Peer reviewed publications

  1. 48.

    A. N. Leistra and L.M. Contreras. “Regulatory Non-coding sRNAs in Bacterial Metabolic Pathway Engineering ” (Submitted)

  1. 47.

    J. Vazquez-Anderson, M. K. Mihailovic, 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” (Submitted)

  2. 46.

    K. Haning, S-H. Cho, J.C. Gonzalez-Rivera, B. Simonsen, L.M. Contreras. “Multiple small RNAs interact to co-regulate ethanol tolerance in Zymomonas mobilis” (Submitted)

  3. 45.

    J. K. Villa, Y. Su, L.M. Contreras and M. Hammond. “Synthetic Biology of Small RNAs and Riboswitches”, Accepted book chapter, in Papenfort, K, Storz, G (eds.), Regulating with RNA in Bacteria and Archaea. ASM.

  4. 44.

    Y. Li, K. Reyes, J. Vazquez-Anderson, Y. Wang, L.M. Contreras , and W. Powell. “A knowledge gradient policy for sequencing experiments to identify the structure of RNA molecules using a sparse additive believe model,” (Accepted, INFORMS Journal on Computing)

  5. 43.

    A. N. Leistra, G. Gelderman, S. W. Sowa, A. Moon-Walker, H. M. Salis, and L.M. Contreras. “A Canonical Biophysical Model of the CsrA Global Regulator Suggests Flexible Regulator-Target Interactions” Scientific Reports. Available from:

  6. 42.

    K. Baldridge, M. Jora, A. Maranhao, M. Quick, B. Addepalli, J. Brodbelt, A. Ellington, P. Limbach and L.M. Contreras. “Directed Evolution of Heterologous tRNAs Leads to Reduced Dependence on Post-transcriptional Modifications” ACS Synthetic Biology, 7(5):1315-1327. Available from:

  7. 41.

    X. Wang, Q He, Y. Yang, J. Wang, K. Hanning, Y. Hu, B. Wu, M. He, Y. Zhang, J. Bao, L.M. Contreras, and S. Yang “Advances and Prospects in Metabolic Engineering of Zymomonas mobilis,” Metabolic Engineering, S1096-7176(18)30036-3. Available from:

  8. 40.

    M. Sherman and L.M. Contreras “Computational approaches in design of nucleic acid-based therapeutics” Current Opinion in Biotechnology, 18(53):232-239. Available from:

  9. 39.

    A. Leistra, M.K Mihailovic and L.M. Contreras “Fluorescence-based Methods for Characterizing RNA interactions in vivo,” in: Arluison V., Valverde C. (eds) Bacterial Regulatory RNA. Methods in Molecular Biology, vol 1737. Humana Press, New York, NY. Available from:

  10. 38.

    A.A. Orr, J.C. Gonzalez-Rivera, M. Wilson, P.R. Bhikha, D. Wang, L.M. Contreras, and P. Tamamis. “A high-throughput and rapid computational method for screening of RNA post-transcriptional modifications that can be recognized by target proteins,” Methods. Available from:


    S-H. Cho, K. Haning, W. Shen, C. Blome, R. Li, S. Yang, and L.M. Contreras, “Identification and characterization of 5′ untranslated regions (5’UTRs) in Zymomonas mobilis as regulatory biological parts,” Frontiers in Microbiology, section Microbial Physiology and Metabolism, 8:2432 (2017). Available from: doi:10.3389/fmicb.2017.02432.

  1. 36.

    A. Chen, L.M. Contreras, and Benjamin Keitz, “Imposed Environmental Stresses Facilitate Cell-free Nanoparticle Formation by Deinococcus radiodurans,” Applied and Environmental Microbiology, 83 (18): e00798-17 (2017). Available from: doi:10.1016/10.1128/AEM.00798-17.

  2. 35.

    J. K. Villa, P. Amador, J. Janovsky, A. Bhuyan, R. Saldanha, T. J. Lamkin, and L.M. Contreras, “Genome-wide search for ionizing radiation responsive 5’UTRs in Deinococcus radiodurans reveals post-transcriptional regulation in the Radiation and Desiccation Response (RDR) for DNA gyrase subunit A,” Applied and Environmental Microbiology, 83(12): e00039-17 (2017). Available from: doi:10.1128/AEM.00039-17.


    A. Leistra, P. Amador, A. Buvanendiran, A. Moon-Walker and L.M. Contreras “Rational modular RNA engineering based on in vivo profiling of structural accessibility” ACS Synthetic Biology (2017). Available from: doi:10.1016/10.1021/acssynbio.7b00185.

  3. 33.

    J. Vazquez-Anderson, M. K. Mihailovic, K.C. Baldridge, K. Reyes, K. Haning, S. H. Cho, P. Amador, W. Powell, and L.M. Contreras, “Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions,” Nucleic Acids Research Journal, 45(9):5523–5538 (2017). Available from: doi:10.1093/nar/gkx115.

  4. 32.

    M.K. Mihailovic, A. Chen, J.C. Gonzalez-Rivera, and L.M. Contreras, “Defective RNPs, mistakes in RNA processing and Diseases,” Biochemistry, 56(10):1367–1382 (2017). (Invited Article). Available from: doi:10.1016/10.1021/acs.biochem.6b01134.

  5. 31.

    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). Available from: doi:10.1093/nar/gkx048.


  1. 30.

    S. Yang, Q. Fei, Y. Zhang, L.M. Contreras , S. M. Utturkar, S. D. Brown, M. E. Himmel and M. Zhang. “Zymomonas mobilis as a Model System for Production of Biofuels and Biochemicals,” Microbial Biotechnology, 9(6): 699–717 (2016). Available from: doi:10.1111/1751-7915.12408.

  2. 29.

    K. Vasquez, T. Hatridge, N. Curtis, and L.M. Contreras, “Modifying translation timing between protein domains by regulating affinity between mRNAs and the ribosomal anti-Shine-Dalgarno sequence results in predictable solubility changes,” ACS Synthetic Biology, 5(2): 133-145 (2016). Available from: doi:10.1021/acssynbio.5b00193. Paper featured in issue’s cover.


web only. Editor: Ranj JEM: Leslie

Artwork by Franklin M. Sandoval


  1. 28.

    S-H. Cho, S-H. Ju, and L.M. Contreras,“Synthetic chimeras with orthogonal ribosomal proteins increase translation yields by promoting mRNA associations with active ribosomes,” Biotechnology Progress, 32(2): 285–293 (2016). Available from: doi:10.1002/btpr.2227

  1. 27.

    S. Sowa, G. Gelderman, and L.M. Contreras, “Advances in synthetic dynamic circuits: using novel synthetic parts to engineer new generations of gene oscillations,”  Current Opinion in Biotechnology, 36:161-167  (2015). (Invited Article). Available from: doi:10.1016/j.copbio.2015.08.020.

  2. 26.
  3. K. Haning, S-H. Cho, and L. M. Contreras,  “Strain Engineering via regulatory noncoding RNA mechanisms: not a one-blueprint fits all,” Current Opinion in Chemical Engineering, 10:25-34 (2015). (Invited Article). Available from: doi:10.1016/j.coche.2015.07.008
  1. 25.

    C-H. Tsai, R. Liao, B. Chou, and L.M. Contreras, “Transcriptional Analysis of Deinococcus radiodurans reveals small RNAs that are differentially expressed under ionizing radiation,” Applied and Environmental Microbiology, 81(5): 1745-55 (2015). Available from: doi:10.1128/AEM.03709-14

  2. 24.

    G. Gelderman, A. Sivakumar, S. Lipp, L.M. Contreras, “Adaptation of Tri-molecular fluorescent complementation allows assaying of regulatory Csr RNA-protein interactions in bacteria,” Biotechnology and bioengineering, 112(2): 365-375 (2015). Available from: doi:10.1002/bit.25351.

  3. 23.

    K. Baldridge, J. Zavala, J. Surratt, K. Sexton, and L.M. Contreras, “Cellular RNA is chemically modified by exposure to air pollution mixtures,” Inhalation Toxicology, 27(1):74-82 (2015). Available from: doi:10.3109/08958378.2014.987361.

  4. 22.

    C-H. Tsai, R. Liao, B. Chou, M. Palumbo, and L.M. Contreras, “Genome-wide analysis in bacteria shows sRNA enrichment in long and conserved intergenic regions,” Journal of Bacteriology, 197(1):40-50  (2015). Available from: doi:10.1128/JB.02359-14.

  5. 21.

    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). Available from: doi:10.1093/nar/gku1191

  1. 20.

    K. Haning, S-H. Cho, and L.M.Contreras, ”Small RNAs in Mycobacteria: an unfolding story,” Frontiers in cellular infection and microbiology, 4(96):1-11 (2014). (Invited Article). Available from: doi:10.3389/fcimb.2014.00096

  2. 19.

    S. Sowa, M. Baldea, and L.M.Contreras, “Optimizing metabolite production using periodic    oscillations,” PLOS Computational Biology, 10(6): e1003658 (2014).  Available from: doi:10.1371/journal.pcbi.1003658

  3. 18.

    S-H. Cho, R. Lei, and L.M. Contreras, “Discovery of ethanol responsive small RNAs in Zymomonas mobilis,” Applied and Environmental Microbiology, 80(14):4189-98 (2014). Available from: doi:10.1128/AEM.00429-14

  4. 17.

    K.Gupta, L.M.Contreras, T. Huang, L. Spruce, S. Seeholzer, M. Belfort, and G. Van Duyne,, “Quaternary arrangement of an active, native group II intron ribonucleoprotein complex revealed by small-angle X-ray scattering,” Nucleic Acids Research, 42(8): 5347-60 (2014). Available from: doi:10.1093/nar/gku140

  5. 16.

    K. Baldridge, and L.M.Contreras, “Functional implications of rRNA methylations in response to environmental stress,” Critical Reviews in Biochemistry and Molecular Biology, 49(1):69-89 (2014). Available from: doi:10.3109/10409238.2013.859229

  1. 15.

    J. Vazquez-Anderson, and L.M. Contreras, “Regulatory RNAs: Charming Gene Management Styles for Synthetic Biology Applications” RNA Biology, 10(12):1778-97 (2013). Available from: doi:10.4161/rna.27102

  2. 14.

    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). Available from: doi:10.1371/journal.pone.0079411

  3. 13.

    L.M. Contreras, T.Huang, C.L. Piazza, D. Smith, G. Qu, G. Gelderman, J. Potratz, R. Russell, M. Belfort, “Group II intron ribosome association protects intron RNA from degradation,” RNA 19 (11): 1497–1509  (2013). Available from: doi:10.1261/rna.039073.113

  4. 12.

    G.Gelderman, and L.M. Contreras, “Discovery of posttranscriptional regulatory RNAs using next generation sequencing technologies,” Methods in Molecular Biology, 985:269-95 (2013). Available from: doi:10.1007/978-1-62703-299-5_14

  5. 11.

    S. Sowa, J. Vazquez-Anderson, and L.M. Contreras, “Capturing cellular regulation in silico using big data: a frontier for systems biology,” Current Synthetic and Systems Biology, 19;1(1):1-4 (2013). Available from: doi:10.4172/2332-0737.1000107

  1. 10.

    L.M. Contreras, J. Kostecki, and M.P. DeLisa, “The ribosomal exit tunnel as a target for optimizing protein expression in Escherichia coli,” Journal of Biotechnology, 7 (3): 354-60 (2012). Available from: doi:10.1002/biot.201100198

Prior to 2012
  1. 9.

    T. Huang, T. Shaikh, K. Gupta, L.M. Contreras, R. Grassucci, G.D.Van Duyne, J. Frank, and M. Belfort, “The group II intron ribonucleoprotein precursor is a large, loosely packed structure,” Nucleic Acids Research, 39(7) : 2845-2854 (2011). Available from: doi: 10.1093/nar/gkq1202

  2. 8.

    W-Y. Wu, A. R.. Gillies, J.F. Hsii, L.M. Contreras, S. Oak, M.B. Perl, and D.W. Wood, “Self-cleaving purification tags re-engineered for rapid Topo® cloning,” Biotechnology Progress, 26(5):1205-12   (2010). Available from: doi:10.1002/btpr.430

  3. 7.

    J.M. Dichiara, L.M. Contreras, D. Smith, and M. Belfort, “Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis,”  Nucleic Acids Research, 38 (12): 4068-4078 (2010). Available from: doi:10.1093/nar/gkq101

  4. 6.

    E.E. Borrero, L.M. Contreras, M.P. DeLisa, “Kinetics and reaction coordinates of the reassembly of protein fragments via forward flux sampling,” BioPhysical Journal, 98(9):1911-20 (2010). Available from: doi:10.1016/j.bpj.2009.12.4329

  5. 5.

    L.M. Contreras, E.E. Borrero, F. Escobedo, and M.P. DeLisa. “In silico protein fragmentation reveals the importance of critical nuclei in domain reassembly,”  BioPhysical Journal, 94(5): 1575-88 (2007). Available from: doi:10.1529/biophysj.107.119651

  6. 4.

    L.M. Contreras-Martinez, M.P DeLisa. “Expression engineering of synthetic antibodies using ribosome display”. In: M. Dyson, Y. Durocher, editors. Expression Systems: Methods Express. 1st ed. Oxfordshire, UK: Scion Publishing; pp. 29-52 (2007).

  7. 3.

    L.M. Contreras and M.P. DeLisa, “Intracellular ribosome display via SecM translation arrest as a selection for antibodies with enhanced cytosolic stability,” Journal of Molecular Biology, 372(2): 513-524 (2007). Available from: doi:10.1016/j.jmb.2007.06.070

  8. 2.

    L.M. Contreras, J. Walls J. “Feedback from workshop participants”. In: R. Gray, S. Hemami, E. Riskin, R. Ward, S. Brainard, P. Cosman, N. Fortenberry, J. Rutledge, T. Whitney, editors. Mentoring for Engineering Academia II. ; pp. 101–124 (2007).

  9. 1.

    L.M. Contreras, F.Martinez-Veracoechea, P. Pohkarel, A.D. Stroock, F. Escobedo and M.P. DeLisa, “Protein translocation through a tunnel induces changes in folding kinetics: a lattice model study,”Biotechnology and Bioengineering, 94: 105-117 (2006).  Available from: doi:10.1002/bit.20832


  1. 2.

    DeLisa MP, Contreras LM. “Protein Discovery Using Intracellular Ribosome Display” (Provisional Patent Application filed on June 21, 2007).  Licensed by Vybion, Inc. 

  2. 1.

    Wood D, HsII J, Oak S, Contreras L, Chestnut J. “Self-Cleaving Affinity Tags and Methods of Use”. (PCT application filed with US Patent Office February 27, 2005).