Contreras, Lydia M. Ph.D.

Associate Professor
Jim and Barbara Miller Endowed Faculty Fellowship in Chemical Engineering

Lydia Contreras

Office: CPE 5.410 Mailing Address:
Phone: 512-471-2453 University of Texas at Austin
Fax: 512-471-7060 McKetta Department of Chemical Engineering
Email: lcontrer@che.utexas.edu 200 E Dean Keeton St. Stop C0400
UT Mail: C0400 Austin, Texas  78712-1589

Research Areas: Biotechnology and Modeling & Simulation

Research Group Website

Research Presentation for Prospective Graduate Students

Educational Qualifications

Ph.D., Chemical and Biomolecular Engineering, Cornell University (2008)
B.S.E., Chemical Engineering, Princeton University (2003)
NIH Postdoctoral Fellow (Infectious Diseases), Division of Developmental Genetics and Bioinformatics, Wadsworth Center-New York State Dept. of Health, Albany, NY (2008-2010)

Courses Taught

CHE 317  Introduction to Chemical Engineering Analysis

Focus

Biomolecular engineering, biotechnology, metabolic and cellular engineering

Research

Our research combines biomolecular engineering, genetic studies and computational modeling to understand molecular features that lead to the specific recognition and interaction of RNAs and proteins. We apply fundamental concepts that emerge from experimental (and computational) work to develop novel applications that could beneficially impact human health.
Overall research goals:

  • RNA-protein interactions, RNA-protein folding
  • Novel molecular tools for intracellular studies of RNA-metabolism
  • Protein engineering for novel mechanisms of molecular recognition
  • Diagnostics for RNA-related diseases
  • Discovery of drugs targeting RNAs
  • Optimization strategies for therapeutic RNA/protein expression

We welcome interest from motivated undergraduate students who want to pursue graduate research and from exceptional graduate students who are interested in postdoctoral research opportunities. Please don’t hesitate to contact Prof. Contreras for additional information.

Awards & Honors

  • FASEB Postdoctoral Development and Enrichment Award, 2009
  • Edna and William Hooey Award, Chemical Engineering Dept. Cornell. University, 2007
  • NSF IGERT Fellow, Cornell University, 2004-2006

 Selected Publications

  • Contreras Martinez, L., Martinez-Veracoechea, F., Pohkarel, P., Stroock, A.D., Escobedo, F. and DeLisa, M.P. (2006) Protein translocation through a tunnel induces changes in folding kinetics:  a lattice model study. Biotechnol Bioeng 94: 105-117.
  • Contreras Martinez, L. and DeLisa MP (2007) Intracellular ribosome display via SecM translation arrest as a selection for antibodies with enhanced cytosolic stability. J.Mol.Biol. 372(2): 513-524.
  • Contreras Martinez, L., Borrero, E.E., Escobedo, F. and DeLisa, M.P. (2007) In silico protein fragmentation reveals the importance of critical nuclei in domain reassembly. BioPhys J. 94(5): 1575-1588.
  • Contreras Martinez, L. and DeLisa, M.P. (2007) Expression engineering of synthetic antibodies using ribosome display. In: Dyson, M. and Durocher, Y., editors. Expression Systems – Methods Express. Oxfordshire, UK: Scion Publishing.
  • Borrero, E.E., Contreras Martinez, L., DeLisa, M.P. (2010) Kinetics and reaction coordinates of the reassembly of protein fragments via forward flux sampling.  BioPhys J. 98(9): 1911-20.
  • Dichiara, J.M., Contreras Martinez, L., Smith D., and Belfort M. (2010) Identification of small RNAs in the TB-complex bacterium Mycobacterium bovis BCG reveals a link to Crp/Cmr related metabolism. NAR, 38 (12): 4068-4078.
  • Wu, W-Y., Gillies, A. R., Hsii, J. F., Contreras, L., Oak, S., Perl, M. B. and Wood, D. W.  Self-cleaving purification tags re-engineered for rapid Topo® cloning (2010). Biotechnol Prog, 26 (5):1205-1212.
  • Huang, T., Shaikh,T., Gupta, K., Contreras-Martin L., Grassucci, R., Van Duyne, G.D., Frank, J., Belfort, M. The group II intron ribonucleoprotein precursor is a large, loosely packed structure ( Nucleic Acids Research, published online of press December, 2010).
  • Contreras-Martin, L., Huang, T., Piazza, CL., Danserau J., Belfort, M. (2010) A protective interaction between the Lactoccocus lactis group II intron RNP and host ribosomes (in preparation).
  • Gupta, K., Contreras-Martin L., Huang, T., Belfort, M., and Van Duyne, G. (2010) SAXS envelope of group II intron RNP provides arrangement of proteins and RNA components (in preparation).
  • Contreras-Martin, L., Dichiara, J., Belfort, M. (2010) A phylogenetic approach to refining sRNAs prediction using Mycobacterium as a model (in preparation).
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