Padhmanand Sudhakar

The paper investigates how antibiotic resistance affects the MexT regulatory switch in Pseudomonas aeruginosa, leading to phenotypic plasticity in virulence and antibiotic resistance.

The paper models the impact of non-coding SNPs on gene regulatory networks in IBD to stratify patients based on gene dysregulation and therapeutic response.

This study shows that extracellular vesicles from Bacteroides thetaiotaomicron affect host immune pathways differently in various cell types and disease states, with implications for IBD therapy.

SalmoNet2 provides an updated multi-layered network resource for 20 Salmonella strains, enhancing strain comparisons through protein-protein, transcriptional regulatory, and metabolic interactions.

ViralLink is a systems biology workflow that reconstructs and analyzes intracellular signaling networks affected by viruses, using transcriptomics data to identify key pathways and proteins in the cellular response to infection.

The paper identifies distinct regulatory mechanisms and functions of ULK1 and ULK2, showing they are less redundant than previously thought.

MicrobioLink integrates microbial-host protein interactions with host networks to predict functional effects on cellular processes using network diffusion, applied to Crohn's disease gut metaproteomic data.

The paper uses transcriptomics and network analysis to study regulatory networks in Paneth and goblet cell enriched gut organoids, identifying key regulators and their links to inflammatory bowel disease.

This paper introduces iSNP, a workflow to identify patient-specific pathogenic pathways in ulcerative colitis by integrating SNP profiles with regulatory networks.

The paper integrates proteomic and transcriptomic data from intestinal organoids to identify autophagy-dependent processes in Paneth cells, showing that autophagy impairment affects protein abundance and key cellular functions.