Results 91 to 100 of about 786,474 (343)
Reconstruct gene regulatory network using slice pattern model
BMC Genomics, 2009 Background Gene expression time series array data has become a useful resource for investigating gene functions and the interactions between genes.
Yang Bo +6 more
doaj +1 more source
, 2020 Gene network inference is the task of reconstructing regulatory networks among genes from high-throughput (in particular transcriptomic) data. Here we introduce the main concepts of this rich and rapidly evolving field. In order to illustrate the basic principles of gene network inference we simulate gene expression patterns using two distinct ...
Hütt, Marc-Thorsten, Lesne, Annick
openaire +1 more source
The newfound relationship between extrachromosomal DNAs and excised signal circles
FEBS Letters, EarlyView.Extrachromosomal DNAs (ecDNAs) contribute to the progression of many human cancers. In addition, circular DNA by‐products of V(D)J recombination, excised signal circles (ESCs), have roles in cancer progression but have largely been overlooked. In this Review, we explore the roles of ecDNAs and ESCs in cancer development, and highlight why these ...
Dylan Casey, Zeqian Gao, Joan Boyes
wiley +1 more source
Homeostasis in gene regulatory networks
International Journal of BiomathematicsGene regulatory networks lie at the heart of many important intracellular signal transduction processes. A Gene Regulatory Network (GRN) is abstractly defined as a directed graph, where the nodes represent genes and the edges represent the causal regulatory interactions between genes. It can be used to construct mathematical models describing the time-
Fernando Antoneli +3 more
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Entropy of complex relevant components of Boolean networks
, 2007 Boolean network models of strongly connected modules are capable of capturing the high regulatory complexity of many biological gene regulatory circuits.
A. Faure +6 more
core +1 more source
Quantitative analysis of the ThrbCRM1-centered gene regulatory network
Biology Open, 2019 Enhancer activity is determined by both the activity and occupancy of transcription factors as well as the specific sequences they bind. Experimental investigation of this dynamic requires the ability to manipulate components of the system, ideally in as
Benjamin Souferi, Mark M. Emerson
doaj +1 more source
FEBS Letters, EarlyView.This study reveals how the mitochondrial protein Slm35 is regulated in Saccharomyces cerevisiae. The authors identify stress‐responsive DNA elements and two upstream open reading frames (uORFs) in the 5′ untranslated region of SLM35. One uORF restricts translation, and its mutation increases Slm35 protein levels and mitophagy.
Hernán Romo‐Casanueva +5 more
wiley +1 more source
Gene-Centered Regulatory Network Mapping [PDF]
, 2011 The Caenorhabditis elegans hermaphrodite is a complex multicellular animal that is composed of 959 somatic cells. The C. elegans genome contains ∼20,000 protein-coding genes, 940 of which encode regulatory transcription factors (TFs). In addition, the worm genome encodes more than 100 microRNAs and many other regulatory RNA and protein molecules.
openaire +3 more sources
Estimating gene regulatory networks with pandaR [PDF]
Bioinformatics, 2017 Abstract PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that begins with a model of transcription factor–target gene interactions and uses message passing to update the network model given available transcriptomic and protein–protein interaction data.
Schlauch, Daniel +4 more
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Stable Gene Regulatory Network Modeling From Steady-State Data
Bioengineering, 2016 Gene regulatory networks represent an abstract mapping of gene regulations in living cells. They aim to capture dependencies among molecular entities such as transcription factors, proteins and metabolites.
Joy Edward Larvie +5 more
doaj +1 more source