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Lydia M. Contreras, Ph.D. - Publications

Affiliations: 
2008 Cornell University, Ithaca, NY, United States 
Area:
Chemical Engineering, Biochemistry
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53 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Taylor KE, Miller LG, Contreras LM. RNA-binding proteins that preferentially interact with 8-oxoG-modified RNAs: our current understanding. Biochemical Society Transactions. PMID 38174726 DOI: 10.1042/BST20230254  0.537
2023 Rojano-Nisimura AM, Simmons TR, Leistra AN, Mihailovic MK, Buchser R, Ekdahl AM, Joseph I, Curtis NC, Contreras LM. CsrA selectively modulates sRNA-mRNA regulator outcomes. Frontiers in Molecular Biosciences. 10: 1249528. PMID 38116378 DOI: 10.3389/fmolb.2023.1249528  0.331
2023 Miller LG, Demny M, Tamamis P, Contreras LM. Characterization of epitranscriptome reader proteins experimentally and : Current knowledge and future perspectives beyond the YTH domain. Computational and Structural Biotechnology Journal. 21: 3541-3556. PMID 37501707 DOI: 10.1016/j.csbj.2023.06.018  0.411
2023 Buchser R, Sweet P, Anantharaman A, Contreras L. RNAs as Sensors of Oxidative Stress in Bacteria. Annual Review of Chemical and Biomolecular Engineering. 14: 265-281. PMID 37289561 DOI: 10.1146/annurev-chembioeng-101121-070250  0.375
2023 Rojano-Nisimura AM, Simmons TR, Leistra AN, Mihailovic MK, Buchser R, Ekdahl AM, Joseph I, Curtis NC, Contreras LM. CsrA Shows Selective Regulation of sRNA-mRNA Networks. Biorxiv : the Preprint Server For Biology. PMID 37034808 DOI: 10.1101/2023.03.29.534774  0.333
2022 Han R, Jiang J, Fang J, Contreras LM. PNPase and RhlB Interact and Reduce the Cellular Availability of Oxidized RNA in . Microbiology Spectrum. e0214022. PMID 35856907 DOI: 10.1128/spectrum.02140-22  0.548
2022 Ekdahl AM, Rojano-Nisimura AM, Contreras LM. Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria. Journal of Molecular Biology. 167689. PMID 35717997 DOI: 10.1016/j.jmb.2022.167689  0.479
2021 Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, ... ... Contreras LM, et al. Noncoding RNAs: biology and applications-a Keystone Symposia report. Annals of the New York Academy of Sciences. PMID 34791665 DOI: 10.1111/nyas.14713  0.561
2021 Chandler M, Johnson B, Khisamutdinov E, Dobrovolskaia MA, Sztuba-Solinska J, Salem AK, Breyne K, Chammas R, Walter NG, Contreras LM, Guo P, Afonin KA. The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field. Acs Nano. PMID 34677049 DOI: 10.1021/acsnano.0c10240  0.491
2021 Mihailovic MK, Ekdahl AM, Chen A, Leistra AN, Li B, González Martínez J, Law M, Ejindu C, Massé É, Freddolino PL, Contreras LM. Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study. Frontiers in Cellular and Infection Microbiology. 11: 696533. PMID 34327153 DOI: 10.3389/fcimb.2021.696533  0.414
2021 Villa JK, Han R, Tsai CH, Chen A, Sweet P, Franco G, Vaezian R, Tkavc R, Daly MJ, Contreras LM. A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation. Scientific Reports. 11: 12949. PMID 34155239 DOI: 10.1038/s41598-021-91335-8  0.367
2020 Gonzalez-Rivera JC, Sherman MW, Wang DS, Chuvalo-Abraham JCL, Hildebrandt Ruiz L, Contreras LM. RNA oxidation in chromatin modification and DNA-damage response following exposure to formaldehyde. Scientific Reports. 10: 16545. PMID 33024153 DOI: 10.1038/s41598-020-73376-7  0.818
2020 Gonzalez-Rivera JC, Baldridge KC, Wang DS, Patel K, Chuvalo-Abraham JCL, Hildebrandt Ruiz L, Contreras LM. Post-transcriptional air pollution oxidation to the cholesterol biosynthesis pathway promotes pulmonary stress phenotypes. Communications Biology. 3: 392. PMID 32699268 DOI: 10.1038/s42003-020-01118-6  0.72
2020 Han R, Haning K, Gonzalez-Rivera JC, Yang Y, Li R, Cho SH, Huang J, Simonsen BA, Yang S, Contreras LM. Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in . Frontiers in Bioengineering and Biotechnology. 8: 155. PMID 32195236 DOI: 10.3389/Fbioe.2020.00155  0.759
2020 Bowman EK, Mihailovic MK, Li B, Contreras LM. Bioinformatic Application of Fluorescence-Based In Vivo RNA Regional Accessibility Data to Identify Novel sRNA Targets. Methods in Molecular Biology (Clifton, N.J.). 2113: 41-71. PMID 32006307 DOI: 10.1007/978-1-0716-0278-2_5  0.558
2020 Lukasiewicz AJ, Contreras LM. Antisense probing of dynamic RNA structures. Methods (San Diego, Calif.). PMID 31991194 DOI: 10.1016/J.Ymeth.2020.01.015  0.612
2020 Gonzalez-Rivera JC, Orr AA, Engels SM, Jakubowski JM, Sherman MW, O'Connor KN, Matteson T, Woodcock BC, Contreras LM, Tamamis P. Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding. Computational and Structural Biotechnology Journal. 18: 137-152. PMID 31988703 DOI: 10.1016/J.Csbj.2019.12.003  0.808
2019 Haning K, Engels SM, Williams P, Arnold M, Contreras LM. Applying a New REFINE Approach in Identifies Novel sRNAs That Confer Improved Stress Tolerance Phenotypes. Frontiers in Microbiology. 10: 2987. PMID 31998271 DOI: 10.3389/Fmicb.2019.02987  0.47
2019 Rojano Nisimura AM, Haning K, Janovsky J, Vasquez KA, Thompson JP, Contreras LM. Codon selection affects recruitment of ribosome-associating factors during translation. Acs Synthetic Biology. PMID 31769967 DOI: 10.1021/Acssynbio.9B00344  0.346
2019 Chen A, Sherman M, Contreras LM. Discovery and Characterization of Native Promoters for Tunable Gene Expression. Applied and Environmental Microbiology. PMID 31471304 DOI: 10.1128/Aem.01356-19  0.306
2018 Leistra AN, Curtis NC, Contreras LM. Regulatory non-coding sRNAs in bacterial metabolic pathway engineering. Metabolic Engineering. 52: 190-214. PMID 30513348 DOI: 10.1016/J.Ymben.2018.11.013  0.478
2018 Mihailovic MK, Vazquez-Anderson J, Li Y, Fry V, Vimalathas P, Herrera D, Lease RA, Powell WB, Contreras LM. High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites. Nature Communications. 9: 4084. PMID 30287822 DOI: 10.1038/S41467-018-06207-Z  0.603
2018 Contreras LM. Methods and advances in RNA characterization and design. Methods (San Diego, Calif.). 143: 1-3. PMID 30017060 DOI: 10.1016/J.Ymeth.2018.06.003  0.527
2018 Leistra AN, Gelderman G, Sowa SW, Moon-Walker A, Salis HM, Contreras LM. A Canonical Biophysical Model of the CsrA Global Regulator Suggests Flexible Regulator-Target Interactions. Scientific Reports. 8: 9892. PMID 29967470 DOI: 10.1038/S41598-018-27474-2  0.367
2018 Villa JK, Su Y, Contreras LM, Hammond MC. Synthetic Biology of Small RNAs and Riboswitches. Microbiology Spectrum. 6. PMID 29932045 DOI: 10.1128/Microbiolspec.Rwr-0007-2017  0.633
2018 Baldridge KC, Jora M, Maranhao AC, Quick MM, Addepalli B, Brodbelt JS, Ellington AD, Limbach PA, Contreras LM. Directed Evolution of Heterologous tRNAs Leads to Reduced Dependence on Post-transcriptional Modifications. Acs Synthetic Biology. PMID 29694026 DOI: 10.1021/Acssynbio.7B00421  0.776
2018 Sherman M, Contreras L. Computational approaches in design of nucleic acid-based therapeutics. Current Opinion in Biotechnology. 53: 232-239. PMID 29562215 DOI: 10.1016/J.Copbio.2017.12.001  0.323
2018 Leistra AN, Mihailovic MK, Contreras LM. Fluorescence-Based Methods for Characterizing RNA Interactions In Vivo. Methods in Molecular Biology (Clifton, N.J.). 1737: 129-164. PMID 29484592 DOI: 10.1007/978-1-4939-7634-8_9  0.604
2018 Orr AA, Gonzalez-Rivera JC, Wilson M, Reena Bhikha P, Wang D, Contreras LM, Tamamis P. "A high-throughput and rapid computational method for screening of RNA post-transcriptional modifications that can be recognized by target proteins". Methods (San Diego, Calif.). PMID 29408626 DOI: 10.1016/J.Ymeth.2018.01.015  0.813
2018 Li Y, Reyes KG, Vazquez-Anderson J, Wang Y, Contreras LM, Powell WB. A Knowledge Gradient Policy for Sequencing Experiments to Identify the Structure of RNA Molecules Using a Sparse Additive Belief Model Informs Journal On Computing. 30: 750-767. DOI: 10.1287/Ijoc.2017.0803  0.492
2017 Cho SH, Haning K, Shen W, Blome C, Li R, Yang S, Contreras LM. Identification and Characterization of 5' Untranslated Regions (5'UTRs) in Zymomonas mobilis as Regulatory Biological Parts. Frontiers in Microbiology. 8: 2432. PMID 29375488 DOI: 10.3389/Fmicb.2017.02432  0.44
2017 Leistra AN, Amador P, Buvanendiran A, Moon-Walker A, Contreras LM. Rational Modular RNA Engineering Based on In Vivo Profiling of Structural Accessibility. Acs Synthetic Biology. PMID 28796489 DOI: 10.1021/Acssynbio.7B00185  0.451
2017 Villa JK, Amador P, Janovsky J, Bhuyan A, Saldanha R, Lamkin TJ, Contreras LM. Genome-wide search for ionizing radiation responsive elements in Deinococcus radiodurans reveals regulatory role of the DNA gyrase subunit A 5' UTR in the Radiation and Desiccation Response (RDR). Applied and Environmental Microbiology. PMID 28411225 DOI: 10.1128/Aem.00039-17  0.408
2017 Vazquez-Anderson J, Mihailovic MK, Baldridge KC, Reyes KG, Haning K, Cho SH, Amador P, Powell WB, Contreras LM. 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. PMID 28334800 DOI: 10.1093/Nar/Gkx115  0.81
2017 Mihailovic MK, Chen A, Gonzalez-Rivera JC, Contreras LM. Defective RNPs, Mistakes in RNA Processing and Diseases. Biochemistry. PMID 28206738 DOI: 10.1021/Acs.Biochem.6B01134  0.788
2017 Sowa SW, Gelderman G, Leistra AN, Buvanendiran A, Lipp S, Pitaktong A, Vakulskas CA, Romeo T, Baldea M, Contreras LM. Integrative FourD omics approach profiles the target network of the carbon storage regulatory system. Nucleic Acids Research. PMID 28126921 DOI: 10.1093/Nar/Gkx048  0.338
2016 Cho SH, Ju SH, Contreras LM. Synthetic chimeras with orthogonal ribosomal proteins increase translation yields by recruiting mRNA for translation as measured by profiling active ribosomes. Biotechnology Progress. PMID 26749267 DOI: 10.1002/Btpr.2227  0.358
2015 Vasquez KA, Hatridge TA, Curtis NC, Contreras L. Slowing translation between protein domains by increasing affinity between mRNAs and the ribosomal anti-Shine-Dalgarno sequence improves solubility. Acs Synthetic Biology. PMID 26607828 DOI: 10.1021/Acssynbio.5B00193  0.32
2015 Baldridge KC, Zavala J, Surratt J, Sexton KG, Contreras LM. Cellular RNA is chemically modified by exposure to air pollution mixtures. Inhalation Toxicology. 27: 74-82. PMID 25600141 DOI: 10.3109/08958378.2014.987361  0.783
2015 Tsai CH, Liao R, Chou B, Contreras LM. Transcriptional analysis of Deinococcus radiodurans reveals novel small RNAs that are differentially expressed under ionizing radiation. Applied and Environmental Microbiology. 81: 1754-64. PMID 25548054 DOI: 10.1128/Aem.03709-14  0.412
2015 Sowa SW, Vazquez-Anderson J, Clark CA, De La Peña R, Dunn K, Fung EK, Khoury MJ, Contreras LM. Exploiting post-transcriptional regulation to probe RNA structures in vivo via fluorescence. Nucleic Acids Research. 43: e13. PMID 25416800 DOI: 10.1093/Nar/Gku1191  0.563
2015 Tsai CH, Liao R, Chou B, Palumbo M, Contreras LM. Genome-wide analyses in bacteria show small-RNA enrichment for long and conserved intergenic regions. Journal of Bacteriology. 197: 40-50. PMID 25313390 DOI: 10.1128/Jb.02359-14  0.436
2015 Gelderman G, Sivakumar A, Lipp S, Contreras L. Adaptation of Tri-molecular fluorescence complementation allows assaying of regulatory Csr RNA-protein interactions in bacteria. Biotechnology and Bioengineering. 112: 365-75. PMID 25080893 DOI: 10.1002/Bit.25351  0.493
2015 Sowa SW, Gelderman G, Contreras LM. Advances in synthetic dynamic circuits design: Using novel synthetic parts to engineer new generations of gene oscillations Current Opinion in Biotechnology. 36: 161-167. DOI: 10.1016/J.Copbio.2015.08.020  0.335
2015 Cho SH, Haning K, Contreras LM. Strain engineering via regulatory noncoding RNAs: Not a one-blueprint-fits-all Current Opinion in Chemical Engineering. 10: 25-34. DOI: 10.1016/J.Coche.2015.07.008  0.41
2014 Haning K, Cho SH, Contreras LM. Small RNAs in mycobacteria: an unfolding story. Frontiers in Cellular and Infection Microbiology. 4: 96. PMID 25105095 DOI: 10.3389/Fcimb.2014.00096  0.531
2014 Cho SH, Lei R, Henninger TD, Contreras LM. Discovery of ethanol-responsive small RNAs in Zymomonas mobilis. Applied and Environmental Microbiology. 80: 4189-98. PMID 24795378 DOI: 10.1128/Aem.00429-14  0.406
2014 Gupta K, Contreras LM, Smith D, Qu G, Huang T, Spruce LA, Seeholzer SH, Belfort M, Van Duyne GD. Quaternary arrangement of an active, native group II intron ribonucleoprotein complex revealed by small-angle X-ray scattering. Nucleic Acids Research. 42: 5347-60. PMID 24567547 DOI: 10.1093/Nar/Gku140  0.589
2014 Baldridge KC, Contreras LM. Functional implications of ribosomal RNA methylation in response to environmental stress. Critical Reviews in Biochemistry and Molecular Biology. 49: 69-89. PMID 24261569 DOI: 10.3109/10409238.2013.859229  0.817
2013 Vazquez-Anderson J, Contreras LM. Regulatory RNAs: charming gene management styles for synthetic biology applications. Rna Biology. 10: 1778-97. PMID 24356572 DOI: 10.4161/Rna.27102  0.6
2013 Tsai CH, Baranowski C, Livny J, McDonough KA, Wade JT, Contreras LM. Identification of novel sRNAs in mycobacterial species. Plos One. 8: e79411. PMID 24244498 DOI: 10.1371/Journal.Pone.0079411  0.359
2013 Contreras LM, Huang T, Piazza CL, Smith D, Qu G, Gelderman G, Potratz JP, Russell R, Belfort M. Group II intron-ribosome association protects intron RNA from degradation. Rna (New York, N.Y.). 19: 1497-509. PMID 24046482 DOI: 10.1261/Rna.039073.113  0.711
2013 Gelderman G, Contreras LM. Discovery of posttranscriptional regulatory RNAs using next generation sequencing technologies. Methods in Molecular Biology (Clifton, N.J.). 985: 269-95. PMID 23417809 DOI: 10.1007/978-1-62703-299-5_14  0.534
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