Cynthia Mira Sharma

Interdependent mode of RNA recognition by the interacting KH-domain proteins KhpA and KhpB

This study shows KhpA and KhpB in Campylobacter jejuni depend on each other for RNA recognition, with KhpA using a KH domain and KhpB an atypical R3H domain.

Human-targeted drugs impact antibiotic sensitivity and growth of Campylobacter jejuni

This study shows that human-targeted drugs can both enhance antibiotic resistance and inhibit Campylobacter jejuni growth through efflux pump activation and direct toxicity.

Human-targeted drugs extensively reshape regulatory networks controlling virulence and antibiotic resistance in Salmonella Typhimurium

The paper investigates how human-targeted drugs alter regulatory networks in Salmonella Typhimurium, revealing non-antibiotic compounds reshape virulence and antibiotic resistance through specific transcriptional responses.

Unveiling the small protein landscape of uropathogenic E. coli

This study identifies 338 previously unannotated small open reading frames in UPEC strain CFT073, with functional evidence for nine intergenic sORFs and potential roles in stress response.

A revised genome annotation of the model cyanobacterium Synechocystis based on start and stop codon-enriched ribosome profiling and proteogenomics

This paper revises the genome annotation of Synechocystis using ribosome profiling and proteogenomics, identifying new genes and correcting existing annotations.

Molecular genetic characterization of bacterial KH-domain proteins

The paper characterizes the molecular interactions of KH-domain proteins KhpA and KhpB across bacterial species, revealing conserved protein-protein interactions and species-specific RNA-binding behaviors.

Molecular model of a bacterial flagellar motor in situ reveals a "parts-list" of protein adaptations to increase torque

The paper determines the in situ structure of a high-torque bacterial flagellar motor using cryogenic electron microscopy, revealing protein adaptations and universal principles of torque generation.

Pre-trained molecular representations enable antimicrobial discovery

This paper introduces a deep learning framework for antimicrobial discovery that identifies new compounds with antimicrobial potential using pre-trained molecular representations.

A small protein essential for flagellar assembly and virulence of Campylobacter jejuni

This study identifies a small protein, PflE, essential for flagellar assembly and virulence in Campylobacter jejuni by using transposon sequencing in a humanized tissue model.

Statistical end-to-end analysis of large-scale microbial growth data with DGrowthR

DGrowthR provides a statistical framework for analyzing large-scale microbial growth data, enabling differential growth analysis and discovery of compounds affecting bacterial growth.

Small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti

The paper expands the known proteome of Sinorhizobium meliloti by identifying 48 novel small proteins using Ribo-seq and proteogenomics.

Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni

The paper uses complementary Ribo-seq methods to map the translatome of Campylobacter jejuni, identifying novel small open reading frames and refining gene annotations.

RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria

The paper benchmarks ORF prediction tools for bacterial Ribo-seq data, finding DeepRibo performs well but none detect all novel sORFs with high sensitivity.

HRIBO - High-throughput analysis of bacterial ribosome profiling data

HRIBO is a workflow for analyzing bacterial Ribo-seq data to discover novel ORFs, using annotation-independent methods and integrating additional features for prioritization.