Contreras Research Lab

Publications

2024

  1. Ruan, M., Engels, S. M., Burroughs, M. R., Bloch, D., Fanari, O., Akeson, S., Eyler, D. E., Li, X., Weidmann, C. A., Rouhanifard, S., Jain, M., Contreras, L. M. & Koutmou, K. S. PUS7 cytoplasmic localization directs a pseudouridine-mediated cellular stress response. (Submitted).
  2. Rojano-Nisimura, A. M., Simmons, T. R., Lukasiewicz, A. J., Buchser, R., Ruzek, J. S., Avila, J. L. & Contreras, L. M. Concentration dependent CsrA regulation of the uxuB transcript leads to development of post-transcriptional BANDPASS Filter. (Submitted).
  3. Lukasiewicz, A. J., Leistra, A. N., Hoefner, L., Monzon, E., Gode, C. J., Zorn, B. T., Janssen, K. H., Yahr, T. L., Wolfgang, M. C. & Contreras, L. M. Thermodynamic modeling of Csr/Rsm- RNA interactions capture novel, direct binding interactions across the Pseudomonas aeruginosa transcriptome. (Submitted).
  4. Park, R., Demny, M., Miller, L. G., Pedraza, C., Xenophontos, X., Hunt, R. K., Orr, A. A., Perez, L. M., Contreras, L. M. and Tamamis, P. Elucidating Mechanisms of HNRNPA2B1 Binding in the Context of Unmodified and m6A-modified RNAs. (Submitted).
  5. Ekdahl, A. M., Julien, T., Suraj, S., Kribelbauer, J., Tavazoie, S., Freddolino, P. L. & Contreras, L. M. Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs. (Submitted).
  6. Wongwiset, N., Quinones-Diaz, B. I., Mehboudi, A., Contreras, L. M. & Sreenivasan, S. V. High-throughput combinatorial microfluidics enabled by parallel dispensing system. (Submitted).
  7. Rojano-Nisimura, A. M., Miller, L. G., Anantharaman, A., Middleton, A. T., Kibret, E., Jung, S. H., Russell, R. & Contreras, L. M. A high-throughput search for intracellular factors that affect RNA folding identifies E. coli proteins PepA and YagL as RNA chaperones that promote RNA remodeling. (Accepted).
  8. Burroughs, M. R., Sweet, P. J. & Contreras, L. M. Optimized chemical labeling method for isolation of 8-oxoG-modified RNA, ChLoRox-Seq, identifies mRNAs enriched in oxidation and transcriptome-wide distribution biases of oxidation events post environmental stress. RNA Biol. 21, 132–148 (2024).
  9. Miller, L. G., Kim, W., Schowe, S., Taylor, K., Han, R., Jain, V., Park, R., Sherman, M., Fang, J., Ramirez, H., Ellington, A., Tamamis, P., Resendiz, M. J. E., Zhang, Y. J. & Contreras, L. Selective 8-oxo-rG stalling occurs in the catalytic core of polynucleotide phosphorylase (PNPase) during degradation. PNAS 121, e2317865121 (2024).
  10. Sweet, P., Burroughs, M., Jang, S. & Contreras, L. TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs. Microbiol. Spectr. 12, e03838-23 (2024).
  11. Simmons, T. R., Partipilo, G., Buchser, R., Stankes, A. C., Srivastava, R., Chiu, D., Keitz, B. K. & Contreras, L. M. Rewiring native post-transcriptional global regulators to achieve designer, multi-layered genetic circuits. Nat. Commun. 15, 8752 (2024).
Ref. 80
  1. Cordova, A., Niese, B., Sweet, P., Kamat, P., Phillip, J. M., Gordon, V. & Contreras, L. M. Quantitative morphological analysis of Deinococcus radiodurans elucidates complex dose-dependent nucleoid condensation during recovery from ionizing radiation. Appl. Environ. Microbiol. 90, e00108-24 (2024).
  2. Rojano-Nisimura, A. M., Grismore, K. B., Ruzek, J. S., Avila, J. L. & Contreras, L. M. The Post-Transcriptional Regulatory Protein CsrA Amplifies Its Targetome through Direct Interactions with Stress-Response Regulatory Hubs: The EvgA and AcnA Cases. Microorganisms 12, 636 (2024).
  3. Taylor, K. E., Miller, L. G. & Contreras, L. M. RNA-binding proteins that preferentially interact with 8-oxoG-modified RNAs: our current understanding. Biochem. Soc. Trans. (2024).

2023

  1. Rojano-Nisimura, A. M., Simmons, T. R., Leistra, A. N., Mihailovic, M. K., Buchser, R., Ekdahl, A. M., Joseph, I., Curtis, N. C. & Contreras, L. M. CsrA selectively modulates sRNA-mRNA regulator outcomes. Front. Mol. Biosci. 10, 1249528 (2023).
  2. Engels, S. M., Kamat, P., Pafilis, G. S., Li, Y., Agrawal, A., Haller, D. J., Phillip, J. M. & Contreras, L. M. Particulate matter composition drives differential molecular and morphological responses in lung epithelial cells. PNAS Nexus 3, pgad415 (2023).
  3. Miller, L. G., Demny, M., Tamamis, P. & Contreras, L. M. Characterization of epitranscriptome reader proteins experimentally and in silico: Current knowledge and future perspectives beyond the YTH domain. Comput. Struct. Biotechnol. J. 21, 3541–3556 (2023).
Ref. 74
  1. Buchser, R., Sweet, P., Anantharaman, A. & Contreras, L. RNAs as Sensors of Oxidative Stress in Bacteria. Annu. Rev. Chem. Biomol. Eng. 14, 265–281 (2023).
  2. Sweet, P., Blacutt, J., Gordon, V. & Contreras, L. Exposure of Shewanella oneidensis MR-1 to Sublethal Doses of Ionizing Radiation Triggers Short-Term SOS Activation and Longer-Term Prophage Activation. Appl Environ Microb e01716-22 (2023).

2022

  1. Han, R., Jiang, J., Fang, J. & Contreras, L. M. PNPase and RhlB Interact and Reduce the Cellular Availability of Oxidized RNA in Deinococcus radiodurans. Microbiol Spectr 10, e02140-22 (2022).
  2. Ekdahl, A. M., Rojano-Nisimura, A. M. & Contreras, L. M. Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria. J. Mol. Biol. 434, 167689 (2022).
Ref. 70
  1. Simmons, T. R., Ellington, A. D. & Contreras, L. M. “RNP-Based Control Systems for Genetic Circuits in Synthetic Biology Beyond CRISPR” in Riboregulator Design and Analysis. Methods Mol Biology 1–31 (2022).
  2. Hillsley, A., Santoso, M. S., Engels, S. M., Halwachs, K. N., Contreras, L. M. & Rosales, A. M. A strategy to quantify myofibroblast activation on a continuous spectrum. Sci. Rep. 12, 12239 (2022). 

2021

  1. Chandler, M., Johnson, B., Khisamutdinov, E., Dobrovolskaia, M. A., Sztuba-Solinska, J., Salem, A. K., Breyne, K., Chammas, R., Walter, N. G., Contreras, L. M., Guo, P. & Afonin, K. A. The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field. ACS Nano 15, 16957–16973 (2021). 
  2. Burroughs, M. R., Gonzalez-Rivera, J. C., Cordova, A. & Contreras, L. M. “Experimental and Computational Methods for Guiding Identification and Characterization of Epitranscriptome Proteins” in Epitranscriptomics. Rna Technologies 593–632 (2021).
  3. Chen, A., Hernandez-Vargas, J., Han, R., Cortazar-Martínez, O., Gonzalez, N., Patel, S., Keitz, B. K., Luna-Barcenas, G. & Contreras, L. M. Small RNAs as a New Platform for Tuning the Biosynthesis of Silver Nanoparticles for Enhanced Material and Functional Properties. Acs Appl Mater Inter (2021).
  4. Mihailovic, M. K., Ekdahl, A. M., Chen, A., Leistra, A. N., Li, B., Martínez, J. G., Law, M., Ejindu, C., Massé, É., Freddolino, P. L. & Contreras, L. M. Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study. Front Cell Infect Mi 11, 696533 (2021).
Ref. 68
  1. Villa, J. K., Han, R., Tsai, C.-H., Chen, A., Sweet, P., Franco, G., Vaezian, R., Tkavc, R., Daly, M. J. & Contreras, L. M. A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation. Sci. Rep. 11, 12949 (2021).
  2. Sherman, M. W., Sandeep, S. & Contreras, L. M. The Tryptophan-Induced tnaC Ribosome Stalling Sequence Exposes High Amino Acid Cross-Talk That Can Be Mitigated by Removal of NusB for Higher Orthogonality. ACS Synth. Biol. 10, 1024–1038 (2021).

2020

  1. Han, R., Fang, J., Jiang, J., Gaidamakova, E. K., Tkavc, R., Daly, M. J. & Contreras, L. M. Signal Recognition Particle RNA Contributes to Oxidative Stress Response in Deinococcus radiodurans by Modulating Catalase Localization. Front. Microbiol. 11, 613571 (2020).
  2. Gonzalez-Rivera, J. C., Sherman, M. W., Wang, D. S., Chuvalo-Abraham, J. C. L., Ruiz, L. H. & Contreras, L. M. RNA oxidation in chromatin modification and DNA-damage response following exposure to formaldehyde. Sci. Rep. 10, 16545 (2020).
  3. Contreras, L. M., Gonzalez-Rivera, J. C., Baldridge, K. C., Wang, D. S., Chuvalo-Abraham, J. & Ruiz, L. H. Understanding the Functional Impact of VOC-Ozone Mixtures on the Chemistry of RNA in Epithelial Lung Cells. Res. Rep. (Heal. Eff. Inst.) (2020). https://pubmed.ncbi.nlm.nih.gov/32845096/.
  4. Gonzalez-Rivera, J. C., Baldridge, K. C., Wang, D. S., Patel, K., Chuvalo-Abraham, J. C. L., Ruiz, L. H. & Contreras, L. M. Post-transcriptional air pollution oxidation to the cholesterol biosynthesis pathway promotes pulmonary stress phenotypes. Commun Biology 3, 392 (2020).
Ref. 58
  1. Gimenez, A. J., Medellín-Rodríguez, F. J., Contreras-Martinez, L. M., López-Romero, J. M., Sanchez, I. C., Villaseñor-Ortega, F. & Luna-Bárcenas, G. Turbidimetry by Image Degradation Analysis. IEEE Trans. Instrum. Meas. 69, 7574–7579 (2020).
  2. Han, R., Haning, K., Gonzalez-Rivera, J. C., Yang, Y., Li, R., Cho, S. H., Huang, J., Simonsen, B. A., Yang, S. & Contreras, L. M. Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis. Front. Bioeng. Biotechnol. 8, 155 (2020).
  3. Lukasiewicz, A. J. & Contreras, L. M. Antisense probing of dynamic RNA structures. Methods 183, 76–83 (2020).
  4. Bowman, E. K., Mihailovic, M. K., Li, B. & Contreras, L. M. “Bioinformatic Application of Fluorescence-Based In Vivo RNA Regional Accessibility Data to Identify Novel sRNA Targets” in RNA Spectroscopy, Methods and Protocols. Methods Mol. Biol. 2113, 41–71 (2020).
  5. Gonzalez-Rivera, J. C., Orr, A. A., Engels, S. M., Jakubowski, J. M., Sherman, M. W., O’Connor, K. N., Matteson, T., Woodcock, B. C., Contreras, L. M. & Tamamis, P. Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding. Comput Struct Biotechnology J 18, 137–152 (2020).
  6. Haning, K., Engels, S. M., Williams, P., Arnold, M. & Contreras, L. M. Applying a New REFINE Approach in Zymomonas mobilis Identifies Novel sRNAs That Confer Improved Stress Tolerance Phenotypes. Front. Microbiol. 10, 2987 (2020).
  7. Rojano-Nisimura, A. M., Haning, K., Janovsky, J., Vasquez, K. A., Thompson, J. P. & Contreras, L. M. Codon Selection Affects Recruitment of Ribosome-Associating Factors during Translation. ACS Synth. Biol. 9, 329–342 (2020).
Ref. 51 featured in issue’s cover

2019

  1. Chen, A., Sherman, M. W., Chu, C., Gonzalez, N., Patel, T. & Contreras, L. M. Discovery and Characterization of Native Deinococcus radiodurans Promoters for Tunable Gene Expression. Appl. Environ. Microbiol. 85, e01356-19 (2019).
Ref. 50 featured in issue’s cover
  1. Leistra, A. N., Curtis, N. C. & Contreras, L. M. Regulatory non-coding sRNAs in bacterial metabolic pathway engineering. Metab. Eng. 52, 190–214 (2019).

2018

  1. Chen, A., Keitz, B. K. & Contreras, L. M. Biological links between nanoparticle biosynthesis and stress responses in bacteria. Mex. J. Biotechnol. 3, 44–69 (2018).
  2. Li, Y., Reyes, K. G., Vazquez-Anderson, J., Wang, Y., Contreras, L. M. & Powell, W. B. A Knowledge Gradient Policy for Sequencing Experiments to Identify the Structure of RNA Molecules Using a Sparse Additive Belief Model. Inf. J. Comput. 30, 750–767 (2018).
  3. Mihailovic, M. K., Vazquez-Anderson, J., Li, Y., Fry, V., Vimalathas, P., Herrera, D., Lease, R. A., Powell, W. B. & Contreras, L. M. High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites. Nat. Commun. 9, 4084 (2018).
  4. Villa, J. K., Su, Y., Contreras, L. M. & Hammond, M. C. Synthetic Biology of Small RNAs and Riboswitches. Microbiol. Spectr. 6, 10.1128/microbiolspec.rwr-0007–2017 (2018).
  5. Contreras, L. M. Methods and advances in RNA characterization and design. Methods 143, 1–3 (2018).
  1. Leistra, A. N., Gelderman, G., Sowa, S. W., Moon-Walker, A., Salis, H. M. & Contreras, L. M. A Canonical Biophysical Model of the CsrA Global Regulator Suggests Flexible Regulator-Target Interactions. Sci. Rep. 8, 9892 (2018).
  2. Baldridge, K. C., Jora, M., Maranhao, A. C., Quick, M. M., Addepalli, B., Brodbelt, J. S., Ellington, A. D., Limbach, P. A. & Contreras, L. M. Directed Evolution of Heterologous tRNAs Leads to Reduced Dependence on Post-transcriptional Modifications. ACS Synth. Biol. 7, 1315–1327 (2018).
  3. Wang, X., He, Q., Yang, Y., Wang, J., Haning, K., Hu, Y., Wu, B., He, M., Zhang, Y., Bao, J., Contreras, L. M. & Yang, S. Advances and prospects in metabolic engineering of Zymomonas mobilis. Metab. Eng. 50, 57–73 (2018).
  4. Sherman, M. & Contreras, L. Computational approaches in design of nucleic acid-based therapeutics. Curr Opin Biotech 53, 232–239 (2018).
  5. Leistra, A. N., Mihailovic, M. K. & Contreras, L. M. Methods in Molecular Biology- Fluorescence-Based Methods for Characterizing RNA Interactions In Vivo. Methods Mol Biology Clifton N J 1737, 129–164 (2018).
  6. Orr, A. A., Gonzalez-Rivera, J. C., Wilson, M., Bhikha, P. R., Wang, D., Contreras, L. M. & Tamamis, P. A high-throughput and rapid computational method for screening of RNA post-transcriptional modifications that can be recognized by target proteins. Methods 143, 34–47 (2018).

2017

  1. Cho, S. H., Haning, K., Shen, W., Blome, C., Li, R., Yang, S. & Contreras, L. M. Identification and Characterization of 5′ Untranslated Regions (5′UTRs) in Zymomonas mobilis as Regulatory Biological Parts. Front. Microbiol. 8, 2432 (2017). 
  2. Chen, A., Contreras, L. M. & Keitz, B. K. Imposed Environmental Stresses Facilitate Cell-Free Nanoparticle Formation by Deinococcus radiodurans. Appl. Environ. Microbiol. 83, e00798-17 (2017).
  3. Villa, J. K., Amador, P., Janovsky, J., Bhuyan, A., Saldanha, R., Lamkin, T. J. & Contreras, L. M. A Genome-Wide Search for Ionizing-Radiation-Responsive Elements in Deinococcus radiodurans Reveals a Regulatory Role for the DNA Gyrase Subunit A Gene’s 5′ Untranslated Region in the Radiation and Desiccation Response. Appl. Environ. Microbiol. 83, e00039-17 (2017).
  4. Leistra, A. N., Amador, P., Buvanendiran, A., Moon-Walker, A. & Contreras, L. M. Rational Modular RNA Engineering Based on In Vivo Profiling of Structural Accessibility. ACS Synth. Biol. 6, 2228–2240 (2017).
Ref. 34
  1. Vazquez-Anderson, J., Mihailovic, M. K., Baldridge, K. C., Reyes, K. G., Haning, K., Cho, S. H., Amador, P., Powell, W. B. & Contreras, L. M. 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 Res. 45, 5523–5538 (2017).
  2. Mihailovic, M. K., Chen, A., Gonzalez-Rivera, J. C. & Contreras, L. M. Defective Ribonucleoproteins, Mistakes in RNA Processing, and Diseases. Biochemistry 56, 1367–1382 (2017). 
  3. Sowa, S. W., Gelderman, G., Leistra, A. N., Buvanendiran, A., Lipp, S., Pitaktong, A., Vakulskas, C. A., Romeo, T., Baldea, M. & Contreras, L. M. Integrative FourD omics approach profiles the target network of the carbon storage regulatory system. Nucleic Acids Res. 45, 1673–1686 (2017).

2016

  1. Yang, S., Fei, Q., Zhang, Y., Contreras, L. M., Utturkar, S. M., Brown, S. D., Himmel, M. E. & Zhang, M. Zymomonas mobilis as a model system for production of biofuels and biochemicals. Microb. Biotechnol. 9, 699–717 (2016).
  2. Vasquez, K. A., Hatridge, T. A., Curtis, N. C. & Contreras, L. M. Slowing Translation between Protein Domains by Increasing Affinity between mRNAs and the Ribosomal Anti-Shine–Dalgarno Sequence Improves Solubility. ACS Synth. Biol. 5, 133–145 (2016).
Ref. 29 featured in issue’s cover. Art by Franklin M. Sandoval
  1. Cho, S. H., Contreras, L. M. & Ju, S. H. Synthetic chimeras with orthogonal ribosomal proteins increase translation yields by recruiting mRNA for translation as measured by profiling active ribosomes. Biotechnol. Prog. 32, 285–293 (2016).

2015

  1. Sowa, S. W., Gelderman, G. & Contreras, L. M. Advances in synthetic dynamic circuits design: using novel synthetic parts to engineer new generations of gene oscillations. Curr. Opin. Biotechnol. 36, 161–167 (2015).
  2. Cho, S. H., Haning, K. & Contreras, L. M. Strain engineering via regulatory noncoding RNAs: not a one-blueprint-fits-all. Curr. Opin. Chem. Eng. 10, 25–34 (2015).
  3. Tsai, C.-H., Liao, R., Chou, B. & Contreras, L. M. Transcriptional Analysis of Deinococcus radiodurans Reveals Novel Small RNAs That Are Differentially Expressed under Ionizing Radiation. Appl. Environ. Microbiol. 81, 1754–1764 (2015).
  4. Gelderman, G., Sivakumar, A., Lipp, S. & Contreras, L. Adaptation of Tri-molecular fluorescence complementation allows assaying of regulatory Csr RNA-protein interactions in bacteria. Biotechnol. Bioeng. 112, 365–375 (2015).
  5. Baldridge, K. C., Zavala, J., Surratt, J., Sexton, K. G. & Contreras, L. M. Cellular RNA is chemically modified by exposure to air pollution mixtures. Inhal. Toxicol. 27, 74–82 (2015).
  6. Tsai, C.-H., Liao, R., Chou, B., Palumbo, M. & Contreras, L. M. Genome-Wide Analyses in Bacteria Show Small-RNA Enrichment for Long and Conserved Intergenic Regions. J. Bacteriol. 197, 40–50 (2014).
  7. Sowa, S. W., Vazquez-Anderson, J., Clark, C. A., Peña, R. D. L., Dunn, K., Fung, E. K., Khoury, M. J. & Contreras, L. M. Exploiting post-transcriptional regulation to probe RNA structures in vivo via fluorescence. Nucleic Acids Res. 43, e13–e13 (2015).

2014

  1. Haning, K., Cho, S. H. & Contreras, L. M. Small RNAs in mycobacteria: an unfolding story. Front. Cell. Infect. Microbiol. 4, 96 (2014).
  2. Sowa, S. W., Baldea, M. & Contreras, L. M. Optimizing Metabolite Production Using Periodic Oscillations. PLoS Comput. Biol. 10, e1003658 (2014). 
  3. Cho, S. H., Lei, R., Henninger, T. D. & Contreras, L. M. Discovery of Ethanol-Responsive Small RNAs in Zymomonas mobilis.
  4. Gupta, K., Contreras, L. M., Smith, D., Qu, G., Huang, T., Spruce, L. A., Seeholzer, S. H., Belfort, M. & Duyne, G. D. V. Quaternary arrangement of an active, native group II intron ribonucleoprotein complex revealed by small-angle X-ray scattering. Nucleic Acids Res. 42, 5347–5360 (2014).
  5. Baldridge, K. C. & Contreras, L. M. Functional implications of ribosomal RNA methylation in response to environmental stress. Crit. Rev. Biochem. Mol. Biol. 49, 69–89 (2014).

2013

  1. Vazquez-Anderson, J. & Contreras, L. M. Regulatory RNAs: Charming Gene Management Styles for Synthetic Biology Applications. RNA Biol. 10, 1778–1797 (2013).
  2. Tsai, C.-H., Baranowski, C., Livny, J., McDonough, K. A., Wade, J. T. & Contreras, L. M. Identification of Novel sRNAs in Mycobacterial Species. PLoS ONE 8, e79411 (2013).
  3. Contreras, L. M., Huang, T., Piazza, C. L., Smith, D., Qu, G., Gelderman, G., Potratz, J. P., Russell, R. & Belfort, M. Group II intron–ribosome association protects intron RNA from degradation. RNA 19, 1497–1509 (2013).
  4. Gelderman, G. & Contreras, L. M. “Discovery of posttranscriptional regulatory RNAs using next generation sequencing technologies” in Systems Metabolic Engineering, Methods and Protocols. Methods Mol. Biol. 985, 269–295 (2013).
  5. 1.Sowa, S., Vazquez-Anderson, J. & Contreras, L. M. Capturing Full Cellular Regulation In silico using “Big” Data: A Frontier for Systems Biology Perspectives. Curr. Synth. Syst. Biol. 01, (2013).

2012 and prior

  1. Contreras-Martinez, L. M., Boock, J. T., Kostecki, J. S. & DeLisa, M. P. The ribosomal exit tunnel as a target for optimizing protein expression in Escherichia coli. Biotechnol. J. 7, 354–360 (2012).
  2. Huang, T., Shaikh, T. R., Gupta, K., Contreras-Martinez, L. M., Grassucci, R. A., Duyne, G. D. V., Frank, J. & Belfort, M. The group II intron ribonucleoprotein precursor is a large, loosely packed structure. Nucleic Acids Res. 39, 2845–2854 (2011).
  3. Wu, W., Gillies, A. R., Hsii, J. F., Contreras, L., Oak, S., Perl, M. B. & Wood, D. W. Self-cleaving purification tags re-engineered for rapid Topo® cloning. Biotechnol. Prog. 26, 1205–1212 (2010).
  4. DiChiara, J. M., Contreras-Martinez, L. M., Livny, J., Smith, D., McDonough, K. A. & Belfort, M. Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis. Nucleic Acids Res. 38, 4067–4078 (2010).
  5. Borrero, E. E., Contreras-Martínez, L. M., DeLisa, M. P. & Escobedo, F. A. Kinetics and Reaction Coordinates of the Reassembly of Protein Fragments Via Forward Flux Sampling. Biophys. J. 98, 1911–1920 (2010).
  6. Contreras-Martínez, L. M., Quintana, E. E. B., Escobedo, F. A. & DeLisa, M. P. In Silico Protein Fragmentation Reveals the Importance of Critical Nuclei on Domain Reassembly. Biophys. J. 94, 1575–1588 (2008).
  7. Contreras-Martinez, L. M. & DeLisa, M. P. “Expression engineering of synthetic antibodies using ribosome display” in Expression Systems: Methods Express 29–52 (2007).
  8. Contreras-Martínez, L. M. & DeLisa, M. P. Intracellular Ribosome Display Via SecM Translation Arrest as a Selection for Antibodies with Enhanced Cytosolic Stability. J. Mol. Biol. 372, 513–524 (2007).
  9. Contreras, L. M. & Walls, J. “Feedback from Workshop Participants” in Mentoring for Engineering Academia II: BIRS 2007 Workshop. 101–124 (2007).
  10. Contreras-Martínez, L. M., Martínez-Veracoechea, F. J., Pohkarel, P., Stroock, A. D., Escobedo, F. A. & DeLisa, M. P. Protein translocation through a tunnel induces changes in folding kinetics: A lattice model study. Biotechnol. Bioeng. 94, 105–117 (2006).

Patents

  1. DeLisa MP, Contreras LM. “Protein Discovery Using Intracellular Ribosome Display” (Provisional Patent Application filed on June 21, 2007).  Licensed by Vybion, Inc. 
  2. 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).