Ines Thiele

StereoMapper: Clarifying Metabolite Identity Through Stereochemically Aware Relationship Assignment

StereoMapper clarifies metabolite identity by assigning stereochemically aware relationships, achieving high performance in benchmark datasets and improving GEM accuracy.

XomicsToModel: Multiomics data integration and generation of thermodynamically consistent metabolic models

XomicsToModel integrates multi-omics data with a generic metabolic model to generate context-specific, thermodynamically consistent metabolic models.

Elucidating a potential role of the infant gut microbiome on the bioavailability of L-tyrosine in phenylketonuria

The paper uses metabolic models to show that gut microbiome composition affects L-tyrosine availability in PKU, suggesting microbiome-targeted therapies.

Personalised whole-body modelling links gut microbiota to metabolic perturbations in Alzheimer's disease

The paper uses whole-body metabolic models to link gut microbiota to metabolic changes in Alzheimer's disease, identifying key microbial drivers and metabolites involved.

The MicroMap is a network visualisation resource for microbiome metabolism

The paper introduces the MicroMap, a curated metabolic network visualization resource for microbiome metabolism, integrating with existing tools and providing educational and comparative capabilities.

APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites

APOLLO provides 247,092 genome-scale metabolic models of human microbes, enabling strain-level taxonomic prediction and disease-associated metabolite analysis.

fluxTrAM: Integration of tracer-based metabolomics data into atomically resolved genome-scale metabolic networks for metabolic flux analysis

fluxTrAM automates processing of tracer-based metabolomics data and integrates it with genome-scale metabolic models for flux analysis.

Dynamic whole-body models for infant metabolism

The paper develops dynamic whole-body models for infants to simulate metabolism and predict biomarker concentrations, showing they exceed newborn screening thresholds for isovaleric aciduria.

Conserved moiety fluxomics

This paper introduces a new method for genome-scale metabolic flux inference using conserved moieties, demonstrating its computational efficiency and accuracy with isotopic labeling data.

Personalised metabolic whole-body models for newborns and infants predict growth and biomarkers of inherited metabolic diseases

Coupling of metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and resulting traits and diseases

The paper identifies gene-metabolite associations using exome sequencing and metabolomics, revealing graded effects of rare variants on traits and diseases.

Longitudinal flux balance analyses of a patient with Crohn's disease highlight microbiome metabolic alterations

This study uses longitudinal flux balance analysis of a Crohn's disease patient's microbiome to identify time-correlated metabolic alterations and their systemic effects.

Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication

This study uses whole-body metabolic models to show that isoleucine availability limits SARS-CoV-2 virus shedding and identifies potential therapeutic strategies.

Mechanistic model-driven exometabolomic characterisation of human dopaminergic neuronal metabolism

The paper develops genome-scale metabolic models of human dopaminergic neurons to study metabolic dysfunction in Parkinson's disease using exometabolomic and transcriptomic data.

Causal inference on microbiome-metabolome relations via in silico in vivo association pattern analyses

This paper develops a method to infer causal relationships between microbiome and metabolome in observational data using in silico in vivo association pattern analyses and validates it on a multi-omics dataset.

Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of Fusobacteria species on community butyrate production

This study integrates constraint-based community modeling with fecal metabolomics to show Fusobacteria negatively impact butyrate production in gut microbiomes.

AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities.

AGORA2 reconstructs the human microbiome at scale, revealing individual-specific drug metabolism capabilities and correlations with clinical parameters.

Pan-organ model integration of metabolic and regulatory processes in type 1 diabetes

The paper develops a whole-body model of T1D integrating metabolic and regulatory processes to predict pathophysiological mechanisms and potential therapeutic targets.

Identifying differences in bile acid pathways for cholesterol clearance in Alzheimer’s disease using metabolic networks of human brain regions

The paper identifies differences in bile acid pathways for cholesterol clearance in Alzheimer’s disease by analyzing transcriptomes and metabolomics data from brain samples.

Systematic interrogation of the distinct metabolic potential in gut microbiomes of inflammatory bowel disease patients with dysbiosis

The paper develops a computational approach to analyze metabolic potential in gut microbiomes of IBD patients with dysbiosis, finding distinct metabolite profiles compared to healthy controls and non-dysbiotic patients.

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

The paper introduces a toolbox for modeling microbial interactions and communities using metagenomic data and extends the COBRA Toolbox.

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

The paper introduces the Virtual Metabolic Human database, which integrates human and gut microbiome metabolism with nutrition and disease data to support biomedical research.

When metabolism meets physiology: Harvey and Harvetta

The paper presents two gender-specific whole-body metabolism models, Harvey and Harvetta, that integrate physiological and omics data to predict metabolic processes and interactions across organs.

Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individuals

The paper uses personalized microbial community models to analyze bile acid metabolism in healthy and IBD individuals, revealing distinct metabolic potentials and strain contributions.