Genome-scale metabolic modeling of the human microbiome in the era of personalized medicine
The human microbiome plays an important role in human health and disease. Meta-omics
analyses provide indispensable data for linking changes in microbiome composition and …
analyses provide indispensable data for linking changes in microbiome composition and …
[HTML][HTML] Toward modeling metabolic state from single-cell transcriptomics
Background Single-cell metabolic studies bring new insights into cellular function, which can
often not be captured on other omics layers. Metabolic information has wide applicability …
often not be captured on other omics layers. Metabolic information has wide applicability …
Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools
Individual cells within an otherwise genetically homogenous population constantly undergo
fluctuations in their molecular state, giving rise to non-genetic heterogeneity. Such diversity …
fluctuations in their molecular state, giving rise to non-genetic heterogeneity. Such diversity …
[HTML][HTML] Integration of single-cell RNA-seq data into population models to characterize cancer metabolism
Metabolic reprogramming is a general feature of cancer cells. Regrettably, the
comprehensive quantification of metabolites in biological specimens does not promptly …
comprehensive quantification of metabolites in biological specimens does not promptly …
[HTML][HTML] INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation
Metabolism is directly and indirectly fine-tuned by a complex web of interacting regulatory
mechanisms that fall into two major classes. On the one hand, the expression level of the …
mechanisms that fall into two major classes. On the one hand, the expression level of the …
[HTML][HTML] Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN
Altered metabolism is associated with many human diseases. Human genome-scale
metabolic models (GEMs) were reconstructed within systems biology to study the …
metabolic models (GEMs) were reconstructed within systems biology to study the …
[HTML][HTML] The role of metabolic ecosystem in cancer progression—Metabolic plasticity and mTOR hyperactivity in tumor tissues
A Sebestyén, T Dankó, D Sztankovics… - Cancer and Metastasis …, 2021 - Springer
Despite advancements in cancer management, tumor relapse and metastasis are
associated with poor outcomes in many cancers. Over the past decade, oncogene-driven …
associated with poor outcomes in many cancers. Over the past decade, oncogene-driven …
[HTML][HTML] GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction
Metabolic network models are increasingly being used in health care and industry. As a
consequence, many tools have been released to automate their reconstruction process de …
consequence, many tools have been released to automate their reconstruction process de …
Dystrophin deficiency affects human astrocyte properties and response to damage
In addition to progressive muscular degeneration due to dystrophin mutations, 1/3 of
Duchenne muscular dystrophy (DMD) patients present cognitive deficits. However, there is …
Duchenne muscular dystrophy (DMD) patients present cognitive deficits. However, there is …
[HTML][HTML] Constraint-based reconstruction and analyses of metabolic models: open-source python tools and applications to cancer
The influence of metabolism on signaling, epigenetic markers, and transcription is highly
complex yet important for understanding cancer physiology. Despite the development of …
complex yet important for understanding cancer physiology. Despite the development of …