Results 51 to 60 of about 38,521 (297)

13C-metabolic flux analysis reveals metabolic rewiring in HL-60 neutrophil-like cells through differentiation and immune stimulation

Metabolic Engineering Communications
Neutrophils are innate immune cells and the first line of defense for the maintenance of homeostasis. However, our knowledge of the metabolic rewiring associated with their differentiation and immune stimulation is limited.
Takeo Taniguchi, Nobuyuki Okahashi, Fumio Matsuda   +2 more
doaj   +1 more source

ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis

Journal of Integrative Bioinformatics, 2008
y ReMatch is a web-based, user-friendly tool that constructs stoichiometric network models for metabolic flux analysis, integrating user-developed models into a database collected from several comprehensive metabolic data resources, including KEGG ...
Pitkänen Esa, Åkerlund Arto, Rantanen Ari, Jouhten Paula, Ukkonen Esko   +4 more
doaj   +1 more source

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

BMC Bioinformatics, 2017
Background Modeling of microbial metabolism is a topic of growing importance in biotechnology. Mathematical modeling helps provide a mechanistic understanding for the studied process, separating the main drivers from the circumstantial ones, bounding the
Garrett W. Birkel, Amit Ghosh, Vinay S. Kumar, Daniel Weaver, David Ando, Tyler W. H. Backman, Adam P. Arkin, Jay D. Keasling, Héctor García Martín   +8 more
doaj   +1 more source

Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions.

PLoS Computational Biology, 2021
Metabolic engineering in the post-genomic era is characterised by the development of new methods for metabolomics and fluxomics, supported by the integration of genetic engineering tools and mathematical modelling.
Claudio Tomi-Andrino, Rupert Norman, Thomas Millat, Philippe Soucaille, Klaus Winzer, David A Barrett, John King, Dong-Hyun Kim   +7 more
doaj   +1 more source

Metabolic flux reprogramming in Mycobacterium tuberculosis-infected human macrophages

Frontiers in Microbiology, 2023
Metabolic fluxes are at the heart of metabolism and growth in any living system. During tuberculosis (TB) infection, the pathogenic Mycobacterium tuberculosis (Mtb) adapts its nutritional behaviour and metabolic fluxes to survive in human macrophages and
Khushboo Borah Slater, Luana Moraes, Luana Moraes, Luana Moraes, Ye Xu, Daniel Kim   +5 more
doaj   +1 more source

Hyperpolarized 13C-pyruvate MRI detects real-time metabolic flux in prostate cancer metastases to bone and liver: a clinical feasibility study. [PDF]

, 2020
BackgroundHyperpolarized (HP) 13C-pyruvate MRI is a stable-isotope molecular imaging modality that provides real-time assessment of the rate of metabolism through glycolytic pathways in human prostate cancer.
Aggarwal, Rahul, Bok, Robert A, Carvajal, Lucas, Chen, Hsin-Yu, Gordon, Jeremy W, Kurhanewicz, John, Larson, Peder EZ, Lee, Philip, Ohliger, Michael A, Slater, James B, Small, Eric J, van Criekinge, Mark, Vigneron, Daniel B, Zhu, Zi   +13 more
core  

Algorithms to infer metabolic flux ratios from fluxomics data [PDF]

, 2013
In silico cell simulation approaches based in the use of genome-scale metabolic models (GSMMs) and constraint-based methods such as Flux Balance Analysis are gaining importance, but methods to integrate these approaches with omics data are still greatly ...
Carreira, Rafael, Rocha, I., Rocha, Miguel, Villas-Bôas, S. G.   +3 more
core   +1 more source

Flux-P: Automating Metabolic Flux Analysis

Metabolites, 2012
Quantitative knowledge of intracellular fluxes in metabolic networks is invaluable for inferring metabolic system behavior and the design principles of biological systems.
Birgitta E. Ebert, Anna-Lena Lamprecht, Bernhard Steffen, Lars M. Blank   +3 more
doaj   +1 more source

Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis

BMC Bioinformatics, 2022
Background Elucidating cellular metabolism led to many breakthroughs in biotechnology, synthetic biology, and health sciences. To date, deriving metabolic fluxes by 13C tracer experiments is the most prominent approach for studying metabolic fluxes ...
Kulwadee Thanamit, Franziska Hoerhold, Marcus Oswald, Rainer Koenig   +3 more
doaj   +1 more source

Quantifying Dynamic Regulation in Metabolic Pathways with Nonparametric Flux Inference [PDF]

, 2019
One of the central tasks in systems biology is to understand how cells regulate their metabolism. Hierarchical regulation analysis is a powerful tool to study this regulation at the metabolic, gene-expression, and signaling levels.
He, Fei, Stumpf, Michael P H
core   +1 more source