Pradipta Ghosh

Peripheral nerve-derived extracellular vesicles are dynamically regulated in chemotherapy-induced painful peripheral neuropathy

The paper identifies and characterizes Schwann cell-derived extracellular vesicles in chemotherapy-induced neuropathy, showing changes in their proteome and function.

A Druggable G Protein Checkpoint in Cholesterol Efflux

The paper identifies GIV as a macrophage checkpoint suppressing reverse cholesterol transport and shows its inhibition restores cholesterol efflux, reducing plaque burden and systemic lipid overload.

COMPASS enables cohort-independent digital biomarker discovery and pathway quantification

The paper introduces COMPASS, a method to quantify pathway activity from gene expression without reference cohorts, showing improved consistency and robustness compared to existing methods.

A stromal-state dichotomy governs recalcitrance or remission in inflammatory bowel disease

This paper identifies two stromal states in IBD that predict clinical outcomes and shows that targeting one state can reverse disease pathology.

An Endocytic Checkpoint Controls Macrophage PD-1 Function and Immunotherapy Fate

This paper identifies GIV as a macrophage-intrinsic factor that controls PD1 endocytosis, determining durable response versus hyperprogressive disease to PD1 blockade.

A NOD2-Encoded Toggle Switch Resolves the Host-Microbe Battle Over Cyclic AMP Control

This paper identifies a host-encoded toggle switch involving NOD2 and GIV that controls cAMP levels in macrophages, converting tolerant cells into microbicidal machines to restore microbial clearance and gut barrier integrity.

Distinct Colitis-Associated Macrophages Drive NOD2-Dependent Bacterial Sensing and Gut Homeostasis

The paper identifies niColAMs as critical for IBD recovery and shows GIV-NOD2 interaction is essential for microbial sensing and gut homeostasis.

F.O.R.W.A.R.D: A Data-Driven Framework for Network-Based Target Prioritization in Drug Discovery

F.O.R.W.A.R.D is a network-based target prioritization framework that uses clinical outcomes and transcriptomic data to predict drug efficacy in IBD, achieving 100% predictive accuracy in benchmarking.

Molecular Signatures for Microbe-Associated Colorectal Cancers

The paper identifies a Microbe-Associated Colorectal Cancer Signature (MACS) induced by Fusobacterium nucleatum in genetically predisposed hosts, linking microbial infection to early CRC initiation.

Machine Learning Identifies Signatures of Macrophage Reactivity and Tolerance that Predict Disease Outcomes

The paper identifies a 338-gene signature of macrophage reactivity and tolerance that predicts disease outcomes across diverse conditions and species.

Artificial Intelligence Guided Discovery of Gastric Cancer Continuum

The paper develops predictive models of gastric cancer progression using Boolean implication networks and identifies gene clusters associated with different stages of the disease.

Design principles of dose-response alignment in coupled GTPase switches

This paper investigates design principles for dose-response alignment in signaling motifs with negative feedback loops, showing how kinetic parameters and activation levels affect performance.

Artificial Intelligence-rationalized balanced PPARα/γ dual agonism resets the dysregulated macrophage processes in inflammatory bowel disease

The paper uses BoNE to identify dual PPARα/γ agonism as a therapeutic strategy for IBD, validated in preclinical models and patient-derived cells.

AI-guided discovery of the invariant host response to viral pandemics

The paper identifies a conserved 166-gene host immune signature across viral pandemics, with a 20-gene subset predicting disease severity and guiding therapeutic strategies.

A Circuit for Secretion-coupled Cellular Autonomy in Multicellular Eukaryotes

The paper identifies a GTPase circuit that enables secretion-coupled cellular autonomy in cancer cells through feedback loops and dose response alignment of growth factor sensing and secretion.

Guanine-nucleotide Exchange Modulator, GIV/Girdin, Serves as a Tunable Valve for Growth Factor-Stimulated Cyclic AMP Signals

The paper presents a network-based model of GIV/Girdin-dependent cAMP signaling, revealing its role as a tunable control valve distinct from GPCRs and PDEs.

Dysregulation of the engulfment pathway in the gut fuels Inflammatory Bowel Disease

This study shows that ELMO1 dysregulation in the gut epithelium and macrophages contributes to IBD by promoting bacterial internalization and pro-inflammatory cytokine production.