Venkata Satagopam

User-driven development and evaluation of an agentic framework for analysis of large pathway diagrams

The paper describes the development and evaluation of an agentic framework using LLMs to explore molecular interaction maps through user-driven prototyping and testing.

Sex-specific microRNA regulators of Parkinson disease: insights from cohort-stratified simulations of compensatory pathway dynamics

This study uses Boolean modeling on PD cohorts to show sex-specific miRNA dysregulation affects mitochondrial biogenesis, mitophagy, and autophagy in Parkinson's disease.

Multi-omic triangulation identifies molecular candidates of atopic dermatitis severity

This study identifies 440 genes/proteins associated with atopic dermatitis severity through multi-omics analyses and highlights four with significant cross-evidence, including CEP85, which may contribute to severity via impaired phagocytosis.

Association of ulcerative colitis with atopic dermatitis: identification of shared and unique mechanisms by construction and computational analysis of disease maps

This paper constructs and compares computational disease maps of ulcerative colitis and atopic dermatitis to identify shared and unique molecular mechanisms and potential therapeutic targets.

Deciphering shared molecular dysregulation across Parkinson's disease variants using a multi-modal network-based data integration and analysis

The paper integrates multi-modal data to identify shared molecular dysregulation across Parkinson's disease variants, finding common transcriptomic features in glial cells and potential involvement of ROBO signalling.

FAIRification of computational models in biology

The paper proposes adapting FAIR indicators to assess and improve the quality and transparency of computational models in biology.

The inflammatory skin disease map (ISD map): an interactive computational resource focused on psoriasis and atopic dermatitis molecular mechanisms

The paper presents the ISD map, an interactive resource modeling molecular mechanisms of psoriasis and atopic dermatitis, and identifies potential therapeutic targets through hypothesis generation.

Using interactive platforms to encode, manage and explore immune-related adverse outcome pathways

The paper develops a systems immunotoxicology workflow to model and predict adverse outcomes in immunotoxicology using a molecular interaction model and the MINERVA Platform.

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

Cohort-specific Boolean models highlight different regulatory modules during Parkinson's disease progression

This study uses Boolean models to analyze Parkinson's disease progression and identifies subtype-specific regulatory modules and biomolecules.

FAIR assessment of MINERVA as an opportunity to foster open science and scientific crowdsourcing in systems biomedicine

The paper assesses the FAIRness of the MINERVA platform using the RDA FAIR Data Maturity Model, focusing on the Parkinson's Disease Map and the COVID-19 Disease Map.

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

The paper presents a computational framework for analyzing SARS-CoV-2-host interactions to identify drug targets and model disease mechanisms.

COBREXA.jl: constraint-based reconstruction and exascale analysis

COBREXA.jl is a Julia package for scalable constraint-based metabolic modeling, designed for high-performance computing environments and multi-organism community models.

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

The paper describes the development of a computational knowledge repository, the COVID-19 Disease Map, which curates SARS-CoV-2 virus-host interaction mechanisms and provides tools for their analysis and application.

PredictProtein - Predicting Protein Structure and Function for 29 Years

PredictProtein provides protein sequence analysis tools, offering structure and function predictions with updates including deep learning and DNA/RNA/protein binding predictions.

GigaSOM.jl: High-perfomance clustering and visualization of huge cytometry datasets

GigaSOM.jl provides a scalable solution for clustering and visualizing large cytometry datasets, achieving high performance with distributed computing.

BioKC: a collaborative platform for systems biology model curation and annotation

BioKC provides a collaborative platform for curating and annotating systems biology models using SBML standards.