Plants framework gene regulatory networks. Medical search. Frequent questions

The experimental part of the project will produce a data set of gene expression measurements from various Arabidopsis mutants with altered wounding responses. (uea.ac.uk)
A transcriptional and metabolic framework for secondary wall formation in arabidopsis. (mpg.de)
To better understand this rewiring of gene expression we undertook RNA- and DNaseI-SEQ on de-etiolating seedlings of C 4 Gynandropsis gynandra , which is sister to C 3 Arabidopsis. (sciety.org)
C 3 photosynthesis and C 4 genes showed similar induction patterns, but C 4 genes from G. gynandra were more strongly induced than orthologs from Arabidopsis. (sciety.org)
The main finding is the cistrome of C4 genes in G. gynandra has likely diverged from its orthologs in Arabidopsis. (sciety.org)
In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. (nature.com)
Organ formation during flower development in Arabidopsis is regulated by only few genes, what can be summarized by the so-called 'ABC' model. (ens-lyon.fr)

Gene regulatory network inference using fused LASSO on multiple data sets. (mpg.de)
We have ongoing interests in the systems level analysis and reconstruction of regulatory networks, inference of enhancer-promoter contacts, predictive models of gene expression and integration of three-dimensional chromatin structure with one-dimensional epigenetic measurements in the context of cancer, malaria, asthma and several autoimmune diseases. (ucsd.edu)
This project will focus on developing regulatory network inference methods for the joint analysis of gene expression and histone modification data from several different types of tumor infiltrating lymphocytes, which are gathered from a cohort of patients with solid tumors. (ucsd.edu)
Inference of inter-species gene regulatory networks based on gene expression data is an important computational method to predict pathogen-host interactions (PHIs). (rna-seqblog.com)

Understand and simulate the development of complex traits such as biological pathways (Senescence and Jasmonate) and plant morphology. (niab.com)
Traditional regulatory and commercialisation pathways to licensed products seem to be prohibitive for ultra-small patient populations. (cdc.gov)

The isoform encoded by the unspliced mRNA, XBP1(U), is constitutively expressed, and thought to function as a negative feedback regulator of XBP1(S), which shuts off transcription of target genes during the recovery phase of ER stress. (cancerindex.org)
A cis-acting mechanism mediates transcriptional memory at Polycomb target genes in mammals. (babraham.ac.uk)

Subsequent transcriptomic analysis identified genes differentially regulated by MeJA+NaCl treatment and NaCl alone. (frontiersin.org)
Multiple miRNA-mRNA prediction databases were searched by differentially expressed genes (DEGs) to obtain pairs of a miRNA-DEG regulatory network. (frontiersin.org)
Using a treatment and sex interaction model, 13 and 4 differentially expressed genes were identified in liver and muscle respectively. (biomedcentral.com)
Sex-specific differentially expressed (DE) genes were identified in both sexes. (biomedcentral.com)

We provide a temporal and spatial framework for integrating the flowering GRN with cellular changes at the SAM and highlight the role of local regulation of GA. (jic.ac.uk)
Gene-Expression Analysis of Cell-Cycle Regulation Genes in Virus-Infected Rice Leaves. (routledge.com)
PageMan analysis revealed several significantly enriched categories altered by MeJA+NaCl treatment, compared with NaCl treatment alone, including genes involved in secondary metabolism, glutathione-based redox regulation, cell cycle, transcription factors (TFs), and other signal transductions (such as calcium and ROS). (frontiersin.org)
Our observations suggest that latent phenotypes are pervasive in regulatory circuits, and may thus be an important source of evolutionary adaptations and innovations involving gene regulation. (biomedcentral.com)
Alongside, the commission intends to allocate approximately €50 million via the Horizon 2020 Framework Program for Research and Innovation for around 10 basic and applied-research projects to better understand endocrine disruption and develop tools for their assessment and regulation. (medscape.com)

Her lab has recently worked with gene expression patterns during sexual reproduction and regeneration of syllids. (uni-goettingen.de)
My research focuses on the study of macroevolutionary patterns of taxononomic diversity, morphological disparity and biogeographic distribution in a phylogenetic framework. (uni-goettingen.de)
Elucidating multi-input processing 3-node gene regulatory network topologies capable of generating striped gene expression patterns. (vliz.be)
Experimental [ 21 ] and theoretical [ 22 ] studies hint that gene regulatory circuits harbor latent phenotypes because their gene expression patterns often vary when a circuit is exposed to distinct external stimuli. (biomedcentral.com)
Surprisingly, we discover using ODeGP that increasing cell density results in rapid generation of oscillations in the Bmal1 gene, thus highlighting our method's ability to discover unexpected and new patterns. (edu.in)
For an organism that lacks a high-quality reference genome, the de novo assembly of its transcriptome is a useful method for researchers to find the transcripts or genes responsive to various treatments and to better understand the expression patterns of the candidate genes. (biomedcentral.com)
Strong selection pressures experienced during one stage of development may differ from those experienced in other stages, and with consequences for the underlying patterns of gene expression. (lu.se)
We want to understand differences in life stage-specific gene expression in the peacock fly and relate these patterns to signatures of selection across the genome. (lu.se)

Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. (nature.com)
These differences largely result from limited knowledge regarding the optimized sequencing depth and assembler for transcriptome assembly of structurally complex plant species genomes. (biomedcentral.com)
We employed different amounts of RNA-sequencing data, ranging from 4 to 84 Gb, to assemble the tea plant transcriptome using five well-known and representative transcript assemblers. (biomedcentral.com)
The present study compares the performance of five representative transcript assemblers and investigates the key factors that affect the assembly quality of the transcriptome of the tea plants. (biomedcentral.com)

The species-specific plant Pathway Genome Databases (PGDBs) based on the BioCyc platform provide a conceptual model of the cellular metabolic network of an organism. (oregonstate.edu)
However, that influence is hard to see from the traditional standpoint, so we need to encourage alternative conceptual frameworks. (uncommondescent.com)

The goal of this project is to model the natural variation in gene expression across many immune cell types using an already established database at LJI ( https://dice-database.org ) and to identify cell type-specific epigenetic regulators of important immune genes. (ucsd.edu)
A particular focus has been the Polycomb epigenetic system, where we have proposed an all-or-nothing epigenetic switching mechanism, with epigenetic gene silencing directly antagonised by transcription. (babraham.ac.uk)
Epigenetic mechanisms lead to functionally relevant changes in gene expression without altering the genetic code and have been implicated in permanent effects of transient environmental hazardous exposures/stressors on health. (fellowshipbard.com)
The most stable epigenetic change is DNA (de)methylation, which can persist for years and has been associated with long-lasting alterations in gene expression. (fellowshipbard.com)

High levels of Na + in the rhizosphere can cause detrimental effects on plants, leading to photosynthetic inhibition, enzyme deactivation, and metabolic alterations ( Yang and Guo, 2018 ). (frontiersin.org)
They exist in biological systems as different as promiscuous enzymes and genome-scale metabolic reaction networks, and can give rise to evolutionary adaptations and innovations. (biomedcentral.com)
Of interest, we have observed in a rodent transgenerational model of intrauterine growth restriction (IUGR) that a diet supplemented with essential nutrients, yet unaltered in its caloric content, prevents adult metabolic disease and is associated with abrogation of reprogrammed gene expression. (nih.gov)
The jQMM library presented here provides an open-source, Python-based framework for modeling internal metabolic fluxes and leveraging other -omics data for the scientific study of cellular metabolism and bioengineering purposes. (biomedcentral.com)

Comparing these synthetic profiles to empirically measured gene expression data gives some indication how well a computational RGN model corresponds to the real RGN. (uea.ac.uk)

Pharmacogenomics provides an opportunity to identify candidate genes for studying disease progression and outcomes. (cambridge.org)

Plant J . 2022 Apr;110(2):529-547. (nih.gov)
Current Opinion in Plant Biology (2022) 69: 102262. (biologists.com)

It regulates Sp7 protein expression and induces expression of major bone matrix protein genes, such as Col1a1, Spp1, Ibsp, Bglap2, and Fn1 ( 7 , 8 ). (frontiersin.org)

Soil salinization is progressively becoming a detrimental constraint on plant growth and productivity ( Singh, 2021 ). (frontiersin.org)
Plants (2021) 11 (1): 56. (biologists.com)

The analysis is focused also in transcription factor genes and their potential regulatory networks associated with genes participating in C3 and C4 photosynthesis. (sciety.org)
This gene encodes a transcription factor that regulates MHC class II genes by binding to a promoter element referred to as an X box. (cancerindex.org)
This gene product is a bZIP protein, which was also identified as a cellular transcription factor that binds to an enhancer in the promoter of the T cell leukemia virus type 1 promoter. (cancerindex.org)

Regulatory gene networks are generally a central biological mechanism of decoding genetic information that confers adaptive capabilities into phenotypic responses and other traits. (uea.ac.uk)
High-Throughput Approaches for Characterization and Efficient Use of Plant Genetic Resources. (routledge.com)
Both circuits and gene expression phenotypes that are robust to genetic change are associated with a greater number of latent phenotypes. (biomedcentral.com)
So, as new evolutionary optima have been set by environmental changes (e.g., domestication, management practices, biotic or abiotic pressures) or major shifts in genetic background, plant breeders have selected better-adapted genotypes while pursuing faster genetic gains through technological innovations and scientific breakthroughs. (springer.com)
These domestication traits likely consisted of a few major genes controlling dramatic changes in crop physiology, as is suggested by genetic studies comparing maize to its ancestor teosinte (Doebley et al. (springer.com)
Synthetic genetic circuits are powerful tools for programing these computations, where transcription-regulatory networks and DNA recombination are the two dominant paradigms for implementing these systems. (biorxiv.org)
Dose adjustments have been recommended for efavirenz due to genetic variations in CYP2B6 gene, which results in HIV patients in SSA requiring a reduced dose [ Reference Mukonzo 4 , Reference Dhoro 5 ]. (cambridge.org)
In the last decade, many studies have generated the transcriptomes of tea plants at different developmental stages or under abiotic and/or biotic stresses to investigate the genetic basis of secondary metabolites that determine tea quality. (biomedcentral.com)
The student will evaluate gene expression in relation to measures of genetic diversity, differentiation, and neutrality across the genome to evaluate whether the sequences or the flanking regions of genes with stage-specific expression demonstrate signs of selection. (lu.se)
A framework for identifying targets for individualized therapy in genetic disease. (cdc.gov)
This framework identified multiple eligible mutations among 235 people with the genetic disorder ataxia-telangiectasia. (cdc.gov)

2020). Genotypic variation in leaf and whole-plant water use efficiencies are close related in bread wheat genotypes under well-watered and water-limited conditions during grain filling. (niab.com)
Plants (2020) 9 (5): 585. (biologists.com)
Plant Communications (2020) 1 (5): 100080. (biologists.com)

In this context, we work with both histone modification memory systems, as well as on DNA methylation, collaborating with experimentalists in systems ranging from plants to mammalian stem cells. (babraham.ac.uk)
In this chapter, we describe a generic stochastic modeling framework that can be used to capture histone modification dynamics and associated molecular processes-including transcription and read-write feedback by chromatin modifying complexes-at individual genomic loci. (babraham.ac.uk)

In this respect, he is using a broad range of methods including immunohistochemical analyses, histological staining procedures and ultrastructural investigations as well as gene expression analyses and phylogenomic approaches. (uni-goettingen.de)
This paper analyses the de-etiolation process in Gynandropsis gynandra as a proxy to catch photosynthesis genes whose expression is affected using time course RNA-seq and DNaseI-seq. (sciety.org)
Few nutrigenomics studies have used a high-throughput RNA-Sequencing (RNA-Seq) approach, despite great potential of RNA-Seq data in gene expression quantification and in co-expression network analyses. (biomedcentral.com)
This will include co-expression network analyses to identify groups of genes that are expressed similarly and might belong to the same or linked gene regulatory networks. (lu.se)

DAP-Seq of MYB14/MYB15 was combined with aggregate gene co-expression networks (GCNs) built from more than 1400 transcriptomic datasets from leaves, fruits, and flowers to narrow down bound genes to a set of high confidence targets. (nih.gov)
Gene co-expression networks are usually constructed using datasets generated by high-throughput gene expression profiling technologies such as Microarray or RNA-Seq. (wikipedia.org)
Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
Methods: We utilized bulk RNA-sequencing data from The Cancer Genome Atlas Breast Cancer Cohort and the GSE42568 and GSE146558 datasets to identify BC-specific m7G-modification regulators and associated genes. (bvsalud.org)
Although the total number of assembled transcripts increased with increasing sequencing data, the proportion of unassembled transcripts became saturated as revealed by plant BUSCO datasets. (biomedcentral.com)

MicroRNA-mRNA co-sequencing identifies transcriptional and post-transcriptional regulatory networks underlying muscle wasting in cancer Cachexia. (vliz.be)
It has been found that upon accumulation of unfolded proteins in the endoplasmic reticulum (ER), the mRNA of this gene is processed to an active form by an unconventional splicing mechanism that is mediated by the endonuclease inositol-requiring enzyme 1 (IRE1). (cancerindex.org)
Recently, miRNA-messenger RNA (mRNA) regulatory relationships have been confirmed during biological processes, including osteogenic differentiation. (frontiersin.org)
The miRNA-mRNA interactions were verified by dual-luciferase reporter gene assays and experiments using mimics miRNA or their inhibitors. (frontiersin.org)

Compared to a GRN, a GCN does not attempt to infer the causality relationships between genes and in a GCN the edges represent only a correlation or dependency relationship among genes. (wikipedia.org)

The Plant Cell (2023) 35 (8): 2929. (biologists.com)
Plants (2023) 12 (5): 1128. (biologists.com)

In addition, circRNAs can regulate gene expression at transcriptional or post-transcriptional levels by titrating microRNAs (miRNAs), regulating transcription and interfering with splicing [ 13 , 14 ]. (ijbs.com)

The integration of DAP-Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome-wide approaches in the context of non-model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism. (nih.gov)
The idea that genes associated with C4 photosynthesis required changes in cis-regulatory elements to be incorporated in different gene regulatory networks during the evolution of C4 photosynthesis in certain species is intuitive, as the authors mention during the discussion. (sciety.org)
Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology. (nature.com)
The study of specialized tissue domains and their interactions is essential for a comprehensive understanding of the function of biological systems, including the wide variety of plant species. (nature.com)
Advanced machine learning not only detects diseases but also helps to discover gene regulatory networks and select the genomic sequence to develop resistance in crop species and to mark pathogen effectors. (plantprotection.pl)
Leaf-Net: A computer vision system for automatic plant species identification. (plantprotection.pl)
Early plant breeders domesticated useful species and unintentionally promoted domestication traits, such as reduced shattering in maize (Stitzer and Ross-Ibarra 2018 ) and grain composition in rice (Kovach et al. (springer.com)
Flower are present in a great number of different plants in nature, including over 200,000 species of dicotyledonous plants. (ens-lyon.fr)
Basically, if miRNA repression is evolutionarily important for a gene, we expect the miRNA binding sites to be shared across closely related species. (lu.se)
The student will create a pipeline for identifying conserved miRNA binding sites across several sparrow species using TargetScan as a framework. (lu.se)

Breeding for Sustainability: Utilizing High-Throughput Genomics to Design Plants for a New Green Revolution. (routledge.com)
In recent years, thanks to the development of high-throughput sequencing technology and other techniques [ 3 ], an increasing number of circRNAs have been identified in thousands of living organisms including archaea, plants and animals [ 4 - 7 ]. (ijbs.com)
However, two major problems in de novo assembly have obstructed progress in high-throughput transcript identification: 1) most of the transcripts assembled are not full-length, and 2) only a certain proportion of the genes can be assembled. (biomedcentral.com)

To these ends his team is also developing methods to characterize gene function in this nontraditional model organism. (uni-goettingen.de)
Recently, co-expression networks are used to analyze single cell RNA-Seq data, in order to better characterize the gene to gene relations in a cohort of cells from a specific cell type. (wikipedia.org)
Heterogeneous network flow and Petri nets characterize multilayer complex networks. (unifi.it)

2018) Functional Mapping of Quantitative Trait Loci (QTLs) Associated with Plant Performance in a Wheat MAGIC Mapping Population. (niab.com)

Such frameworks allow analysis of the genome-scale expression data to understand changes in the overall metabolisms of an organism (or organs, tissues, and cells) in response to various extrinsic (e.g. developmental and differentiation) and/or extrinsic signals (e.g. pathogens and abiotic stresses) from the surrounding environment. (oregonstate.edu)

Light responsive elements, especially G-, E- and GT-boxes were over-represented in accessible chromatin around C 4 genes. (sciety.org)
We hypothesized that a high fat diet in non-human primates would induce changes in hepatic chromatin structure resulting in altered expression of fetal genes critical to the development of childhood and adult obesity. (nih.gov)

MicroRNAs (miRNAs) are well-recognized for their abilities to regulate gene expression post-transcriptionally in plants and animals. (frontiersin.org)

Ability to deploy across high performance computing systems sophisticated mathematical modeling frameworks, data analysis pipelines and bioinformatics workflows to address complex biological phenomena. (vliz.be)

The resulting matrix, called the adjacency matrix, represents the graph of the constructed gene co-expression network. (wikipedia.org)

The application of such technologies will require to reliably estimate the effect of loci in plant genomes by avoiding the situation where the number of loci assayed ( p ) surpasses the number of plant genotypes ( n ). (springer.com)
Ewan led the analysis of the Human Genome gene set, mouse and chicken genomes and the ENCODE project, focusing on non-coding elements of the human genome. (nottingham.ac.uk)

25 years after establishing Nature Genetics as the founding editor, he launched The CRISPR Journal , a new peer-review journal on gene editing (published by Mary Ann Liebert Inc.) He has also served as editor-in-chief of Cell Press and publisher of Chemical & Engineering News . (nottingham.ac.uk)

An MC3T3-E1-based microarray dataset (accessioned as GSE46400) downloaded from the Gene Expression Omnibus included MC3T3-E1 cells with or without 14-day osteoblast differentiation osteoblast induction. (frontiersin.org)

Modules or the highly connected subgraphs in gene co-expression networks correspond to clusters of genes that have a similar function or involve in a common biological process which causes many interactions among themselves. (wikipedia.org)
A developmental systems perspective on epistasis: computational exploration of mutational interactions in model developmental regulatory networks. (vliz.be)
Interactions between these genes and with other non-ABC genes are necessary to establish the final pattern of concentric circles of ABC gene expression. (ens-lyon.fr)
To understand this process, the expression and the interactions between these genes in the early stages of development are investigated experimentally. (ens-lyon.fr)

In this project we will develop and use a statistsical approach to discriminate alternative RGN models based on the consistence of their synthetic profiles with a data set of empirical gene expression measurements. (uea.ac.uk)
They gathered the measurement data of medical laboratory tests (e.g. hemoglobin level ) for a number of patients and they calculated the Pearson correlation between the results for each pair of tests and the pairs of tests which showed a correlation higher than a certain level were connected in the network (e.g. insulin level with blood sugar). (wikipedia.org)
Butte and Kohane used this approach later with mutual information as the co-expression measure and using gene expression data for constructing the first gene co-expression network. (wikipedia.org)
The input data for constructing a gene co-expression network is often represented as a matrix. (wikipedia.org)
If we have the gene expression values of m genes for n samples (conditions), the input data would be an m×n matrix, called expression matrix. (wikipedia.org)
Overall, the data support a model in which rapid and robust C 4 gene expression following light exposure is generated through modifications in cis to allow integration into high-level transcriptional networks including those underpinned by conserved light responsive elements. (sciety.org)
Although these techniques can provide spatially resolved or cell-type-specific gene expression data, they each have inherent limitations. (nature.com)
Our aim is to use the potential of RNA-Sequencing data in order to evaluate the effect of an EO supplementary diet on gene expression in both lamb liver and muscle. (biomedcentral.com)
The student will analyze gene expression in a reference-based pipeline using existing RNA sequencing data from larvae, pupae, and adult flies from each of the two host forms. (lu.se)
A concluding section stresses the need for a new framework of safety assessment that relies on a characterization of food in terms of its molecular, biological, and chemical properties, and uses the resulting data to determine the need for toxicity tests. (who.int)

The analysis of MYB14, MYB15, and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 of 47 STS family genes. (nih.gov)
We used multiple m7G databases and RNA interference to validate the relationships between BC-specific m7G-modification regulators (METTL1 and WDR4) and related genes. (bvsalud.org)
From the article: 'In the past two years, two gene therapies have been withdrawn from the European market for business reasons after earning regulators' approval. (cdc.gov)

A good number of methods have been developed for constructing gene co-expression networks. (wikipedia.org)
Pearson's correlation coefficient, Mutual Information, Spearman's rank correlation coefficient and Euclidean distance are the four mostly used co-expression measures for constructing gene co-expression networks. (wikipedia.org)

Transcription Factors, Gene Regulatory Networks, and Agronomic Traits. (routledge.com)
There are other hypothesis on how transcriptional networks could be rewired to generate novel traits that are not explored during this work. (sciety.org)
Here, we discuss approaches to avoid this curse of dimensionality ( n ≪ p ), which will involve analyzing intermediate phenotypes such as molecular traits and component traits related to plant morphology or physiology. (springer.com)
2007 ). Early domestication phases were followed by long periods of deliberate selection for increased performance, probably involving mass selection for traits with a complex polygenic basis, such as plant environmental adaptations and yield (Breeding 1.2). (springer.com)

Having gene expression profiles of a number of genes for several samples or experimental conditions, a gene co-expression network can be constructed by looking for pairs of genes which show a similar expression pattern across samples, since the transcript levels of two co-expressed genes rise and fall together across samples. (wikipedia.org)
And when it overlaid with a segmented image of the experimental area, only points identified as plants had their temperature values maintained. (preprints.org)

Using network based analysis, different clusters of co-expressed genes that were highly correlated to the diet were detected in males vs. females, in agreement with DE analysis. (biomedcentral.com)

In W. Busch (Ed.), Plant Genomics (pp. 251-266). (ncsu.edu)

On convergence for hybrid models of gene regulatory networks under polytopic uncertainties: a Lyapunov approach. (unifi.it)

CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs. (mpg.de)

Early identification of plant diseases can be achieved through machine learning approaches. (plantprotection.pl)
In this review, new advancements in plant science through machine learning approaches have been discussed. (plantprotection.pl)
Solving current limitations of deep learning based approaches for plant disease detection. (plantprotection.pl)
Nutrigenomics investigations represent innovative approaches in understanding the relation between diet effect and gene expression related to the animal performance. (biomedcentral.com)

whereas in a gene regulatory network (GRN) a directed edge connects two genes, representing a biochemical process such as a reaction, transformation, interaction, activation or inhibition. (wikipedia.org)
Propagation of kinetic uncertainties through a canonical topology of the TLR4 signaling network in different regions of biochemical reaction space. (vliz.be)

In all cases, gene expression is modified such that C 4 proteins accumulate to levels matching those of the photosynthetic apparatus. (sciety.org)
The FACS and INTACT methods require plant transgenic lines respectively expressing fluorescent proteins or the biotinylated nuclear envelope protein in the cell type of interest. (nature.com)
Potential hazards identified include the activation of silent genes and the creation of new toxins, changes in nutritional content or in the bioavailability of nutrients, and allergic reactions to new or altered proteins. (who.int)

For instance, in a microarray experiment the expression values of thousands of genes are measured for several samples. (wikipedia.org)

This study will be of significance in helping the tea research community obtain better sequencing and assembly of tea plant transcriptomes under conditions of interest and may thus help to answer major biological questions currently facing the tea industry. (biomedcentral.com)

This work provides a transcriptional framework to study de-etiolation in G. gynandra and genomic and epigenomic insights on the gene regulatory networks underlying this process. (sciety.org)

Gene co-expression networks are of biological interest since co-expressed genes are controlled by the same transcriptional regulatory program, functionally related, or members of the same pathway or protein complex. (wikipedia.org)

Based on the state-of-play in Belgium, this chapter discusses examples of regulatory journeys of applications with genetically modified viral vectors and novel vaccine candidates that have been reviewed by GMO national competent authorities in Belgium and in Europe. (intechopen.com)

The Arhgap11a, H2afx, Chek2, Dlgap5, and Chek1 were hub genes downregulated in MC3T3-E1 cells after osteogenic differentiation, verified by RT-qPCR results. (frontiersin.org)
We develop methods that are based in statistics, machine learning, optimization and graph theory to understand how changes in the 3D genome affect cellular outcome such as development, differentiation and gene expression. (ucsd.edu)

A network property necessary for concentration robustness. (mpg.de)

Cells can sense the presence of interaction partners by a range of receptors and, via complex regulatory networks, specifically react by changing the expression of many of their genes. (rna-seqblog.com)

Computational models of regulatory networks can be used in "forward" simulations to generate synthetic gene expression profiles. (uea.ac.uk)
The MDP will use transsys, a computational framework for RGN modelling. (uea.ac.uk)

My paper on reconstruction of Gene Regulatory Networks reports the SimGenex framework which can be used to in silico simulate both the wetlab and artificial life, from cell to organ to plant. (niab.com)

In this study, a heterogeneous network was constructed by employing the circRNA expression profiles, disease phenotype similarity and Gaussian interaction profile kernel similarity. (ijbs.com)
A Resilient Consensus Protocol for Networks with Heterogeneous Confidence and Byzantine Adversaries. (unifi.it)

The Use of Omics Databases for Plants. (routledge.com)
A subset of high quality and rare information, retrieved and organized by systematic literature- searching tools from existing databases, and related to a subset of genes functioning together in '-omic' sciences. (genomicglossaries.com)

Changes in chloroplast ultrastructure and C 4 gene expression were coordinated and rapid. (sciety.org)

His efforts are focused on the identification of the complete set of biomineralizing effector genes in the pulmonate gastropod Lymnaea stagnalis , and on identifying the gene regulatory and cellular communication events that coordinate the initiation of shell formation in the early snail embryo. (uni-goettingen.de)

Ongoing studies find more parallels between the complex apoptosis regulatory networks of vertebrates with locusts and beetles, but not with dipteran flies. (uni-goettingen.de)

Nonlinear dynamics and noise actuated by the cycle of gene inactivation in stochastic transcription. (zbmath.org)

Anatomy17

Organisms21

Chemicals and Drugs21

Analytical, Diagnostic and Therapeutic Techniques and Equipment25

Psychiatry and Psychology2

Phenomena and Processes63

Disciplines and Occupations4

Information Science17

Health Care9

Arabidopsis7

Inference4

Pathways2

Target genes2

Differentially4

Regulation5

Patterns8

Transcriptome4

Conceptual2

Epigenetic4

Metabolic4

Measured gene expression1

Candidate genes1

20222

Protein genes1

20212

Transcription factor3

Genetic11

20203

Histone modification2

Analyses4

Datasets5

MRNA4

Infer1

20232

Post-transcriptional1

Species10

High-throughput3

Characterize3

20181

Genome-scale1

Chromatin2

Regulate gene expression1

Bioinformatics1

Constructed gene co-expression network1

Genomes2

Genetics1

Expression Omnibus1

Interactions4

Data10

Regulators3

Constructing gene co-expression2

Traits4

Experimental2

Clusters1

Genomics1

Models of gene1

Subgraphs1

Approaches4

Biochemical2

Proteins3

Microarray1

Sequencing1

Epigenomic1

Functionally1

Genetically modified1

Differentiation2

Robustness1

Complex regulatory1

Computational2

Reconstruction1

Heterogeneous2

Databases2

Chloroplast1

Cellular1

Apoptosis1

Stochastic1