Rama Shankar

In Vivo Transcriptomics-Based Framework for Systematic Indication Expansion

This paper presents a drug repurposing framework using in vivo transcriptomics to expand indications by matching drug signatures with disease signatures, successfully recovering established uses of semaglutide and proposing new ones.

Automating scientific annotations for open transcriptomic profiles via multi-stage agents

GEOMeta automates metadata curation for GEO transcriptomic data, generating standardized annotations for 600,000 human bulk RNA-seq samples and benchmarking LLMs for annotation quality.

Comparative immuno-biology at clinical recognition of early multiple organ dysfunction syndrome in pediatric and adult patients using single-cell transcriptomics

The paper uses single-cell transcriptomics to identify S100 gene expression patterns and cell-type changes in MODS patients, showing diagnostic potential and therapeutic implications.

Computational discovery of co-expressed antigens as dual targeting candidates for cancer therapy through bulk, single-cell, and spatial transcriptomics

The paper develops a computational pipeline to identify bispecific antibody targets by integrating bulk, single-cell, and spatial transcriptomics data, finding GPC3 and MUC13 as promising candidates in hepatocellular carcinoma.

Detection of viral infection in cell lines using ViralCellDetector

The paper develops a tool to detect viral infections in cell lines using RNA-seq data and machine learning, finding 10% of MCF7 experiments were likely infected.

Analysis of Infected Host Gene Expression Reveals Repurposed Drug Candidates and Time-Dependent Host Response Dynamics for COVID-19