Our Research:

Our research combines biomolecular engineering, genetic studies and computational modeling to understand molecular features that lead to the specific recognition and interaction of regulatory RNAs and proteins. We apply fundamental concepts that emerge from experimental (and computational) work to develop novel applications that could beneficially impact human health and biotechnology. Overall research interests: *transcriptional regulation, *regulatory RNA networks, *epitranscriptomics,  * RNA-protein interactions, RNA-protein folding * Novel molecular tools for intracellular studies of RNA-metabolism *  * Diagnostics for RNA-related diseases * Molecular mechanisms of stress-responses

Our Team Values:

Our lab strives to be at the forefront of exciting scientific discoveries in the field of RNA biology. To accomplish this, we value a strongly cohesive and team-oriented environment where we encourage and respect each other. We value the contribution of every member towards creating and sustaining a safe, stimulating, and engaging environment for intellectual growth. 

We believe that a collaborative, professional, and diverse environment fosters creativity and excellence in our field. Therefore, the Contreras group is committed to maintaining an inclusive environment for every student, at every level, regardless of race, age, citizenship status, national origin, gender, gender-identity, sexual orientation, religion, marital/parental status, veteran status, or physical/ mental abilities.

Sample  Publications:

J.C. Gonzalez-Rivera, K.C. Baldridge, D.S. Wang, K.H. Patel, J.C.L. Chuvalo-Abraham, L. Hildebrandt Ruiz, and L.M. Contreras. “Post-transcriptional air pollution oxidation to the cholesterol biosynthesis pathway promotes pulmonary stress phenotypes” Communications Biology 3, 392 (2020).

Han, K. Haning, J.C. Gonzalez-Rivera, Y. Yang,  R. Li, S-H. Cho, J. Huang, B. Simonsen, S. Yang, L.M. Contreras. “Multiple small RNAs interact to co-regulate ethanol tolerance in Zymomonas mobilis” Frontiers in Bioengineering and Biotechnology, 8 (2020).

Lukasiewicz, A. and L.M. Contreras . “Antisense probing of dynamic RNA structures” Methods (2020).

 J.C. Gonzalez-Rivera, A.A. Orr, S.M. Engels, J.M. Jakubowski, M.W. Sherman, K.N. O’Connor, T. Matteson, B.C. Woodcock, L.M. Contreras and P. Tamamis. “Computational evolution of an RNA-binding protein towards enhanced oxidized RNA binding” Computational and Structural Biotechnology Journal, 28:137-152 (2020).

A.M. Rojano-Nisimura , K. Haning,  J. Janovsky, K.A. Vasquez, J.P. Thompson, and  L.M. Contreras (2019).” Codon selection affects recruitment of ribosome-associating factors during translation”. ACS Synthetic Biology 

A. N. Leistra, N.C. Curtis and L.M. Contreras. “Regulatory Non-coding sRNAs in Bacterial Metabolic Pathway Engineering ”Metabolic Engineering, 52:190-214 (2019). 

K. Mihailovic, J. Vazquez-Anderson, Y. Li, P. Vimalathas, V. Fry, R.A. Lease, W. Powell, and L.M. Contreras. “High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites.” Nature Communications, 9:4084 (2018)

S. Sowa, G. Gelderman, A. N. Leistra, A. Buvanendiran, S. Lipp, A. Pitaktong, T. Romeo, M. Baldea, and L.M. Contreras, “Integrative FourDomics approach profiles the target network of the carbon storage regulatory system,” Nucleic Acids Research Journal, 45(4): 1673-1686 (2017)

S. Sowa, J. Vazquez-Anderson, C. Clark, R. De La Peña, K. Dunn, E. Fung, M. Khoury, and L.M.Contreras,“Exploiting post-transcriptional regulation to probe RNA structures in vivo via fluorescence,” Nucleic Acids Research, 43(2):e13  (2015). 

C-H. Tsai, C. Baranowski, J. Livny, K. McDonough, J. Wade, and L.M. Contreras, “Identification of novel sRNAs in Mycobacterial species”, Plos One  4;8(11):e79411 (2013)