforts in systems biology, which aim to understand biology through modelling. It can also provide helpful clues toward resolving other fundamental scientific issues, ranging from evolutionary mechanisms to experimental design in functional genomics, and is the driving force behind our emphasis on multidisciplinary research strategies.

    Often target proteins for individual analyses are suggested through collaborations with colleagues investigating them in the laboratory. Even more important than the actual biological insight gained is, to us, that we are working toward a better understanding of sequence-structure-function relationships in these cases – in protein families that may have special features, i.e. are “non-standard” by comparison to proteins for which structures have been solved experimentally. The awareness of, for example, repetitive structure and how it may affect the results of standard bioinformatics programs, is important if these programs are to be applied to a wider range of molecules than they were developed for, and tested upon


    Web Resources


    Selected publications

    H. Barysz, J.H. Kim, Z.A. Chen, D.F. Hudson, J. Rappsilber, D.L. Gerloff, W.C. Earnshaw (2015).
    3D topology of the SMC2/SMC4 sub-complex from chicken condensin I revealed by cross-linking and molecular modelling. Open Biology, in the press.

    J.D. Magasin and D.L. Gerloff (2015).
    Pooled assembly of marine metagenomic data sets: Enriching annotation through chimerism. Bioinformatics 31, 311-317.
    doi:10.1093/bioinformatics/btu546

    N.F. Goodacre, D.L. Gerloff and P.Uetz (2014).
    Domains of unknown function are essential in bacteria. mBio 5, e00744-13.
    doi:10.1128/mBio.00744-13

    J.L. Sharman and D.L. Gerloff (2013).
    MaGnET: Malaria Genome Exploration Tool. Bioinformatics 29, 2350-2352.
    doi:10.1093/bioinformatics/btt384

    D.L. Gerloff, N. T. Woods, A. Farago, A.N.A. Monteiro (2012) .
    BRCT Domains: a little more than kin, and less than kind. FEBS Lett 586, 2711-2716.
    doi:10.1016/j.febslet.2012.05.005

    D.T. Pathak, X. Wei, A. Bucuvalas, D.H. Haft, D.L. Gerloff, D. Wall (2012).
    Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism. PLoS Genetics 8, e1002626.
    doi:10.1371/journal.pgen.1002626

    D.A. Liberles, S.A. Teichmann et al. [NESCENT Catalysis Group on Modeling Protein Structural and Snergetic Constraints on Sequence Evolution] (2012).
    The interface of protein structure, protein biophysics, and molecular evolution. Protein Science 21, 769-785.
    doi:10.1002/pro.2071

    T. Juettemann and D. L. Gerloff (2011).
    BISC: binary subcomplexes in proteins database. Nucleic Acids Res., 39, D705-711.
    doi:10.1093/nar/gkq859.

    F. Kippert and D. L. Gerloff (2009).
    Highly sensitive detection of individual HEAT and ARM repeats with HHpred and COACH. PLoS ONE, 4, e7148.
    doi:10.1371/journal.pone.0007148.

    A. M. B. Tadeu, S. Ribeiro, J. Johnston, I. Goldberg, D. Gerloff, W. C. Earnshaw (2008).
    CENP-V is required for centromere organization, chromosome alignment and cytokinesis. EMBO J. 27, 2510-2522.

    X. Quan, C. Walton, D. L. Gerloff, J. L. Sharman and D. Robertson (2006).
    Peer-to-peer experimentation in protein structure prediction: an architecture, experiment and initial results. International Workshop on Distributed, High-Performance and Grid Computing in Computational Biology (GCCB 2006), pp. 75-98.

    D. L. Gerloff, A. Creasey, S. Maslau and R. Carter (2005).
    Structural models for the protein family characterised by the Pfs230 gamete surface protein of Plasmodium falciparum. Proc. Natl. Acad. Sci. USA 102, 13598-603.

    D. C. Soares, D. L. Gerloff, N. R. Syme, A. F. W. Coulson, J. Parkinson and P. N. Barlow (2005).
    Large-scale modelling as a route to multiple surface comparisons of the CCP module family. Prot. Eng. Des. Sel. 18, 379-88.

    R. J. Orton, W. I. Sellers and D. L. Gerloff (2004).
    YETI: Yeast Exploration Tool Integrator (www.yeastgenomeexplorer.org - also check out our malarial genome explorer MaGnET (www.malariagenomeexplorer.org)! Bioinformatics 20, 284-285.

    F. Kippert and D. L. Gerloff (2004).
    Timeless and Armadillo - a link too far [comment]. Curr. Biol. 14, R650-R651.

    R. Schmid and D. L. Gerloff (2004).
    Functional properties of the alternative NADH:ubiquinone oxidoreductase from E.coli through comparative modelling. FEBS Letts. 578, 163-8