Results 101 to 110 of about 474,387 (314)

Integrated signaling pathway and gene expression regulatory model to dissect dynamics of Escherichia coli challenged mammary epithelial cells [PDF]

, 2014
Cells transform external stimuli, through the activation of signaling pathways, which in turn activate gene regulatory networks, in gene expression. As more omics data are generated from experiments, eliciting the integrated relationship between the ...
den Breems, NY, den Breems, Nicoline Y., Kulasiri, Don, Nguyen, LK, Nguyen, Lan K.   +4 more
core   +1 more source

α‐Synuclein aggregation landscape from phase separation to neurotoxic intermediates

FEBS Letters, EarlyView.
Alpha‐synuclein aggregation in Parkinson's disease involves a complex landscape of transient intermediates, including oligomers, fibrils and liquid–liquid phase separation (LLPS). A view is emerging in which LLPS maturation into solid‐like condensates may contribute to the formation of neurotoxic species.
Silvia Arino, Giuliana Fusco, Alfonso De Simone   +2 more
wiley   +1 more source

Linking Cytoscape and the corynebacterial reference database CoryneRegNet

, 2008
Baumbach J, Apeltsin L. Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008;9(1): 184.Background: Recently, the research community has seen an influx of data relating to transcriptional regulatory interactions of
Baumbach Jan, Jan Baumbach, Apeltsin, Leonard, Baumbach, Jan, Apeltsin Leonard, Leonard Apeltsin   +5 more
core   +1 more source

Three phosphatase families form a community: The phosphohydrolases that act upon inositol pyrophosphates

FEBS Letters, EarlyView.
Inositol pyrophosphates are energy‐rich signaling molecules that perform critical functions in cells. Three different families of phosphatases hydrolyze the β phosphate of the inositol pyrophosphate molecules: two have narrow specificities and one is promiscuous.
Ronda J. Rolfes
wiley   +1 more source

Correcting for link loss in causal network inference caused by regulator interference [PDF]

, 2014
Motivation: There are a number of algorithms to infer causal regulatory networks from time-series (gene expression) data. Here we analyse the phenomena of regulator interference, where regulators with similar dynamics mutually suppress both the ...
Penfold, Christopher A., Hodgson, D. A., Christopher A. Penfold, Wang, Ying, Ying Wang, David A. Hodgson, Burroughs, Nigel John, Miriam L. Gifford, Nigel J. Burroughs, Gifford, Miriam L.   +9 more
core   +1 more source

Modelling stem cell differentiation related processes—A practical overview for biologists

FEBS Letters, EarlyView.
Stem cell differentiation is complex and difficult to control experimentally. This review introduces suitable computational modelling approaches that can support stem cell research, from mechanistic ODE and abstract models to multiscale and deep learning methods.
Ricco Zeegelaar, Xinqi Yan, Lucas Jansen Klomp, Stefano Schivo, Janine N. Post   +4 more
wiley   +1 more source

Differential System Approach to Gene Regulatory Network Modeling

AppliedMath
The system of ordinary differential equations that arises in models of genetic networks is considered. This system has both nonlinear and linear parts. As a nonlinear part, we use a piecewise linear function. This allows us to treat systems with multiple
Olga Kozlovska, Felix Sadyrbaev
doaj   +1 more source

Design and analysis strategies for robust microbiome ageing research

FEBS Letters, EarlyView.
The gut microbiome changes with age and associates with age‐related morbidity and mortality, establishing it as a potential biomarker and intervention target for ageing. Realising this potential requires methodological rigour, yet distinguishing biological signals from methodological artefacts remains challenging across cohorts. This review provides an
Mark Olenik, İsmail Güderer, Yi Wang, Tayyaba Alvi, Prasoon Pandey, Handan Melike Dönertaş   +5 more
wiley   +1 more source

Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks

PLOS Computational Biology, 2015
Human gene regulatory networks (GRN) can be difficult to interpret due to a tangle of edges interconnecting thousands of genes. We constructed a general human GRN from extensive transcription factor and microRNA target data obtained from public databases.
Vipin Narang, Muhamad Azfar Ramli, Amit Singhal 0003, Pavanish Kumar, Gennaro de Libero, Michael Poidinger, Christopher P. Monterola   +6 more
openaire   +5 more sources

Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana

BMC Bioinformatics, 2011
Background Photosynthetic light acclimation is an important process that allows plants to optimize the efficiency of photosynthesis, which is the core technology for green energy.
Chen Bor-Sen, Hsu Ban-Dar, Yao Cheng-Wei
doaj   +1 more source