Jean‐Marc Schwartz

SIMOFF: Discovering the metabolic objective of the cell

SIMOFF infers metabolic objectives from flux data, improving gene essentiality predictions in yeast and CHO cells.

Transcriptome-Driven Constraint-Based Modelling Reveals Metabolic Targets for Ovarian Cancer

This study uses transcriptome-driven constraint-based modeling to identify metabolic targets in ovarian cancer, revealing TPI1 as a potential therapeutic target supported by experimental validation.

Human pluripotent stem cell model of multiple epiphyseal dysplasia with MATN3 mutation identifies altered Matrix organisation and upregulation of the cholesterol biosynthesis pathway

This study uses hPSCs to model MED with MATN3 mutations, revealing altered matrix organisation and upregulated cholesterol biosynthesis pathway.

HIHISIV: a database of gene expression in HIV and SIV host immune response

HIHISIV is a database that integrates and provides tools to analyze gene expression data from HIV and SIV host immune responses in humans and nonhuman primates.

Development of a genome scale metabolic model for the lager hybrid yeast S. pastorianus to understand evolution of metabolic pathways in industrial settings.

The paper develops a genome-scale metabolic model for S. pastorianus to predict metabolic pathway evolution and aid industrial strain optimization.

Constraint-based modelling predicts metabolic signatures of low- and high-grade serous ovarian cancer

This study uses constraint-based modeling to predict metabolic differences between low- and high-grade serous ovarian cancer subtypes, supported by CRISPR-Cas9 and literature data.

SubcellulaRVis: an app to visualize subcellular compartment enrichment

SubcellulaRVis visualizes subcellular compartment enrichment of gene lists using a eukaryotic cell diagram, improving interpretation of protein localization from enrichment analyses.

Transcriptional network of the industrial hybrid Saccharomyces pastorianus reveals temperature-dependent allele expression bias and preferential orthologous protein assemblies

Using Multilayer Heterogeneous Net-works to Infer Functions of Phosphorylated Sites

The paper introduces a method to infer functions of phosphorylated sites using a heterogeneous multilayer network and validates it on phosphoproteomics data.

HybridMine: pipeline for allele inheritance and gene copy number prediction in industrial yeast hybrids

HybridMine annotates hybrid aneuploid genomes by predicting parental alleles, enabling functional analysis of complex yeast hybrids.

Modelling the role of dual specificity phosphatases in Herceptin resistant breast cancer cell lines

The paper models how DUSP overexpression contributes to Herceptin resistance in breast cancer and identifies potential therapeutic strategies.

Network controllability: viruses are driver agents in dynamic molecular systems

This paper applies network controllability theory to study how HIV-1 and HCV infections control host cell networks by targeting critical nodes more efficiently than uninfected states.

Using set theory to reduce redundancy in pathway sets

The paper reduces pathway redundancy using set cover, achieving significant reductions in redundancy while maintaining gene coverage.