Evolutionary gene expression regulation bioinformatics gene regulatory networks. Medical search. Frequent questions

His current research interests focus on natural genetic variation and evolutionary genomics of plants. (elifesciences.org)
To better understand conservation of enhancer activity, we recently used a comparative genomics approach that integrates temporal expression and epigenetic profiles in an innate immune system. (umassmed.edu)
2023. Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives. (openwetware.org)
Bioinformatics Plant genomics and genome evolution, transposable elements, and regulatory gene evolution. (uga.edu)
Plant Biology Genome bioinformatics, ecological and evolutionary genomics of yeast. (uga.edu)
Hannenhalli's current research focuses on comparative genomics, transcriptional regulation, and evolution. (umd.edu)
Dirk Schübeler has done important work in epigenomics and regulatory genomics, in particular with the dynamics of genome-wide methylation patterns, their role in gene regulation, and the interplay between chromatin state and the actions of transcription factors. (unibas.ch)
In addition, I am looking into the genome annotation and comparative genomics of Tembusu to identify genes selected when adapting to nutrient poor soils. (helsinki.fi)
The group uses integrative interdisciplinary approaches-merging systems and molecular biology, and functional genomics-to map, reconstruct, and characterize gene networks that control fundamental biological processes ranging from transcription and signal transduction to cellular response to changes in the environment. (rajajothi.com)

Each time a cell divides, two cells result which, although they contain the same genome in full, can differ in which genes are turned on and making proteins. (wikipedia.org)
With the availability of the high-quality chromosome-level genome assembly for BT that we developed recently, we identified 91 RwFAR1/FRS-like genes, a significant expansion in contrast to 52 in Rosa chinensis 'Old Blush' (OB), a founder genotype in modern rose domestication. (kib.ac.cn)
The Human Genome Project (HGP) was the international, collaborative research program whose goal was the complete mapping and understanding of all the genes of human beings. (umassmed.edu)
Genome wide association studies (GWAS) have identified mutations in non-coding regulatory regions as the most common features associated with human disease. (umassmed.edu)
These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. (biomedcentral.com)
We examined each of these small RNA classes with respect to the newly assembled tammar wallaby genome for gene and repeat features, salient features that define their canonical sequences, and the constitution of both highly conserved and species-specific members. (biomedcentral.com)
Mapping all miRNAs to the tammar genome and comparing target genes among tammar, mouse and human, we identified 163 conserved target genes. (biomedcentral.com)
Small RNAs play important roles in many aspects of pre- and post-transcriptional gene regulation, epigenetic modifications, chromosome segregation and genome structure. (biomedcentral.com)
The comparative genome-wide analysis and mode of evolution of KCS and ELO gene families have not been investigated in tetraploid Brassica carinata and its diploid progenitors. (nature.com)
She has a strong background in evolutionary bioinformatics and examined problems related to the origin and genome evolution of eukaryotic microbes and archaea. (unibas.ch)
Assembly of the human genome is one of the greatest achievements of bioinformatics. (ind.in)
As whole genome sequences became available, again with the pioneering work of Frederick Sanger, the term bioinformatics was re-discovered to refer to the creation of databases such as GenBank in 1982. (ind.in)
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)
A total of 117 genes encoding MATE transporters were identified from the whole genome sequence of soybean ( Glycine max ), which were denominated as GmMATE1 - GmMATE117 . (biomedcentral.com)
1 It turns out that the bacterial genome has a few high-level instructions that control a few middle-level processes, that in turn control a massive number of protein-coding genes. (creation.com)
Therefore, to address the growing volumes of available genomic sequence, a number of algorithms that identify putative cis-regulatory modules and transcription factor binding sites using evolutionary comparisons, whole-genome data, and known descriptions of transcription factor binding sites, have been successfully developed. (biomedcentral.com)
I am interested in evolutionary history and population genetics of plants and animals, especially in the reorganization of genome elements in accompany with species divergence. (helsinki.fi)
These genes which are identified could then be used in genome editing in other tree species for reforestation projects. (helsinki.fi)
The transcriptomic and epigenomic regulatory landscape of the MAC genome, which has 80% protein-coding genes and short intergenic regions, is poorly understood. (uni-frankfurt.de)
In this thesis, we developed novel tools, and employed several bioinformatics and machine learning methods to characterise the regulatory landscape of the Paramecium's (epi)genome. (uni-frankfurt.de)
100.000 cCREs in total), dispersed within the genome and present in cis-regulatory regions of ~81% of human genes, as calculated following gene enrichment analysis. (mdpi.com)
Integrated multi-omics analyses and genome-wide association studies reveal prime candidate genes of metabolic and vegetative growth variation in canola. (ipk-gatersleben.de)
Candidate clusters are cloned into reporter genes, transformed into the genome, and tested for in vivo activity by in situ hybridization experiments. (nyu.edu)

GRN also play a central role in morphogenesis, the creation of body structures, which in turn is central to evolutionary developmental biology (evo-devo). (wikipedia.org)
She is currently a Senior Investigator leading the Chromosome Structure and Epigenetics Mechanism Unit within the Laboratory of Receptor Biology and Gene Expression at the Center for Cancer Research of the NCI/NIH in Bethesda. (elifesciences.org)
Sridhar Hannenhalli is a professor in the Department of Cell Biology and Molecular Genetics and holds joint appointments in the Center for Bioinformatics and Computational Biology (CBCB) and UMIACS. (umd.edu)
He has served on program committee for numerous bioinformatics conferences and chaired Workshop on Algorithms in Bioinformatics (WABI) and Research in Computational Molecular Biology (RECOMB) conferences. (umd.edu)
The BioVis aims to educate, inspire, and engage bioinformatics and biology researchers in state-of-the-art visualization research and visualization researchers in problems in biological data visualization. (iscb.org)
Bioinformatics is a distinct science from biological computation , the latter being a computer science and computer engineering subfield using bioengineering and biology to build biological computers , whereas bioinformatics simply uses computers to better understand biology. (ind.in)
Bioinformatics is similar to computational biology and has similar aims to it but differs on scale: whereas bioinformatics works with basic biological data (e.g. (ind.in)
Understanding the origin of novel and beneficial traits - evolutionary adaptations and innovations - is a challenge central to biology. (biomedcentral.com)
Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. (biomedcentral.com)
We first give an overview of network representation frequently used in biology: what nodes and edges represent, and review its application in preclinical research to date. (biomedcentral.com)
Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. (biomedcentral.com)
From the clinicians' point of view, it is necessary to bridge the gap between theoretical network biology and practical biomedical research, in order to improve the diagnosis, prevention, and treatment of the world's major diseases. (biomedcentral.com)
Network representations have been widely used in physics and social science for decades, and are now among the most frequently used tools in systems biology. (biomedcentral.com)
In this review, we aim to improve the understanding of challenges in biomedical research and establish a common ground between clinicians and systems biologists to further promote the application of network biology in translational medicine. (biomedcentral.com)
I am interested in the evolutionary biology and especially how genes and genomes evolve. (helsinki.fi)
Over the years, the group has successfully identified and characterized many genes with previously unknown roles in ES cell biology. (rajajothi.com)
STARR-seq can be used to test thousands of enhancer candidates in parallel, systematically identify enhancers directly based on their activity across large genomic regions or entire genomes, and to ask fundamental questions of transcriptional regulation and enhancer biology. (starklab.org)
One of the most enduring concepts in the field of developmental biology is the idea that expression gradients contain multiple thresholds that control and position different cell fates. (nyu.edu)
Network Biology Approaches to Identify Molecular and Systems-Level Difference. (earlham.ac.uk)

Post-transcriptional regulation in multicellular organisms is mediated by microRNAs. (frontiersin.org)
Transcriptional regulation of the genes in metabolic pathways is a highly successful strategy, which is virtually universal in microorganisms. (lu.se)
With a minimalist model of metabolism, cell growth and transcriptional regulation in a microorganism, we explore how the interaction between environmental conditions and gene regulation set the growth rate of cells in the phase of exponential growth. (lu.se)
Citation: Troein C, Ahre´n D, Krogh M, Peterson C (2007) Is Transcriptional Regulation of Metabolic Pathways an Optimal Strategy for Fitness? (lu.se)
INTRODUCTION broken, which in realistic situations can severly constrain the Transcriptional regulation of effector genes is a highly successful regulatory options. (lu.se)
He studies the process of cell diversification via transcriptional and post-transcriptional regulation, with the help of targeted transcriptomic approaches and specific gene disruption. (embl.de)
Pierre and his group's main focus is to understand principles of transcriptional regulation in development and cancer. (embl.de)

A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the function of the cell. (wikipedia.org)
Some proteins though serve only to activate other genes, and these are the transcription factors that are the main players in regulatory networks or cascades. (wikipedia.org)
In parallel with this process of building structure, the gene cascade turns on genes that make structural proteins that give each cell the physical properties it needs. (wikipedia.org)
At one level, biological cells can be thought of as "partially mixed bags" of biological chemicals - in the discussion of gene regulatory networks, these chemicals are mostly the messenger RNAs (mRNAs) and proteins that arise from gene expression. (wikipedia.org)
A typical gene regulatory network looks something like this: The nodes of this network can represent genes, proteins, mRNAs, protein/protein complexes or cellular processes. (wikipedia.org)
Edges between nodes represent interactions between the nodes, that can correspond to individual molecular reactions between DNA, mRNA, miRNA, proteins or molecular processes through which the products of one gene affect those of another, though the lack of experimentally obtained information often implies that some reactions are not modeled at such a fine level of detail. (wikipedia.org)
In this work, we present a different paradigm for predicting miRNA-regulated genes based on the encoded proteins. (frontiersin.org)
With the wealth of data accumulated from completely sequenced genomes and other high-throughput experiments, global studies of biological systems, by simultaneously investigating multiple biological entities (e.g. genes, transcripts, proteins), has become a routine. (biomedcentral.com)
Such technological improvements enable a large number of molecules, including genes, transcripts, and proteins to be simultaneously measured in different conditions over time. (biomedcentral.com)
It controls the interaction network of hundreds of thousands of proteins. (creation.com)
Specific sites within such regions are recognized by regulatory proteins (transcription factors), which act upon binding as transcriptional repressors or activators, controlling the rate of transcription. (biomedcentral.com)
A substantial portion of the regulatory interactions in the higher eukaryotic cell are mediated by simple sequence motifs in the regulatory segments of genes and (pre-)mRNAs, and in the intrinsically disordered regions of proteins. (biomedcentral.com)
Our working hypothesis is that there are repressors that interfere with Bcd-dependent activation, and that combinations of activating and repressing proteins position and register multiple target gene expression boundaries. (nyu.edu)

Post-genomic analysis techniques such as next-generation sequencing have produced vast amounts of data about micro organisms including genetic sequences, their functional annotations and gene regulatory interactions. (uni-bielefeld.de)
Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions. (uni-bielefeld.de)
Kelly Dyer Professor Genetics Molecular evolution and evolutionary genetics, in particular genetic conflict, sex chromosome evolution, genetics of adaptation and speciation, and host-parasite interactions. (uga.edu)
Both circuits and gene expression phenotypes that are robust to genetic change are associated with a greater number of latent phenotypes. (biomedcentral.com)
Successful development of ES cell-based therapies not only depends on our understanding of the genes and pathways that constitute the genetic network governing ES cell homeostasis, but also the mechanisms that maintain the intricate homeostatic balance between self-renewal and differentiation. (rajajothi.com)
Mechanisms that coordinate the activities of master regulators, signaling pathways, and epigenetic features remain poorly understood, owing largely to incomplete characterization of the genetic network underlying ES cells. (rajajothi.com)
To better understand the genetic network governing ES cell self-renewal and differentiation, the group uses interdiscplinary approaches to generate testable hypotheses. (rajajothi.com)
We train our algorithms on large resources of genetic variation, DNA binding and gene expression data across multiple species, tissues and treatments. (ipk-gatersleben.de)
We use our toolbox to estimate the regulatory impact of structural genetic variation, highlight gene candidates in GWAS studies and design gene editing strategies for gene expression modulation. (ipk-gatersleben.de)
Our other focus is are methods for integration of multi-omic data and identification of causal/predictive interactions between genetic variation, gene expression, metabolite levels and emergence of crop quality traits. (ipk-gatersleben.de)
In our first experiments, we have used genetic experiments to flatten the Bcd gradient, and then measured the amounts of Bcd required for activating specific target genes. (nyu.edu)
Expansion of gene families facilitates robustness and evolvability of biological processes but impedes functional genetic dissection of signalling pathways. (earlham.ac.uk)
Substantial genetic and biochemical similarities exist between resistance determinants in antimicrobial agent-producing actinomycetes and resistance genes found in gram-positive and gram-negative pathogens ( 6 - 9 ). (cdc.gov)

Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes. (openwetware.org)
Small RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. (biomedcentral.com)
Methods of this type assume that regulatory regions are highly conserved in cross-genomic comparison, and conserved segments can be extracted from evolutionary related genomes. (biomedcentral.com)
Furthermore, it is still an open question as to how many genomes are sufficient for reliable extraction of regulatory regions. (biomedcentral.com)
Genomes contain information from the past, from different climate conditions, and this may help in identifying future "evolutionary winners and losers" and hopefully suggest ways to prevent the impending loss of biodiversity. (helsinki.fi)
STARR-seq allows screening multiple cis-regulatory genomes in a single cell type, i.e. in the same trans-regulatory environment, enabling powerful comparative analyses of differential enhancer activities that arise from sequence variation. (starklab.org)
Screening the genomes of 5 Drosophila species (spanning an evolutionary distance of 30-40 million years) in a single D. melanogaster cell type (S2) revealed that a large portion of D. melanogaster orthologous enhancers is functionally conserved, due to stabilizing turnover of TF motifs. (starklab.org)

Editorial: Insights in evolutionary & genomic microbiology: 2022. (openwetware.org)
Editorial: Rising Stars in Evolutionary and Genomic Microbiology. (openwetware.org)
Though overrepresentation of TFBS motifs in regulatory DNA has been intensively exploited by many algorithms, it is still a difficult problem to distinguish regulatory from other genomic DNA. (biomedcentral.com)
Spicuglia and colleagues captured fragments from sonicated genomic DNA that corresponded to candidate regulatory regions predicted based on chromatin accessibility and TF binding (Vanhille 2015). (starklab.org)
The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution. (mbl.edu)
SARS-CoV-2 contextual data specification for open genomic epidemiology (podcast) Micro Binfie (Microbial Bioinformatics), Aug 12, 2020. (cdc.gov)

Mary Goll Associate Professor Genetics Epigenetic regulation in the context of development and cancer. (uga.edu)

We found that gene expression programs diverge among mildly induced genes, while being highly conserved for strongly induced genes. (umassmed.edu)
Using a combination of miRNA hairpin predictions and co-mapping with miRBase entries, we identified a highly conserved cluster of miRNA genes on the X chromosome in the tammar and a total of 94 other predicted miRNA producing genes. (biomedcentral.com)

2023. The gene regulatory network of Staphylococcus aureus ST239-SCCmecIII strain Bmb9393 and assessment of genes associated with the biofilm in diverse backgrounds. (openwetware.org)

Chromatin looping is important for gene regulation, and studies of 3D chromatin structure across species and cell types have improved our understanding of the principles governing chromatin looping. (nature.com)
These variable loops contribute significantly to corresponding gene expression variability across cells and species, possibly by refining sub-TAD-scale loop contacts responsible for cell-type-specific enhancer-promoter interactions. (nature.com)
Structure of Co-expression Networks of Bifidobacterium species in Response to Human Milk Oligosaccharides. (openwetware.org)
The characterization of new miRNA target genes and a unique profile for crasiRNAs has allowed for insight into multiple RNA mediated processes in the tammar, including gene regulation, species incompatibilities, centromere and chromosome function. (biomedcentral.com)
We conclude that protein function is informative across species in predicting post-transcriptional miRNA regulation in living cells. (frontiersin.org)
Performance of phylogenetic foot-printing depends on the evolutionary distance between given species and on the conservation level of individual genes. (biomedcentral.com)
Systems that contain only relatively small numbers of particles of a certain chemical species, such as in signal transduction or gene expression, are particularly prone to this intrinsic noise. (biomedcentral.com)
The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world's major crops. (earlham.ac.uk)

The fraction of conserved enhancers varies greatly across gene expression programs, with induced genes and early-response genes, in particular, being regulated by a higher fraction of conserved enhancers. (umassmed.edu)
Regulatory regions of higher eukaryotes can be subdivided into proximal regulatory units - promoters - which are located close to and upstream of the gene, and distal transcription regulatory units called enhancers or cis-regulatory modules. (biomedcentral.com)
Andrew's research focusses on NF-Y's role in the regulation of chromatin accessibility at enhancers and promoters. (rajajothi.com)
Cell-type specific enhancers drive differential gene expression, hence, identifying such enhancers can be of utmost importance to our understanding of development and differentiation. (starklab.org)
Importantly, cell type-specific gene expression levels were correlated to the combined activities of the flanking enhancers within each cell type and across cell types, which links differential gene expression to differences in enhancer activity and demonstrates that ectopic assays can accurately assess cell type-specific enhancer activities. (starklab.org)
Interestingly, functional enhancers can also be gained within relatively short evolutionary timespans without apparent adaptive selection, yet can be involved in changes of gene expression in vivo (Arnold & Gerlach 2014). (starklab.org)
In many cases, different parts of each gene's transcription pattern are controlled by cis-acting regulatory elements (enhancers) that contain binding sites for factors positioned higher in the hierarchy. (nyu.edu)
Activation of each target gene involves direct binding of Bicoid to one or more enhancers that appear as rather tightly linked clusters of Bicoid-binding sites. (nyu.edu)
These enhancers direct expression patterns at different positions along the anterior posterior axis (Figure 3), and a major goal is to understand the cis-regulatory logic that controls the differential positioning of different target genes. (nyu.edu)

In the fruit fly Drosophila melanogaster, many genes that control body form were identified more than 25 years ago. (nyu.edu)

Research interest: Fungal gene regulatory and biochemical networks, and biological clocks. (uga.edu)
The Seelig group is interested in understanding how biological organisms process information using complex biochemical networks and how such networks can be engineered to program cellular behavior. (unibas.ch)
Bioinformatics is an interdisciplinary scientific field that develops methods for storing, retrieving, organizing and analyzing biological data. (ind.in)
A major activity in bioinformatics is to develop software tools to generate useful biological knowledge. (ind.in)
Bioinformatics uses many areas of computer science , statistics , mathematics and engineering to process biological data. (ind.in)
This definition placed bioinformatics as a field parallel to biophysics (the study of physical processes in biological systems) or biochemistry (the study of chemical processes in biological systems). (ind.in)
Another early contributor to bioinformatics was Elvin A. Kabat , who pioneered biological sequence analysis in 1970 with his comprehensive volumes of antibody sequences released with Tai Te Wu between 1980 and 1991. (ind.in)
The primary goal of bioinformatics is to increase the understanding of biological processes. (ind.in)
The type of biological networks that studies gene coexpression, known as Gene Coexpression Networks, consist of an undirected graph depicting genes and their coexpression relationships. (mdpi.com)
However, these tools are not directly employable by researchers working on non-model organisms to answer fundamental biological, and evolutionary questions. (uni-frankfurt.de)
We discuss how co-operativity allows simple static motifs to perform the conditional regulation that underlies decision-making in higher eukaryotic biological systems. (biomedcentral.com)
Biological networks are graphs used to represent the inner workings of a biological system. (earlham.ac.uk)
Networks describe the relationships of the elements of biological systems using edges. (earlham.ac.uk)

By binding to the promoter region at the start of other genes they turn them on, initiating the production of another protein, and so on. (wikipedia.org)
String-based protein-protein interaction analysis suggested that bZIP53, a transcription factor might be involved in the activation of transcription of ELO / KCS genes. (nature.com)
Inferring protein-protein interacting sites using residue conservation and evolutionary information. (paperexplained.cn)
Of note, functionally-relevant differences between humans and chimpanzees are observed regarding the 3 main components of this pathway: i) the protein sequences of immunes TFs binding MER41 LTRs, ii) the insertion sites of MER41 LTRs in the promoter regions of ID-associated genes and iii) the protein sequences of the targeted ID-associated genes. (biorxiv.org)
Finally, a survey of the human proteome has allowed us to map a protein-protein network which links the identified immune/MER41/cognition pathway to FOXP2 (Forkhead Box P2), a key TF involved in the emergence of human speech. (biorxiv.org)
For example, there are methods to locate a gene within a sequence, to predict protein structure and/or function, and to cluster protein sequences into families of related sequences. (ind.in)
Identification of suppressor genes in deleted regions, determination of promoter hypermethylation and their protein expression in tumor biopsies. (dry-lab.org)
The bacterial cell is able to control many protein-coding genes (green lines at bottom) with relatively few controls (yellow and purple lines). (creation.com)
The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. (duke.edu)
Amanda's uses embryonic stem cell as a model system to investigate nuclear export protein CRM1's role in developmental gene regulation. (rajajothi.com)
We are working on a toolbox of deep learning algorithms that can elucidate predictive relationships between sequence of non-coding gene regulatory elements, protein-DNA binding events, and expression patterns of their target genes. (ipk-gatersleben.de)
We observe that each gene and its products have a unique set of DNA, RNA or protein motifs that encode a regulatory program to define the logical circuitry that guides the life cycle of these biomolecules, from transcription to degradation. (biomedcentral.com)
Finally, we contrast the regulatory properties of protein motifs and the regulatory elements of DNA and (pre-)mRNAs, advocating that co-regulation, co-operativity, and motif-driven regulatory programs are common mechanisms that emerge from the use of simple, evolutionarily plastic regulatory modules. (biomedcentral.com)
One of the few antigens against which mammals develop protective immunity is the highly polymorphic OspC protein, encoded by the ospC gene on the cp26 plasmid. (cdc.gov)
By means of DNA sequencing of a large sample collection of the pathogen from across the United States, we studied the gene for the bacterium's highly diverse OspC protein, protective immunity against which develops in animals. (cdc.gov)

Interestingly, ID-associated genes exhibit promoter-localized MER41 LTRs that harbor TF binding sites (TFBSs) for not only STAT1 but also other immune TFs such as, in particular, NFKB1 (Nuclear Factor Kappa B Subunit 1) and STAT3 (Signal Transducer And Activator Of Transcription 3). (biorxiv.org)
These genes comprise 289 Transcription Factors (TFs) representing Basic Helix-loop Helix (bHLH), Ethylene Response Factors (ERFs), myeloblastosis (MYB), No apical meristem (NAC), and WRKY amino acid motif (WRKY) type major families known to be involved in the mechanism of stress tolerance. (frontiersin.org)
Seven stress-responsive cis -elements such as ABRE, ARE, HSE, LTR, MBS, as well as a cis -element of ART1 (Al resistance transcription factor 1), GGNVS, were identified in the upstream region of these eight GmMATE genes. (biomedcentral.com)
The transcription rate of genes is dictated primarily by interactions between DNA-binding transcription factors. (biomedcentral.com)
Comparatively short sequences (several hundred to several thousand base pairs, depending on thespecies) upstream or downstream of the transcription start site often play a major role in the regulation of gene expression. (biomedcentral.com)
Recognition of regulatory DNA regions based on description of known transcription factor binding sites (TFBS). (biomedcentral.com)
Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature. (gao-lab.org)
Expression of PRX36, PMEI6 and SBT1.7 is controlled by complex transcription factor regulatory networks for proper seed coat mucilage extrusion. (gao-lab.org)
Regulation of anthocyanin and proanthocyanidin biosynthesis by Medicago truncatula bHLH transcription factor MtTT8. (gao-lab.org)
During development, various signaling cascades culminate in the activation of key transcription factors and chromatin remodeling enzymes, which collectively establish and/or maintain gene expression programs controlling cell identity. (rajajothi.com)
The Jothi Lab is interested in understanding how transcription regulators and epigenetic modifications regulate gene expression programs during cellular development and differentiation. (rajajothi.com)
The life of a gene product, from transcription to degradation, is controlled by a series of regulatory decisions. (biomedcentral.com)
For example, steroid hormones regulate gene expression through their nuclear receptors, which bind to specific DNA motifs and act as transcription factors, thus influencing the activity of the bound enhancer. (starklab.org)
Most of these genes encode transcription factors that are expressed in bands or stripes at specific positions along the anterior posterior axis. (nyu.edu)
In our first experiments, we have focused on the Bicoid gradient (Figure 2) and on gradients of transcription factors encoded by the gap genes hunchback, Kruppel, knirps, and giant. (nyu.edu)
My research questions have explored different aspects of transposable elements, including their transcription and epigenetic regulation. (lu.se)

Park H, Imoto S , Miyano S. Comprehensive information-based differential gene regulatory networks analysis (CIdrgn): Application to gastric cancer and chemotherapy-responsive gene network identification. (google.com)
Differential gene expression analysis of these eight GmMATE genes in response to Al stress helps us identify GmMATE75 as the candidate gene for Al tolerance in soybean, whose relative transcript abundance increased at 6, 12 and 24 h after Al treatment, with more fold changes in Al-tolerant than Al-sensitive cultivar, which is consistent with previously reported Al-tolerance related MATE genes. (biomedcentral.com)

Over time U-triangle developed on polyploidization of Brassica 's proved its usefulness in studying the evolution of various genes and phenotypes 3 . (nature.com)
We know little about their prevalence in the gene expression phenotypes of regulatory circuits, important sources of evolutionary innovations. (biomedcentral.com)
Here, we study a space of more than sixteen million three-gene model regulatory circuits, where each circuit is represented by a genotype, and has one or more functions embodied in one or more gene expression phenotypes. (biomedcentral.com)
We find that the majority of circuits with single functions have latent expression phenotypes. (biomedcentral.com)
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)
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)

PRODORIC2: the bacterial gene regulation database in 2018. (uni-bielefeld.de)

The first class of small RNAs identified were the micro RNAs (miRNAs), which are small (~22 nt) non-coding RNAs that regulate gene expression by base pairing to mRNAs where they direct either mRNA cleavage or repress translation [ 8 ]. (biomedcentral.com)

The tammar wallaby, a marsupial mammal, is a powerful comparative model for studying the evolution of regulatory networks. (biomedcentral.com)
In this study, 53 KCS genes were identified in B. carinata compared to 32 and 33 KCS genes in B. nigra and B. oleracea respectively, which suggests that polyploidization might has impacted the fatty acid elongation process during Brassica evolution. (nature.com)
Gene structure analysis indicated that the maximum number of genes were intron-less and remained conserved during evolution. (nature.com)
The neutral type of selection seemed to be predominant in both KCS and ELO genes evolution. (nature.com)
The current study provides a basis to understand the evolution of both KCS and ELO genes in fatty acid elongation and their role in stress tolerance. (nature.com)
Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral. (earlham.ac.uk)
This is important for the understanding of human brain evolution as well as diseases with complex networks where transposable elements may play a regulatory role. (lu.se)

Consequently, motifs are indispensable for temporal, spatial, conditional and basal regulation at the transcriptional, post-transcriptional and post-translational level. (biomedcentral.com)

A number of studies have explored how regulation of generally, and at least to a first approximation, it is obvious that metabolic pathways affects the growth rate of microorganisms, gene regulation only is useful if the environmental conditions vary both in the steady state and in response to changes in the local with time. (lu.se)
In this review, we highlight that many of the key regulatory pathways of the cell are recruited by motifs and that the ease of motif acquisition has resulted in large networks of co-regulated biomolecules. (biomedcentral.com)
Signaling pathways often cause changes in gene expression levels. (starklab.org)
Resistance arises by mutation (influencing the target or efflux of the antimicrobial agent) or by the acquisition of resistance genes (encoding antimicrobial or target alteration, or alternate pathways) ( 2 , 3 ). (cdc.gov)

Thus a yeast cell, finding itself in a sugar solution, will turn on genes to make enzymes that process the sugar to alcohol. (wikipedia.org)
A very natural place to study gene detecting and metabolizing lactose, it is known that the overall regulation is in the metabolism of the cell, and then specifically in effect of expressing the lac genes in vain is a drop in the growth rate the regulation of genes that code for enzymes and transporter of as much as 5% [1,6]. (lu.se)

Their ability to maintain cell and tissue homeostasis is critical, with many miRNA genes implicated in human diseases such as metabolic, inflammatory, and neurodegenerative diseases ( Vishnoi and Rani, 2017 ). (frontiersin.org)
The expression of photosynthesis and chlorophyll synthesis related genes were significantly reduced under both types of stresses, which limit the metabolic processes and thus help prolong survival under extreme conditions. (frontiersin.org)
Here we hypothesize that the reported unfavorable classification results in the set-level framework were due to the adoption of unsuitable gene sets defined typically on the basis of the Gene ontology and the KEGG database of metabolic networks. (biomedcentral.com)
a single set may e.g. collect all genes acting in a specific metabolic pathway. (biomedcentral.com)

Diversification in immunogenicity genes caused by selective pressures in invasive meningococci. (cdc.gov)

FAE ( Fatty Acid Elongation ) like genes take part in the biosynthesis of VLCFAs, growth regulation, and stress responses, and are further comprised of KCS ( Ketoacyl-CoA synthase ) and ELO ( Elongation Defective Elongase ) sub-gene families. (nature.com)
Transcriptome data were further confirmed by quantitative real-time PCR for twelve key genes in EFA biosynthesis. (researchsquare.com)
Regulation of anthocyanin biosynthesis in Arabidopsis thaliana red pap1-D cells metabolically programmed by auxins. (gao-lab.org)

Eme is interested in evolutionary microbiology. (unibas.ch)

Furthermore, nucleotide sequences related to the cluster vanHAX are present in this DNA, suggesting that the prolonged use of avoparcin in agriculture led to the uptake of glycopeptide resistance genes by animal commensal bacteria, which were subsequently transferred to humans. (cdc.gov)
The actual origins of acquired resistance genes are unknown, but environmental microbes, including the strains producing antimicrobial agents, are believed to be important sources ( 4 , 5 ). (cdc.gov)

These 117 GmMATE genes were unevenly localized on soybean chromosomes 1 to 20, with both tandem and segmental duplication events detected, and most genes showed tissue-specific expression patterns. (biomedcentral.com)

In the latter, a gene set contains genes whose product acts in a specific cellular pathway. (biomedcentral.com)
Using biologically interrelated experiments to identify pathway genes in Arabidopsis. (gao-lab.org)
Characterization of the cis elements in the proximal promoter regions of the anthocyanin pathway genes reveals a common regulatory logic that governs pathway regulation. (gao-lab.org)
Further, using RAPID, we investigated the aberrations of endo-siRNAs, and their respective transcriptomic alterations caused by an RNAi pathway triggered by feeding small RNAs against a target gene. (uni-frankfurt.de)
We find that the small RNA transcriptome is altered, even if a gene unrelated to RNAi pathway is targeted. (uni-frankfurt.de)

3DSIG focuses on structural bioinformatics and computational biophysics. (iscb.org)

By comparison, we found that various genes associated with acyl editing, fatty acid β-oxidation, triacylglycerol assembly and oil-body formation had greater expression levels at middle developmental stage (38 DAP), which are consistent with the fast accumulation of EFA in V. galamensis developing seed, implying their fundamental roles in EFA production. (researchsquare.com)

These molecules and their interactions comprise a gene regulatory network. (wikipedia.org)
In this article we introduce the updated version 6.0 of CoryneRegNet and describe the updated database content which includes, 6352 corynebacterial regulatory interactions compared with 4928 interactions in release 5.0 and 3235 regulations in release 4.0, respectively. (uni-bielefeld.de)
We also demonstrate how we support the community by integrating analysis and visualization features for transiently imported custom data, such as gene regulatory interactions. (uni-bielefeld.de)
We explore an alternative approach to defining gene sets, based on regulatory interactions, which we expect to collect genes with more correlated expression. (biomedcentral.com)
We define two families of gene sets using information on regulatory interactions, and evaluate them on phenotype-classification tasks using public prokaryotic gene expression data sets. (biomedcentral.com)
We construct intricate molecular networks that serve as the game engines, driving the complex interactions that govern plant life and responses to environmental challenges. (ipk-gatersleben.de)

Here, we report an expansion of the FAR1/FRS-like genes that correlates well with the switch to prostrate-toerect growth of shoots upon flowering in Rosa wichuraiana 'Basye's Thornless' (BT). (kib.ac.cn)

Blencowe's research team studies the mechanisms by which genes are regulated and coordinated to provide critical functions in mammalian cells. (unibas.ch)
They combine computational and experimental approaches to contrast information between healthy and disease states in order to understand mechanisms impacting gene regulation and expression in diseases. (embl.de)

Liberali studies the dynamics of self-organization, and how cellular signaling dictates its spatial-temporal regulation. (unibas.ch)
In the former case, a gene set corresponds to an ontology term (representing a function, process, or a cellular component) and collects all genes annotated by that term. (biomedcentral.com)

However, the principles that determine if a gene is regulated by miRNAs are poorly understood. (frontiersin.org)
MicroRNAs (miRNAs) post-transcriptionally regulate genes across all animals and plants. (frontiersin.org)
MiRNAs are crucial regulators of gene expression found across both the plant and animal kingdoms. (earlham.ac.uk)

Finally, I will be studying the microbiome of Tembusu in the aims of identifying genes which causes Tembusu to associate with symbionts. (helsinki.fi)

Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum. (openwetware.org)

While collecting an ever-growing number of Bcd-dependent elements, we are using data mining techniques to identify sequence motifs or binding site arrangements that correlate with target gene positioning. (nyu.edu)

Here, we present evidence that the promoter regions of intellectual disability-associated genes are uniquely enriched in LTR sequences of the MER41 HERVs. (biorxiv.org)
In the current report, a systematic approach is implemented to catalogue regulatory elements within HERVs, as a roadmap to potential functions of HERV sequences in gene networks. (mdpi.com)
I analyzed the presence of HERV sequences on consensus cis-regulatory elements (cCREs) from ENCODE data. (mdpi.com)

Journal Article Genes (Basel) · December 16, 2021 Origins of DNA replication are specified by the ordered recruitment of replication factors in a cell-cycle-dependent manner. (duke.edu)

We further show that the evolutionary conservation among paralogs does not imply any coherence in miRNA regulation. (frontiersin.org)
We conclude that duplicated paralogous genes that often changed their function, also diverse in their tendency to be miRNA regulated. (frontiersin.org)

The cis -elements and expression patterns of eight soybean MATE genes related to Al detoxification/iron translocation were analyzed, and GmMATE75 was identified as a candidate gene for Al tolerance in soybean. (biomedcentral.com)
They are organized into a hierarchical network that creates finer and finer striped patterns, which eventually foreshadow and control the placement of body structures of the larval and adult stages of this animal (Figure 1). (nyu.edu)
To rigorously test this idea, we are carefully measuring the spatial relationships between potentially morphogenetic gradients and the positions of their target gene expression patterns. (nyu.edu)

Moreover, we have not found such a significant enrichment in the promoter regions of genes that associate with autism spectrum disorder (ASD) or schizophrenia. (biorxiv.org)

A Bibliometric Analysis of Mexican Bioinformatics: A Portrait of Actors, Structure, and Dynamics. (openwetware.org)

Liu Y, Zhang YZ, Imoto S . Microbial Gene Ontology informed deep neural network for microbe functionality discovery in human diseases. (google.com)
Here, we discuss how such methodology can be useful to translational biomedical research, where scientists traditionally focus on one or a small set of genes, diseases, and drug candidates at any one time. (biomedcentral.com)

We further show that the number of instances of these motifs is a strong predictor of the responsiveness of a gene to pathogen detection. (umassmed.edu)
Extracting clustered recognition motifs is one of the most reliable techniques, but is limited to the recognition of similarly regulated cis-regulatory regions. (biomedcentral.com)

Lateral gene transfers resulted in different linkages between the ospC gene and loci of the chromosome or other plasmids. (cdc.gov)

Construction and Analysis of Gene Co-Expression Network in the Pathogenic Fungus Ustilago maydis. (openwetware.org)
The expression analysis of both gene family members reflect their preferential seed-specific expression, especially during the mature embryo development stage. (nature.com)
CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. (uni-bielefeld.de)
With the public availability of data tools for their analysis were quickly developed and described in journals such as Nucleic Acids Research which published specialized issues on bioinformatics tools as early as 1982. (ind.in)
Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data. (ind.in)
Unlike in more conventional gene expression analysis, the set-level approach assumes that high-dimensional vectors of gene expressions are represented by lower-dimensional vectors of aggregated expressions. (biomedcentral.com)
Besides obvious benefits in the interpretability of the learned classifiers, the set-level approach is mainly motivated by the problem of high feature dimension contrasting with the low number of available samples, which has been characteristic of gene expression data analysis. (biomedcentral.com)
Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. (mdpi.com)
Our analysis revealed subsets of genes, whose expression is positively associated with H3K27me3, different to the otherwise reported negative association with gene expression in many other organisms. (uni-frankfurt.de)

Creating this bioinformatics pipeline has helped to make sense of the data collected as a whole, giving new insights into the human brain," explains Raquel. (lu.se)

These may be located far upstream or downstream of the target gene, and are much more difficult to recognise. (biomedcentral.com)

Reddy and colleagues used STARR-seq to assess the enhancer activities of SNP-containing DNA fragments, thereby determining gene regulatory differences in populations (Vockley 2015). (starklab.org)
We found that the distributions and frequencies of types of OspC genes differed between populations of B. burgdorferi in the Northeast, the Midwest, and California. (cdc.gov)

Phylogenetic affiliations of mesopelagic acantharia and acantharian-like environmental 18S rRNA genes off the southern California coast. (mbl.edu)

Anatomy22

Organisms23

Diseases1

Chemicals and Drugs43

Analytical, Diagnostic and Therapeutic Techniques and Equipment41

Psychiatry and Psychology2

Phenomena and Processes97

Disciplines and Occupations9

Anthropology, Education, Sociology and Social Phenomena1

Information Science36

Health Care12

Genomics9

Genome23

Biology19

Transcriptional regulation7

Proteins13

Genetic13

Genomes7

Genomic6

Genetics1

Highly conserved2

20231

Species8

Enhancers9

Drosophila1

Biological13

Protein15

Transcription16

Differential2

Phenotypes6

20181

Regulate gene expression1

Evolution7

Post-transcriptional1

Pathways4

Enzymes2

Metabolic4

Diversification1

Biosynthesis3

Microbiology1

Resistance Genes2

Chromosomes1

Pathway5

Structural1

Developmental1

Interactions6

Correlates1

Mechanisms2

Cellular2

MiRNAs3

Microbiome1

Inference1

Sequence1

Sequences3

20211

MiRNA2

Patterns3

Enrichment1

Dynamics1

Diseases2

Motifs2

Chromosome1

Analysis9

Insights1

Target gene1

Populations2

Phylogenetic1