Alpha Tom Kodamullil

KG-Orchestra enriches biomedical knowledge graphs by combining manual curation and automated LLM methods to improve granularity and evidence quality.

The paper develops TVBase, a platform that projects biomedical knowledge onto a 3D brain atlas to support neuroimaging analysis and hypothesis generation.

The paper investigates how the H1/H1 risk allele at the MAPT locus increases susceptibility to mild chronic oxidative stress in iNeurons and identifies FDA-approved compounds that rescue this vulnerability.

The paper introduces CBM KG, a knowledge graph linking COVID-19 and neurodegenerative diseases through causal mechanisms, integrating 2,800 relationships from 63 studies.

SynDRep predicts synergistic drug partners for disease repurposing using knowledge graphs and machine learning, achieving 84.58% true predictions with HolE and 0.796 ROC-AUC with random forest.

This study identifies shared molecular mechanisms between schizophrenia and somatic disorders using a computational framework based on multi-rank non-negative matrix factorization.

This study identifies shared genetic and biological mechanisms between schizophrenia, bipolar disorder, and type 2 diabetes mellitus using integrative analysis of gene expression datasets.

This work analyzes transcriptomic data across multiple biological contexts to identify unique and shared gene expression patterns using co-expression networks and pathway analysis.

The paper introduces STonKGs, a Transformer model trained on biomedical text and knowledge graphs, which outperforms single-modality models in classification tasks.

DecoPath is a web tool that helps interpret pathway enrichment analysis results by comparing across databases and methods, highlighting consensus and discrepancies.

This paper investigates transcriptomic signatures across diseases by integrating co-expression networks and pathway knowledge to identify disease mechanisms.

This paper uses predictive machine learning models to simulate drug responses by calibrating patient-specific pathway signatures, identifying potential drugs and mechanisms for three cancers.

The paper presents a drug-target-mechanism graph to identify synergistic drug combinations for SARS-CoV-2 treatment, validated through experimental testing.

The paper constructs a cause-and-effect knowledge graph of COVID-19 pathophysiology from scientific literature and provides it as a public resource.

The PTSD Biomarker Database compiles over 900 PTSD biomarkers from 109 studies to enable exploration and comparison of biomarker findings through interactive visualizations.