Chintan Jagdishchandra Joshi

Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data

The paper evaluates algorithms for generating context-specific metabolic models using gene expression data and identifies guidelines for selecting the best models.

Inferring a spatial code of cell-cell interactions across a whole animal body

The paper introduces a computational framework to infer the spatial code of cell-cell interactions using transcriptomic data from C. elegans, validated with experimental confirmation.

What does your cell really do? Model-based assessment of mammalian cells metabolic functionalities using omics data

The paper introduces a framework to predict how changes in omics data affect metabolic functions in mammalian cells using curated metabolic tasks and genome-scale networks.

StanDep: capturing transcriptomic variability improves context-specific metabolic models

StanDep improves context-specific metabolic models by using transcriptomic variability to identify core reactions, increasing inclusion of housekeeping and lowly expressed reactions.

Assessing key decisions for transcriptomic data integration in biochemical networks

The paper evaluates how different decisions in transcriptomic data integration affect the identification of active reactions in biochemical networks across tissues.