Chris T. Evelo

User-friendly transcriptomic data analysis with ArrayAnalysis

ArrayAnalysis provides an interactive web and desktop platform for analyzing microarray and RNA-seq data, offering tools for preprocessing, differential expression, and visualization to support both novice and expert users.

GSEA and the coexpression network approach identify novel pathway connections of molecular processes affected in Porto-sinusoidal vascular disease.

The paper uses GSEA and WGCNA to identify dysregulated pathways in Porto-sinusoidal vascular disease, revealing immune, signaling, and metabolic dysfunctions.

Collaborative network analysis for the interpretation of transcriptomics data in rare diseases, an application to Huntington's disease

This study applies collaborative network analysis to Huntington's disease transcriptomics data to identify enriched pathways and generate hypotheses about disease mechanisms.

Extending Inherited Metabolic Disorder diagnostics with Biomarker Interaction Visualizations

This paper presents a framework integrating metabolic pathway knowledge with patient data to aid in diagnosing inherited metabolic disorders through visualization of biomarker interactions.

Molecular Adverse Outcome Pathways: towards the implementation of transcriptomics data in risk assessments

The paper introduces molecular AOPs to link KEs from AOP-Wiki to biological pathways in WikiPathways, enabling transcriptomics data analysis for KE activation identification.

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.

Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions

The paper semantifies and harmonizes biological pathway diagrams from WikiPathways to enable semantic querying and integration with linked data.

Converging pathways found in copy number variation syndromes with high schizophrenia risk

This study identifies common molecular pathways associated with schizophrenia risk in copy number variation syndromes by analyzing gene interactions and pathways from multiple databases.

History of rare diseases and their genetic causes - a data driven approach

This paper provides a dataset linking rare monogenic diseases to their causative genes, revealing the timeline of discoveries and their relation to methodological and database advancements.

ComMet: A method for comparing metabolic states in genome-scale metabolic models

ComMet is a method for analyzing and comparing metabolic flux states in genome-scale models, identifying distinct network modules and differences in human adipocyte metabolism under varying amino acid uptake conditions.

A cancer pharmacogenomic screen powering crowd-sourced advancement of drug combination prediction

The paper presents a large-scale cancer pharmacogenomic screen with 11,576 experiments on 910 drug combinations across 85 cancer cell lines, enabling crowd-sourced prediction of synergistic drug pairs and biomarkers.

Integrated analysis of human transcriptome data for Rett syndrome finds a network of involved genes

The paper integrates transcriptome data from human cells with impaired MECP2 to identify a network of genes involved in Rett syndrome and their regulatory mechanisms.

Current systems biology approaches in hazard assessment of nanoparticles

This paper reviews systems biology approaches to assess nanoparticle hazards, highlighting their value in understanding NP effects on biological systems.