Publications by authors named "Lydia M Contreras"

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Establishing a Standardized Genetic Toolkit for the Radiation-Resistant Extremophile .
Trevor R Simmons, Antonio Cordova, Kobe B Grismore, Laci C Moline, Anna C Stankes, Lydia M Contreras

ACS Synth Biol· December 2025

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High-Throughput Microfluidic Technologies for Rapidly Screening Pollutant-Induced Cell Health Effects.
Blanca I Quiñones-Díaz, Niphattha Wongwiset, Pratik Kamat, Orian Stapleton, Sean M Engels, Lydia M Contreras

ACS Bio Med Chem Au· October 2025

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RNA Binding Proteins KhpA and KhpB Interact with Small Regulatory RNAs and Affect Global Gene Expression in .
Runhua Han, Blanca I Quinones-Diaz, Antonio Cordova, Brandon Niese, Phillip Sweet, Lydia M Contreras

bioRxiv· September 2025

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Cytoplasmic localization of PUS7 facilitates a pseudouridine-dependent enhancement of cellular stress tolerance.
Minli Ruan, Sean M Engels, Matthew R Burroughs, Xiaoyan Li, Rosella Stower, Lydia M Contreras

bioRxiv· September 2025

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Conserved Heterochromatin-like Structures with Local Regulators Mediate the Iron Stress Response in Mycobacteria.
Alyssa M Ekdahl, Agata Turula, Jeremy W Schroeder, Rebecca Hurto, Quancheng Liu, Lydia M Contreras

bioRxiv· August 2025

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Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs.
Alyssa M Ekdahl, Tatiana Julien, Sahana Suraj, Judith F Kribelbauer-Swietek, Saeed Tavazoie, Lydia M Contreras

Nucleic Acids Res· July 2025

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Concentration-Dependent CsrA Regulation of the Transcript Leads to Development of a Post-Transcriptional Bandpass Filter.
Alejandra M Rojano-Nisimura, Trevor R Simmons, Alexandra J Lukasiewicz, Ryan Buchser, Josie S Ruzek, Lydia M Contreras

ACS Synth Biol· April 2025

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Thermodynamic modeling of RsmA - mRNA interactions capture novel direct binding across the transcriptome.
Alexandra J Lukasiewicz, Abigail N Leistra, Lily Hoefner, Erika Monzon, Cindy J Gode, Lydia M Contreras

Front Mol Biosci· February 2025

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RNA dynamics in oxidative stress: From obscurity to mechanistic understanding in health and disease.
Lydia M Contreras, Marlene Belfort

Proc Natl Acad Sci U S A· November 2024

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Rewiring native post-transcriptional global regulators to achieve designer, multi-layered genetic circuits.
Trevor R Simmons, Gina Partipilo, Ryan Buchser, Anna C Stankes, Rashmi Srivastava, Lydia M Contreras

Nat Commun· October 2024

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Quantitative morphological analysis of elucidates complex dose-dependent nucleoid condensation during recovery from ionizing radiation.
Antonio Cordova, Brandon Niese, Philip Sweet, Pratik Kamat, Jude M Phillip, Lydia M Contreras

Appl Environ Microbiol· July 2024

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Multiscale regulation of nutrient stress responses in from chromatin structure to small regulatory RNAs.
Alyssa M Ekdahl, Tatiana Julien, Sahana Suraj, Judith Kribelbauer, Saeed Tavazoie, Lydia M Contreras

bioRxiv· June 2024

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The Post-Transcriptional Regulatory Protein CsrA Amplifies Its Targetome through Direct Interactions with Stress-Response Regulatory Hubs: The EvgA and AcnA Cases.
Alejandra Matsuri Rojano-Nisimura, Kobe B Grismore, Josie S Ruzek, Jacqueline L Avila, Lydia M Contreras

Microorganisms· March 2024

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RNA-binding proteins that preferentially interact with 8-oxoG-modified RNAs: our current understanding.
Kathleen E Taylor, Lucas G Miller, Lydia M Contreras

Biochem Soc Trans· February 2024

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Particulate matter composition drives differential molecular and morphological responses in lung epithelial cells.
Sean M Engels, Pratik Kamat, G Stavros Pafilis, Yukang Li, Anshika Agrawal, Lydia M Contreras

PNAS Nexus· January 2024

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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.
Matthew R Burroughs, Philip J Sweet, Lydia M Contreras

RNA Biol· January 2024

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A high-throughput search for intracellular factors that affect RNA folding identifies proteins PepA and YagL as RNA chaperones that promote RNA remodelling.
Alejandra Matsuri Rojano-Nisimura, Lucas G Miller, Aparna Anantharaman, Aaron T Middleton, Elroi Kibret, Lydia M Contreras

RNA Biol· January 2024

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CsrA selectively modulates sRNA-mRNA regulator outcomes.
Alejandra Matsuri Rojano-Nisimura, Trevor R Simmons, Abigail N Leistra, Mia K Mihailovic, Ryan Buchser, Lydia M Contreras

Front Mol Biosci· November 2023

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Characterization of epitranscriptome reader proteins experimentally and : Current knowledge and future perspectives beyond the YTH domain.
Lucas G Miller, Madeline Demny, Phanourios Tamamis, Lydia M Contreras

Comput Struct Biotechnol J· June 2023

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Particulate matter composition drives differential molecular and morphological responses in lung epithelial cells.
Sean M Engels, Pratik Kamat, G Stavros Pafilis, Yukang Li, Anshika Agrawal, Lydia M Contreras

bioRxiv· May 2023

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CsrA Shows Selective Regulation of sRNA-mRNA Networks.
Alejandra Matsuri Rojano-Nisimura, Trevor R Simmons, Abigail N Leistra, Mia K Mihailovic, Ryan Buchser, Lydia M Contreras

bioRxiv· March 2023

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Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria.
Alyssa M Ekdahl, Alejandra M Rojano-Nisimura, Lydia M Contreras

J Mol Biol· September 2022

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PNPase and RhlB Interact and Reduce the Cellular Availability of Oxidized RNA in .
Runhua Han, Jessie Jiang, Jaden Fang, Lydia M Contreras

Microbiol Spectr· August 2022

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A strategy to quantify myofibroblast activation on a continuous spectrum.
Alexander Hillsley, Matthew S Santoso, Sean M Engels, Kathleen N Halwachs, Lydia M Contreras

Sci Rep· July 2022

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The challenges in finding your home as a multidisciplinary scientist.
Sijia Wang, Linsey C Marr, Lydia M Contreras, Fabian J Theis, Paul Nurse

Cell· July 2022

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