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 …

Ten quick tips for avoiding pitfalls in multi-omics data integration analyses

D Chicco, F Cumbo, C Angione - PLOS Computational Biology, 2023 - journals.plos.org
Data are the most important elements of bioinformatics: Computational analysis of
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 …

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 …

In silico biomarker analysis of the adverse effects of perfluorooctane sulfonate (PFOS) exposure on the metabolic physiology of embryo-larval zebrafish

RM Nolen, LH Petersen, K Kaiser, A Quigg… - Frontiers in Systems …, 2024 - frontiersin.org
Perfluorooctane sulfonate (PFOS) is a ubiquitous pollutant in global aquatic ecosystems with
increasing concern for its toxicity to aquatic wildlife through inadvertent exposures. To …

Genome‐scale metabolic models applied for human health and biopharmaceutical engineering

F Li, Y Chen, J Gustafsson, H Wang, Y Wang… - Quantitative …, 2023 - Wiley Online Library
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 …

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 …

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 …

Yeast adapts to diverse ecological niches driven by genomics and metabolic reprogramming

H Wang, J Nielsen, Y Zhou, H Lu - bioRxiv, 2024 - biorxiv.org
The widely used model organism, Saccharomyces cerevisiae is ubiquitously present in a
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 …