Results 31 to 40 of about 282,038 (168)

Flux Coupling and the Objective Functions’ Length in EFMs

Metabolites, 2020
Structural analysis of constraint-based metabolic network models attempts to find the network’s properties by searching for subsets of suitable modes or Elementary Flux Modes (EFMs).
Francisco Guil, José F. Hidalgo, José M. García   +2 more
doaj   +1 more source

Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation

Frontiers in Microbiology, 2017
Advances in metagenomics enable high resolution description of complex bacterial communities in their natural environments. Consequently, conceptual approaches for community level functional analysis are in high need. Here, we introduce a framework for a
Shany Ofaim, Shany Ofaim, Maya Ofek-Lalzar, Noa Sela, Jiandong Jinag, Yechezkel Kashi, Dror Minz, Shiri Freilich   +7 more
doaj   +1 more source

A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models

Metabolites, 2017
In this article, we present a protocol for generating a complete (genome-scale) metabolic resource allocation model, as well as a proposal for how to represent such models in the systems biology markup language (SBML). Such models are used to investigate
Alexandra-M. Reimers, Henning Lindhorst, Steffen Waldherr   +2 more
doaj   +1 more source

Totoro: Identifying Active Reactions During the Transient State for Metabolic Perturbations

Frontiers in Genetics, 2022
Motivation: The increasing availability of metabolomic data and their analysis are improving the understanding of cellular mechanisms and how biological systems respond to different perturbations.
Mariana Galvão Ferrarini, Mariana Galvão Ferrarini, Irene Ziska, Irene Ziska, Ricardo Andrade, Ricardo Andrade, Alice Julien-Laferrière, Louis Duchemin, Roberto Marcondes César, Arnaud Mary, Arnaud Mary, Susana Vinga, Marie-France Sagot, Marie-France Sagot   +13 more
doaj   +1 more source

Chemical screens for particle-induced macrophage death identifies kinase inhibitors of phagocytosis as targets for toxicity

Journal of Nanobiotechnology
Background Nanoparticles are increasingly being used in medicine, cosmetics, food, and manufacturing. However, potential toxicity may limit the use of newly engineered nanoparticles.
Uyen Thi Tran, Toshimori Kitami
doaj   +1 more source

Recruitment: A Problem of Entangled Temporal Parts

Frontiers in Bioscience-Landmark, 2022
Recruitment is a pervasive activity of life that is at the center of novelty generation and persistence. Without recruitment, novelties cannot spread and biological systems cannot maintain identity through time.
Gustavo Caetano-Anollés, M. Fayez Aziz, Fizza Mughal, Ibrahim Koç, Kelsey Caetano-Anollés, Derek Caetano-Anollés   +5 more
doaj   +1 more source

Ensemble Modeling of Metabolic Networks [PDF]

Biophysical Journal, 2008
Complete modeling of metabolic networks is desirable, but it is difficult to accomplish because of the lack of kinetics. As a step toward this goal, we have developed an approach to build an ensemble of dynamic models that reach the same steady state.
Tran, Linh M., Rizk, Matthew L., Liao, James C.   +2 more
openaire   +2 more sources

Gaining Insights Into Metabolic Networks Using Chemometrics and Bioinformatics: Chronic Kidney Disease as a Clinical Model

Frontiers in Molecular Biosciences, 2021
Because of its ability to generate biological hypotheses, metabolomics offers an innovative and promising approach in many fields, including clinical research. However, collecting specimens in this setting can be difficult to standardize, especially when
Julien Boccard, Julien Boccard, Domitille Schvartz, Santiago Codesido, Santiago Codesido, Mohamed Hanafi, Yoric Gagnebin, Yoric Gagnebin, Belén Ponte, Fabien Jourdan, Serge Rudaz, Serge Rudaz   +11 more
doaj   +1 more source

Essentiality Landscape of Metabolic Networks [PDF]

Journal of the Korean Physical Society, 2019
Local perturbations of individual metabolic reactions may result in different levels of lethality, depending on their roles in metabolism and the size of subsequent cascades induced by their failure. Moreover, essentiality of individual metabolic reactions may show large variations within and across species.
Kim, P., Han, K., Lee, D. -S., Kahng, B.
openaire   +2 more sources

Optimization strategies for metabolic networks [PDF]

BMC Systems Biology, 2009
Abstract Background The increasing availability of models and data for metabolic networks poses new challenges in what concerns optimization for biological systems. Due to the high level of complexity and uncertainty associated to these networks the suggested models often lack detail and liability, required to ...
Alexandre Domingues, Susana Vinga, João Miranda Lemos   +2 more
openaire   +3 more sources