Lydia M. Contreras

The paper predicts CsrA/RsmA target regulons across 16 γ-proteobacterial species, showing that regulatory evolution occurs through changes in RNA targets rather than the protein itself.

This paper develops a standardized genetic toolkit for Deinococcus radiodurans, enabling tunable gene regulation and genome engineering with various components for plasmid and chromosomal modifications.

The paper identifies intrinsic RNA characteristics that influence 8-oxoG accumulation in E. coli and predicts these patterns in other bacterial species.

This study shows that PUS7's cytoplasmic localization enhances stress tolerance by increasing pseudouridylation of mRNAs involved in metal and ROS homeostasis.

This study identifies and characterizes two sRNA-binding proteins, KhpA and KhpB, in Deinococcus radiodurans, showing their roles in sRNA stability, target interactions, and global gene regulation.

The paper maps the protein-DNA landscape of M. bovis BCG under iron starvation, revealing conserved heterochromatin-like structures and their role in stress response gene regulation.

The paper identifies nutrient stress response mechanisms in E. coli by integrating chromatin structure and small regulatory RNA data, revealing novel transcription factor-sRNA interactions.

The paper designs a post-transcriptional BANDPASS filter using the CsrA-uxuB interaction in E. coli, showing concentration-dependent regulation of uxuB mRNA.

This paper uses machine learning on microscopy images to predict microbial community taxonomic diversity and dominant bacterial classes, achieving high accuracy and low error.

ChLoRox-Seq identifies 8-oxoG-modified RNA regions with high specificity and lower cost, revealing transcriptome-wide oxidation biases in stressed human cells.

This study uses thermodynamic modeling to predict RsmA-mRNA binding interactions in Pseudomonas aeruginosa, identifying 1043 interactions including 457 novel targets, validated through experimental assays.

The paper identifies E. coli proteins PepA and YagL as RNA chaperones that promote RNA remodeling through in vivo screening and in vitro validation.

This paper quantifies geometric changes in D. radiodurans nucleoids under ionizing radiation using a new high-throughput method, revealing sub-population shifts and roles of nucleic acid binding proteins in nucleoid condensation.

The paper shows that different particulate matter mixtures cause distinct molecular and morphological changes in lung epithelial cells, with heavy metals causing more severe effects.

The paper identifies new CsrA interactions with sRNAs and demonstrates their regulatory effects on mRNA targets.