Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations
EL Carter, C Constantinidou… - Briefings in …, 2024 - academic.oup.com
Environmental perturbations are encountered by microorganisms regularly and will require
metabolic adaptations to ensure an organism can survive in the newly presenting …
metabolic adaptations to ensure an organism can survive in the newly presenting …
Ten quick tips for avoiding pitfalls in multi-omics data integration analyses
Data are the most important elements of bioinformatics: Computational analysis of
bioinformatics data, in fact, can help researchers infer new knowledge about biology …
bioinformatics data, in fact, can help researchers infer new knowledge about biology …
From observational to actionable: rethinking omics in biologics production
HO Masson, KJ la Cour Karottki, J Tat, H Hefzi… - Trends in …, 2023 - cell.com
As the era of omics continues to expand with increasing ubiquity and success in both
academia and industry, omics-based experiments are becoming commonplace in industrial …
academia and industry, omics-based experiments are becoming commonplace in industrial …
Multi-omic characterization of antibody-producing CHO cell lines elucidates metabolic reprogramming and nutrient uptake bottlenecks
S Gopalakrishnan, W Johnson… - Metabolic …, 2024 - Elsevier
Characterizing the phenotypic diversity and metabolic capabilities of industrially relevant
manufacturing cell lines is critical to bioprocess optimization and cell line development …
manufacturing cell lines is critical to bioprocess optimization and cell line development …
In silico biomarker analysis of the adverse effects of perfluorooctane sulfonate (PFOS) exposure on the metabolic physiology of embryo-larval zebrafish
Perfluorooctane sulfonate (PFOS) is a ubiquitous pollutant in global aquatic ecosystems with
increasing concern for its toxicity to aquatic wildlife through inadvertent exposures. To …
increasing concern for its toxicity to aquatic wildlife through inadvertent exposures. To …
Genome‐scale metabolic models applied for human health and biopharmaceutical engineering
Over the last 15 years, genome‐scale metabolic models (GEMs) have been reconstructed
for human and model animals, such as mouse and rat, to systematically understand …
for human and model animals, such as mouse and rat, to systematically understand …
Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models
M Jalili, M Scharm, O Wolkenhauer… - NPJ Systems Biology …, 2023 - nature.com
Genome-scale metabolic models (GEMs) are extensively used to simulate cell metabolism
and predict cell phenotypes. GEMs can also be tailored to generate context-specific GEMs …
and predict cell phenotypes. GEMs can also be tailored to generate context-specific GEMs …
Metatranscriptomics-based metabolic modeling of patient-specific urinary microbiome during infection
J Josephs-Spaulding, HC Rettig, J Zimmermann… - bioRxiv, 2024 - biorxiv.org
Urinary tract infections (UTIs) are a major health concern which incur significant
socioeconomic costs in addition to substantial antibiotic prescriptions, thereby accelerating …
socioeconomic costs in addition to substantial antibiotic prescriptions, thereby accelerating …
Yeast adapts to diverse ecological niches driven by genomics and metabolic reprogramming
The widely used model organism, Saccharomyces cerevisiae is ubiquitously present in a
variety of natural and human-associated habitats. Despite extensive studies of this …
variety of natural and human-associated habitats. Despite extensive studies of this …
Reconstruction and analysis of tissue-specific models of Atlantic salmon metabolism
H Nordtorp - 2024 - nmbu.brage.unit.no
The set of all biochemical reactions taking place in a living organism, converting nutrients to
energy and growth, is referred to as metabolism. Metabolism is highly interconnected …
energy and growth, is referred to as metabolism. Metabolism is highly interconnected …