Carissa Bleker

TabularQual provides a spreadsheet-based format for annotating logical models, with tools to convert between spreadsheets and SBML-qual, enhancing model reuse and interoperability.

BoolDog is a Python package for Boolean and semi-quantitative network modeling, enabling simulation, analysis, and integration with continuous ODE systems.

The paper develops a genome-scale metabolic model for potato to study growth-defence trade-offs by integrating primary and secondary metabolism and applying transcriptomics data from stress experiments.

The paper integrates multi-omics and phenotyping data to identify molecular signatures of potato responses to abiotic stresses.

The paper unifies potato gene models using an Apollo web server and provides a collaborative genome browser for annotation updates.

The paper introduces Stress Knowledge Map, a resource with two knowledge graphs for plant stress responses, and demonstrates its use in hypothesis generation and analysis.

This study analyzes over 100,000 E. coli genomes to identify 14 phylogroups, revealing population structure and genomic adaptations in virulence and antibiotic resistance.