Anne Siegel

This study examines how Enterococcus faecalis adjusts its metabolism and transcriptional response when exposed to iron under glutathione deficiency, revealing compensatory mechanisms for oxidative stress.

The paper develops a computational framework to model soil microbiome metabolic potential in the Atacama Desert, identifying key species and functions across different environmental conditions.

The paper develops a computational pipeline to classify gut microbiome states using functional annotations, showing comparable performance to microbial profiles and identifying reliable discriminant variables.

This study analyzes 60 brown algal genomes to identify genomic innovations and evolutionary patterns that enabled their adaptation to coastal ecosystems.

This paper develops a rule-based model of hepatic stellate cell dynamics in fibrosis, showing the critical role of inactivation loops in fibrosis progression and identifying inactivated HSCs as markers of fibrosis.

The paper develops dynamic metabolic models of F. succinogenes S85 using genome data and metabolic network reconstruction to simulate carbohydrate metabolism and metabolite production.

AuCoMe reduces technical biases in metabolic network comparisons across diverse genomes and identifies shared and divergent metabolic traits.

EsMeCaTa estimates consensus proteomes and metabolic functions from taxonomic data, validated on environmental datasets and applied to a methanogenic reactor study.

Regulus infers signed transcriptional regulatory networks from few samples by integrating TF binding, gene expression, and regulatory region data with biological constraints.

The paper analyzes reproducibility issues in the Regulatory Circuits project and proposes solutions for improving reusability and reproducibility of its data integration pipeline.

Metage2Metabo identifies keystone species in large microbiotas by analyzing metabolic networks and complementarity.

This paper presents the genome and metabolic network of Ectocarpus subulatus, a stress-tolerant brown alga, and identifies features contributing to its stress tolerance.

The paper identifies metabolic complementarities between a brown alga and its associated bacteria, showing that selected bacterial consortia enhance algal growth and metabolite exchange.

The paper infers new biochemical reactions and metabolite structures in Chondrus crispus, revealing metabolic pathway drift despite conserved phenotypes.

This study shows that miR-202 is critical for female fecundity in medaka, as its knockout leads to reduced egg production and fertility.