Nagasuma R Chandra

Increased 'selfness' in the tumor emerges as a possible immune sculpting mechanism: A pan-cancer data analysis of 32 solid tumors in TCGA

The paper develops a thymus-like score to assess tumor similarity to thymi and finds it correlates with patient survival and inversely with immune infiltration across 32 solid tumors.

CAcnesDB: A database of Cutibacterium acnes with Integrated Functional Insights derived from Multi-modal Genome Annotation

CAcnesDB provides a comprehensive database of Cutibacterium acnes genome with integrated functional annotations derived from multi-modal genome analysis.

Macrophage Cholesterol Homeostasis Underpins the role of Sertraline as an Adjunctive Agent in Tuberculosis Therapy.

This paper shows sertraline enhances macrophage bactericidal activity against Mtb by rewiring cholesterol metabolism and activating inflammasome pathways.

Balance between autophagy and apoptosis determines anoikis resistance: a mathematical model on cell fate

The paper develops a mathematical model to study how cancer cells balance autophagy and apoptosis to determine anoikis resistance.

Hydrogen sulfide (H2S) coordinates redox balance, carbon metabolism, and mitochondrial bioenergetics to suppress SARS-CoV-2 infection.

Chronic Inflammation Induced Immature Neutrophils Drive Immunopathology During Subsequent Inflammatory Events

The paper shows chronic inflammation increases immature neutrophils, which worsen immunopathology during new inflammatory events, and suggests targeting these cells as a therapeutic strategy.

CRD: a De novo Design algorithm for prediction of Cognate Protein Receptors for small molecule ligands

CRD predicts cognate protein receptors for small molecule ligands using de novo design and structural bioinformatics, accurately recovering known sites and predicting receptor classes for drugs.

Fast Local Alignment of Protein Pockets (FLAPP): A system-compiled program for large-scale binding site alignment

FLAPP rapidly aligns protein binding sites at the atomic level, enabling large-scale structural comparisons for functional and drug discovery insights.

Knock-down of a regulatory barcode shifts macrophage polarization destination from M1 to M2 and increases pathogen burden upon S. aureus infection

The paper identifies three regulatory factors that shift macrophage polarization from M1 to M2 and increase susceptibility to S. aureus infection.

PathExt: a general framework for path-based mining of omics-integrated biological networks

PathExt identifies differentially active paths in biological networks to prioritize context-relevant genes, even with single samples or no control.