Cell gene regulatory networks. Medical search. Frequent questions

To test my hypothesis, I investigated which genes of the auxin and cytokinin pathways are regulated by WOX4, also in comparison to WUSCHEL, a stem cell regulator of the shoot apical meristem. (uni-heidelberg.de)
To systematically study these pathways by modulating individual components-or in the case of synthetic biology, building new network architectures by creating DNA circuit-it is critical to control multiple genes simultaneously under tightly regulated or inducible expression. (atcc.org)
Further, the identified pathways and signaling networks also revealed MWCNT potential to trigger pulmonary and cardiovascular effects as well as carcinogenic outcomes in humans, similar to those previously described in rodents exposed to MWCNTs. (cdc.gov)
Single cell evaluation of endocardial Hand2 gene regulatory networks reveals HAND2-dependent pathways that impact cardiac morphogenesis. (bvsalud.org)
The non-specific lethal complex regulates genes and pathways genetically linked to Parkinson's disease. (medscape.com)

The Plant Cell (2023) 35 (8): 2929. (biologists.com)
Cell Reports, Available online 14 November 2023. (lu.se)
The Lund Stem Cell Center Article of the Year Award (2022 & 2023) ceremony will take place on Friday, 21 September during the SCC Annual Retreat 2023. (lu.se)
m6A-driven SF3B1 translation control steers splicing to direct genome integrity and leukemogenesis", Molecular Cell, 2023. (lu.se)

Furthermore, these components could be additionally regulated by WUSCHEL-RELATED HOMEOBOX4 (WOX4), an important transcription factor for stem cell regulation in the vascular cambium. (uni-heidelberg.de)
WUSCHEL also exerts this type of regulation on type-A ARRs in the shoot apical meristem and therefore this could represent a general concept for the regulation of plant stem cells. (uni-heidelberg.de)
In conclusion, this study suggests that a mechanism of cell fate decision making in vascular cambium stem cells is based on the regulation of cytokinin signalling by WOX4 and by type-A ARRs. (uni-heidelberg.de)
While current state-of-the-art methods are limited by their ability to only predict average networks for cell populations, our approach facilitates the reconstruction of networks down to the level of single cells which can be utilized to characterize the heterogeneity of gene regulation within and across tumors. (bifold.berlin)
We also found an unexpectedly dynamic pattern of transcript isoform regulation, suggesting a critical regulatory role during HSC differentiation, and a cell cycle/DNA repair signature associated with multipotency in MPP2 cells. (lu.se)
The basic motifs used to build more complex networks (that is, simple regulation, reciprocal regulation, feedback loop, feedforward loop, and autoregulation) can be faithfully described and their temporal dynamics can be analyzed. (biomedcentral.com)
A gene expression analysis revealed that deletion of Akt in liver led to the constitutive activation of Foxo1-dependent gene expression, but again, concomitant ablation of Foxo1 restored postprandial regulation, preventing the inhibition of the metabolic response to nutrient intake caused by deletion of Akt . (nature.com)
Figure 5: Nutritional regulation of hepatic gene expression in the absence of Foxo1 alone and in the absence of both Akt and Foxo1. (nature.com)
Finally, we found that transcription factors Jun , Fos , Atf3 , and Egr1 were upregulated in protective cells, especially Egr1 was predicted to be involved in the regulation of genes related to antioxidant stress and angiogenesis, suggesting a role in promoting differentiation into this cell phenotype. (hindawi.com)
These differences are achieved through the regulation of individual genes such that they are only on in particular cell types. (ca.gov)
For instance, the regulation of specific genes allows skin cells to serve their specialized epidermal function. (ca.gov)
Additionally, we find that the ESC genome is organized in such a way as to juxtapose regions of DNA that show similar regulation by demonstrating that spatially associated regions in the genome are associated with the same gene regulatory factors. (ca.gov)
This finding adds a new dimension to our understanding of how ESC-specific gene regulation is maintained and how the genome is organized. (ca.gov)
Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell Type Proliferation and Differentiation. (academictree.org)
In addition to classical gene regulatory networks noted above, we have recently identified a central role for additional biologic mechanisms, namely gene regulation by chromatin regulators and by noncoding RNAs. (stanford.edu)
The coordinated changes in ncRNA and mRNA expression profiles revealed a set of miRNAs and their target genes with roles in cell cycle regulation/progression/control, apoptosis and proliferation. (cdc.gov)
The human forebrain has expanded in size and complexity compared to chimpanzees despite limited changes in protein-coding genes, suggesting that gene expression regulation is an important driver of brain evolution. (lu.se)
Achieving systematic, genome-scale perturbations within intact biological systems is important for elucidating gene function and epigenetic regulation. (cdc.gov)

Here, we use single-cell transcriptomics to identify the molecular signature of NMPs and reverse engineer the mechanism that regulates their differentiation. (mdc-berlin.de)
RA, produced by newly generated mesodermal cells, provides feedback that initiates NMP generation and induces neural differentiation, thereby coordinating the production of neural and mesodermal tissue. (mdc-berlin.de)
DMRs show continuous gain or loss of methylation during differentiation, and the overall change in DNA methylation correlates inversely with gene expression at key loci. (lu.se)
Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages. (cincinnatichildrens.org)
Recently, single cell RNA sequencing (scRNA-seq) analysis has been used to examine cellular fate and function during cellular differentiation and has contributed to elucidating the mechanisms of various diseases. (hindawi.com)
Analysis of dynamic gene expression revealed that Gpx3 was significantly upregulated during cell differentiation into protective cells. (hindawi.com)
In stratified epithelia proliferative basal cells adherent to the underlying basement membrane undergo cell cycle arrest then outward migration and terminal differentiation. (stanford.edu)
This process is mediated by 2 mutually exclusive programs of gene expression: 1) an undifferentiated program supporting proliferation by stem cells within the basal layer and 2) a differentiation program instructing growth arrest and differentiation-associated programmed cell death in suprabasal layers. (stanford.edu)
We are currently pursuing studies of the dominant signaling and gene regulatory networks that control this process, including the Ras/MAPK cascade, which is required for stem cell-mediated self-renewal and the p53 transcription factor family member, p63, which is required for epidermal differentiation. (stanford.edu)
The function of histone modifying epigenetic regulators and noncoding RNA as central mediators of epithelial stem cell renewal and differentiation represent major emerging areas of study in the lab. (stanford.edu)
Faculty in our genetics and cell biology group investigate the genetic basis for animal growth, disease resistance, and nutrient efficiency, and the mechanisms underlying nutrient uptake, cellular differentiation, and lipid secretion. (umd.edu)
Temporal multimodal single-cell profiling of native hematopoiesis illuminates altered differentiation trajectories with age. (lu.se)

They also control and maintain adult bodies through feedback processes, and the loss of such feedback because of a mutation can be responsible for the cell proliferation that is seen in cancer. (wikipedia.org)
The expression of cyclin-dependent kinase inhibitors was profoundly affected with early activation and then repression of p21 cip1/waf1 and persistent activation of both p27 kip1 and p57 kip2 , whereas genes involved in cell survival and proliferation were suppressed. (aacrjournals.org)
During cell growth and proliferation, ubiquitin plays an outsized role in promoting progression through the cell cycle. (intechopen.com)
Notably, the G1/S boundary represents a major barrier to cell proliferation and is universally dysfunctional in cancer cells, allowing for the unbridled proliferation observed in malignancy. (intechopen.com)

A vascular cambium stem cell produces both, wood progenitor cells inward and bast progenitor cells outward. (uni-heidelberg.de)
Here, we identify a KRAB-ZFP transcription factor, ZNF558, that is expressed in human but not chimpanzee forebrain neural progenitor cells. (lu.se)
Per Ludvik Brattås (Jakobsson group) " TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells " (Cell 2017). (lu.se)

Such development pattern shares an overlapping biological behavior with the growth plate, which is a process of mesenchymal stem cells differentiating into chondrogenic cells and then sequentially into fibrocartilage cells ( Killian, 2022 ). (elifesciences.org)

The vertebrate head is a complex tapestry of morphological features woven together during embryonic development from a varied array of specialized cell types. (frontiersin.org)

This has shown that a network of just three genes that regulate each other in a specific way is sufficient to bring about the three cell fate possibilities mentioned above. (uni-heidelberg.de)
These GRNs control temporal patterning in primary progenitors, regulate transition from primary to neurogenic progenitors, and drive specification of each major retinal cell type. (wustl.edu)
We confirm that NFI transcription factors selectively activate expression of genes promoting late-stage temporal identity in primary retinal progenitors and identify other transcription factors that regulate rod photoreceptor specification in postnatal retina. (wustl.edu)
A largely studied class of biological systems is constituted by systems which regulate the expression of genes in an organism. (biomedcentral.com)
Noncoding RNA sequences can regulate gene expression via interactions with epigenetic and other control mechanisms. (stanford.edu)
ZNF558 evolved as a suppressor of LINE-1 transposons but has been co-opted to regulate a single target, the mitophagy gene SPATA18. (lu.se)
Because the environment encountered within a living host will be quite different from the external environment, pathogens must be able to regulate the necessary genes in coordination as they move from the environment to the host and from one host niche to another. (cdc.gov)

Transcriptional networks, regulated by extracellular signals, control cell fate decisions and determine the size and composition of developing tissues. (mdc-berlin.de)
Together with genetic perturbations, this reveals a transcriptional network that integrates opposing retinoic acid (RA) and Wnt signals to determine the rate at which cells enter and exit the NMP state. (mdc-berlin.de)
We have identified a key transcriptional regulator of this process, without which AT1 cells lose their molecular and cellular characteristics and the lung undergoes alveolar simplification as in BPD. (mdanderson.org)
2020) provide an initial framework for understanding the underlying mechanisms by integrating enhancer and transcriptional alterations that occur during the progression of basal cell and squamous cell carcinomas. (nih.gov)
Mapping Transcriptional Networks in Plants: Data-Driven Discovery of Novel Biological Mechanisms. (academictree.org)
Advances in molecular biology and genome analysis now also allow for detailed descriptions of DNA-binding transcription factors and transcriptional regulatory networks. (medscape.com)
We use these engineered Cas9 activation complexes to investigate sgRNA targeting rules for effective transcriptional activation, demonstrate multiplexed activation of 10 genes simultaneously, and upregulate long intergenic non-coding RNA (lincRNA) transcripts. (cdc.gov)

Figure 6: Insulin-regulated expression of Foxo1 target genes was compromised in the Foxo1 −/− and TLKO primary hepatocytes. (nature.com)
An integrative analysis of ncRNA-mRNA correlations was performed to identify target genes, functional relationships, and regulatory networks in MWCNT-exposed workers. (cdc.gov)

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)
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)
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)
Gene regulatory networks are widely used by biologists to describe the interactions among genes, proteins and other components at the intra-cellular level. (biomedcentral.com)
Their behavior is often represented by using gene regulatory networks (GRNs), which describe the interactions among genes, proteins and other components at the intra-cellular level. (biomedcentral.com)
Integral nuclear pore proteins bind to Pol III-transcribed genes and are required for Pol III transcript processing in C. elegans. (cincinnatichildrens.org)
Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization. (ca.gov)
Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)

Here, we examined long-range chromatin interactions genome-wide in mouse embryonic stem cells (ESCs), iPSCs, and fibroblasts and uncovered a pluripotency-specific genome organization that is gradually reestablished during reprogramming. (ca.gov)

Amyotrophic lateral sclerosis (ALS) is a progressive disease associated with neuronal cell death that is thought to involve aberrant immune responses. (nih.gov)
Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors ", Nature Communications, 2020). (lu.se)
SCN1A-deficient excitatory neuronal networks display mutation-specific phenotypes. (medscape.com)

CellexalVR: A virtual reality platform to visualize and analyze single-cell omics data", iScience, 2021. (lu.se)

Microtubule-associated protein MAP1LC3C regulates lysosomal exocytosis and induces zinc reprogramming in renal cancer cells. (uc.edu)

In a genome-wide screen for putative tumor suppressor genes, the EBF3 locus on the human chromosome 10q26.3 was found to be deleted or methylated in 73% of the examined cases of brain tumors. (aacrjournals.org)
A second group of methods, which includes DNA microarrays and proteomics, have advantages that overcome the limitations implicit in signature-tagged mutagenesis and in vivo expression technology, namely, the ability to directly measure expression (gene or protein) levels on a true genome-wide scale, but their application to analysis of bacterial pathogens during real infections is still in its infancy. (cdc.gov)

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)

The basis on which this first cell fate decision is made has not yet been clarified. (uni-heidelberg.de)
Importantly, when ARR7 and ARR15 are mutated, the cell fate decisions of vascular cambium stem cells are altered and more wood cells are produced than in wild type plants. (uni-heidelberg.de)
These cells are thus induced into a new fate, and may even generate other morphogens that signal back to the original cell. (wikipedia.org)
Gene regulatory networks (GRNs), consisting of transcription factors and their target sites, control neurogenesis and cell-fate specification in the developing central nervous system. (wustl.edu)
ETV2 primes hematoendothelial gene enhancers prior to hematoendothelial fate commitment. (cincinnatichildrens.org)
Signaling to Modulate Gastrulation via Regulating Cell Fate Specification and Cell Migration in Xenopus tropicalis. (xenbase.org)
The main purpose of this study was to characterize the fate of cardiac fibroblasts (CFs) and the dynamic gene expression patterns in a model of cardiac pressure overload using scRNA-seq analysis. (hindawi.com)
Finally, we used Cytoscape (3.9.1) to extensively examine the gene regulatory network related to cell fate. (hindawi.com)
Embryonic stem cells (ESCs), on the other hand, have not committed to a particular cell fate and retain the ability to become one of the 200-odd types of specialized cell. (ca.gov)

Figure 2: Aberrant insulin signaling and disrupted expression of Foxo1-regulated genes in DLKO but not 2LKO livers. (nature.com)
We are studying how lung endothelial cells respond to Vegfa during intussusceptive angiogenesis and whether and how the same Vegfa signaling elicits distinct responses from those during the well-characterized retinal sprouting angiogenesis. (mdanderson.org)
Given our demonstration of the unexpected angiogenic role of AT1 cells and their extensive surface area, we hypothesize that AT1 cells have other novel signaling roles. (mdanderson.org)
The authors provided convincing evidence for the heterogeneity of postnatal enthesis growth and the molecular dynamics and signaling networks during enthesis formation. (elifesciences.org)
FOXC1 silencing inhibits the epithelial‑to‑mesenchymal transition of glioma cells: Involvement of β‑catenin signaling. (cancerindex.org)

Enthesis development has historically been studied with lineage tracing of individual genes selected a priori, which does not allow for the determination of single-cell landscapes yielding mature cell types and tissues. (elifesciences.org)
or movements in a free energy landscape such that lineage choices are paths between stable cell states. (lu.se)

This team brings together complementary expertise from quantitative systems biology and stem cell biology to explore their novel hypothesis that membrane-localized proteasome may act as a neuroprotectant in disease-resistant motor neurons. (nyu.edu)
Modeling Methods for Medical Systems Biology: Regulatory Dynamics Underlying the Emergence of Disease Processes. (wiko-berlin.de)
The primary thrust of the Genetics and Cell Biology Group is to illuminate the molecular and cellular basis of complex biological systems using a multi-organismal and multi-faceted approach. (umd.edu)
Can we interest you in a thesis project in artificial neural networks, systems biology, bionanophysics or quantum computing? (lu.se)

The molecular heterogeneity of cancer cells contributes to the often partial response to targeted therapies and relapse of disease due to the escape of resistant cell populations. (bifold.berlin)
Molecular portraits of cell cycle checkpoint kinases in cancer evolution, progression, and treatment responsiveness. (uc.edu)
The significant changes in several miRNAs and mRNAs expression as well as their regulatory networks are important for getting molecular insights into the MWCNT-induced toxicity and pathogenesis in humans. (cdc.gov)

From the predicted single-cell networks our approach reveals characteristic network patterns for tumor cells and normal epithelial cells and identifies subnetworks that are observed only in (subgroups of) tumor cells of certain patients. (bifold.berlin)
Chemical-genetic interactions-observed when the treatment of mutant cells with chemical compounds reveals unexpected phenotypes-contain rich functional information linking compounds to their cellular modes of action. (nih.gov)

These molecules and their interactions comprise a gene regulatory network. (wikipedia.org)
We use Statecharts for modeling small and recurring patterns of interactions in gene regulatory networks, called motifs . (biomedcentral.com)
Didier Trono s'est beaucoup intéressé aux interactions entre les virus et leurs hôtes, ce qui l'a conduit à étudier la biologie de pathogènes comme le VIH et le virus de l''hépatite B, et à créer des outils de transfert génétique dérivés du VIH aujourd'hui utilisés avec succès en thérapie génique. (epfl.ch)
This fine balance is achieved through exquisitely connected networks of regulatory interactions between biological players such as molecules, cells, and tissues. (wiko-berlin.de)
This means that I study the interactions of biological networks through the mathematical framework of dynamical systems theory. (wiko-berlin.de)
Underlining the independence of these networks and their functional relevance for genome organization, loss of the Polycomb protein Eed diminishes interactions between Polycomb-regulated regions without altering overarching chromosome conformation. (ca.gov)

Despite the utility of this approach, integrative analyses of genetic and chemical-genetic interaction networks have not been systematically evaluated. (nih.gov)
To identify new potential therapeutic targets for SARS-CoV-2, the Sanjana lab and researchers at the Icahn School of Medicine at Mount Sinai performed a genome-scale, loss-of-function CRISPR screen to systematically knockout all genes in the human genome. (nyu.edu)

In this study, we present integrated quantitative proteome, transcriptome, and methylome analyses of hematopoietic stem cells (HSCs) and four multipotent progenitor (MPP) populations. (lu.se)

Karolina Pircs (Jakobsson group) " Huntingtin aggregation impairs autophagy, leading to argonaute-2 accumulation and global microRNA dysregulation " (Cell Reports, 2019). (lu.se)

Our experimental focus is on the mammalian setting using multiomics, informatics, mouse genetics, human genetics, single cell studies, and new human tissue platforms. (stanford.edu)

To obtain more functional insights, we propose scGeneRAI, an explainable deep learning approach that uses layer-wise relevance propagation (LRP) to infer gene regulatory networks from static single-cell RNA sequencing data for individual cells. (bifold.berlin)
Our approach successfully demonstrates the use of genetic interaction networks in the high-throughput functional annotation of compounds to biological processes. (nih.gov)

Stem cells have fascinated humans for a long time because of their fundamental importance in building and sustaining many forms of life. (uni-heidelberg.de)
Stem cells are able to divide and maintain themselves while producing new cell types. (uni-heidelberg.de)
Like animal stem cells, plant stem cells are a fascinating research object. (uni-heidelberg.de)
In this study, I specifically focussed on the plant stem cells that produce wood and bast. (uni-heidelberg.de)
These stem cells form a cylindrical stem cell niche, the vascular cambium, which is found in the root, the stem and the tissue that connects the root and stem, the hypocotyl. (uni-heidelberg.de)
To complement the in vivo system of chick embryos, we employ patient omics data, single cell RNA sequencing, human and mouse embryos, human cancer cell cultures, human pluripotent stem cells, chick embryo neural crest-derived in vitro crestosphere cultures, and zebrafish and mouse in vivo models. (lu.se)
Sozzi E, Nilsson F, Kajtez J, Parmar M, Fiorenzano A. Generation of Human Ventral Midbrain Organoids Derived from Pluripotent Stem Cells . (lu.se)
Nicola Guzzi (Bellodi group) " Pseudouridylation of tRNA - Derived Fragments Steers Translational Control in Stem Cells " (Cell 2018). (lu.se)

New studies will need to focus on enhancers and transcription factors, as well as genetic regulatory networks, and how changes in these networks can impact health and disease. (cdc.gov)

We have delineated a two-step AT1 cell morphogenesis process, cell flattening and cell folding, which leads to its ultrathin and yet expansive morphology. (mdanderson.org)

These dCas9-activator fusions targeted to the promoter region of endogenous genes can then modulate gene expression 7 - 11 . (cdc.gov)

gene regulatory network through multi-omic data integration. (xenbase.org)

Epigenetic dysregulation and disruption of gene enhancer networks are both pervasive in human cancers, and yet, their roles in keratinocyte cancers are poorly understood. (nih.gov)
Epigenetic control of gene expression lasts through multiple cell divisions without alterations in primary DNA sequence and can occur via mechanisms that include histone modification and DNA methylation. (stanford.edu)

In some cases this protein will be structural, and will accumulate at the cell membrane or within the cell to give it particular structural properties. (wikipedia.org)
AT1 cells are traditionally considered a passive structural component of the alveoli while attention has been focused on AT2 cells due to their proposed stem cell function. (mdanderson.org)
1) What are the shared structural properties of the regulatory networks that maintain homeostasis in biological systems operating at different scales? (wiko-berlin.de)
Thus, this work provides mechanistic insight into how a cis-acting structural variation establishes a regulatory network that affects human brain evolution. (lu.se)
We trained a Bayesian machine learning neural network model to generate a neuroimaging phenotype and AD score representing the probability of AD using structural MRI data in the Alzheimer's Disease Neuroimaging Initiative (ADNI) Cohort (cut-off 0.5, AUC 0.92, PPV 0.90, NPV 0.93). (cdc.gov)

In this study, we use integrated single-cell RNA and single-cell ATAC sequencing (scATAC-seq) analysis in developing mouse and human retina to identify multiple interconnected, evolutionarily conserved GRNs composed of cell-type-specific transcription factors that both activate genes within their own network and inhibit genes in other networks. (wustl.edu)

Silencing of the EBF3 locus was observed in brain, colorectal, breast, liver, and bone tumor cell lines and its reactivation was achieved on treatment with 5-aza-2′-deoxycytidine and trichostatin A in a significant portion of these tumor cells. (aacrjournals.org)

Front Cell Dev Biol. (xenbase.org)

Growth retardation and increased apoptosis in mice with homozygous disruption of the Akt1 gene. (nature.com)
We show here that expression of EBF3 resulted in cell cycle arrest and apoptosis. (aacrjournals.org)

Different cell fates and groups were fully characterized by Gene Set Enrichment Analysis (GSEA) analysis and Transcription factor (TF) activity analysis. (hindawi.com)

We also present experimental validations of CG-TARGET-predicted tubulin polymerization and cell cycle progression inhibitors. (nih.gov)
Our results suggest that recruitment of inflammatory monocytes plays an important role in disease progression and that modulation of these cells is a potential therapeutic approach. (nih.gov)
Progression through the cell cycle is driven by the oscillating activity of Cyclin Dependent Kinases (CDKs). (intechopen.com)

The proper copying and repair of DNA to maintain the correct sequence and structure of genomes is critical to the proper function of cells, and repair and replication is frequently disrupted in cancers and targeted by cancer treatments. (birmingham.ac.uk)
Our research is defining the normal mechanisms of DNA replication and repair, with the aim of understanding how it is deregulated in cancer cells. (birmingham.ac.uk)
Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution. (lu.se)

Thus, to understand the origin of the vertebrates is to understand how these cell populations became developmentally and evolutionarily coupled in our earliest vertebrate ancestors. (frontiersin.org)
Remarkable progress in science and technology has led to the development of powerful tools for genome sequencing and editing increasing ability to study gene expression and function at multiple levels from cells to populations. (cdc.gov)

Figure 1: Liver-specific deletion of Akt1 in Akt2 whole-body knockout mice resulted in severe hyperglycemia and the disruption of Foxo1-regulated gene expression. (nature.com)
We have generated conditional knockout alleles to test whether AT1 cells may also signal to mesenchymal cells such as myofibroblasts. (mdanderson.org)

Despite their genomic uniformity, cells manage to exhibit an impressive variety of forms and functions that go into producing all the tissues of the human body. (ca.gov)
Two of these methods, signature-tagged mutagenesis and in vivo expression technology, do not directly measure gene expression and do not allow true genomic-scale analysis, but they have been devised to identify genes necessary for pathogens during real infections. (cdc.gov)

In a recent publication, we applied CG-TARGET to a screen of nearly 14,000 chemical compounds in Saccharomyces cerevisiae, integrating this dataset with the global S. cerevisiae genetic interaction network to prioritize over 1500 compounds with high-confidence biological process predictions for further study. (nih.gov)

We benchmark our method with synthetic data and apply it to single-cell RNA sequencing data of a cohort of human lung cancers. (bifold.berlin)
My lab integrates traditional and single-nuclei RNA sequencing to elucidate transcriptome-wide changes to RNA metabolism in clinically relevant post-mortem brain tissue and human induced pluripotent stem cell (hiPSC) models of neurological disease including ALS and autism. (ed.ac.uk)
Define RNA metabolism changes in direct context of human neuropathology: Molecules and networks are characterised at region, cell and pseudotemporal resolution. (ed.ac.uk)
The DNA within the nuclei of our cells carries the information to generate the machinery of the cell, the cell itself, our tissues and then the whole human. (birmingham.ac.uk)
The latter encompass human skin regenerated on immune deficient mice as well as organotypic constructs with epithelial and stromal cells embedded within architecturally faithful mesenchyma in vitro. (stanford.edu)
We also synthesize a library consisting of 70,290 guides targeting all human RefSeq coding isoforms to screen for genes which, upon activation, confer resistance to a BRAF inhibitor. (cdc.gov)
Cell-type specific and multiscale dynamics of human focal seizures in limbic structures. (medscape.com)

Our modeling approach is able to simulate some interesting temporal properties of gene regulatory network motifs: the delay in the activation and the deactivation of the "output" gene in the coherent type-1 feedforward loop, the pulse in the incoherent type-1 feedforward loop, the bistability nature of double positive and double negative feedback loops, the oscillatory behavior of the negative feedback loop, and the "lock-in" effect of positive autoregulation. (biomedcentral.com)
Complex behavior within eukaryotic cells manifest from layered regulatory networks changing the transcription of many genes. (atcc.org)

we applied Single-cell RNA sequencing (scRNA-seq) to delineate the comprehensive postnatal RC enthesis growth and the temporal atlas from as early as postnatal day 1 up to postnatal week 8. (elifesciences.org)

We developed a method, called CG-TARGET (Chemical Genetic Translation via A Reference Genetic nETwork), that integrates large-scale chemical-genetic interaction screening data with a genetic interaction network to predict the biological processes perturbed by compounds. (nih.gov)
We describe sleuth ( http://pachterlab.github.io/sleuth ), a method for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. (nature.com)
We present a Statecharts-based approach for the modeling of gene regulatory network motifs in biological systems. (biomedcentral.com)
Using this approach, it has been possible to contribute to understand, prevent, diagnose, and reverse health-to-disease transitions in complex biological systems ranging from individual cells to whole ecosystems. (wiko-berlin.de)

In single-celled organisms, regulatory networks respond to the external environment, optimising the cell at a given time for survival in this environment. (wikipedia.org)
This process, which we associate with wine-making, is how the yeast cell makes its living, gaining energy to multiply, which under normal circumstances would enhance its survival prospects. (wikipedia.org)
However, we now have a number of methods that allow identification of genes critical for survival in a host as well as methods that allow direct measurement of gene expression during interaction with a host. (cdc.gov)

Olariu V, Manesso E, commitment and Peterson C. 2017 A deterministic method for estimating free energy genetic network reprogramming paths landscapes with applications to cell commitment and reprogramming paths. (lu.se)

Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo! (futurismic.com)

To check their hypothesis, the researchers looked for symmetry in protein complexes, RNA structures, and gene networks. (bigthink.com)

Skin malignancies, including epidermal squamous cell carcinoma (SCC), alone account for nearly as many cancers as all other tissues combined. (stanford.edu)
Central to this investigation is an understanding of what gene products are required and expressed during a natural infection and how this expression changes over time (from initial colonization to causation of disease and spread of the pathogen to new hosts) and space (in different cells or tissues within the host). (cdc.gov)

Anatomy18

Organisms23

Diseases1

Chemicals and Drugs26

Analytical, Diagnostic and Therapeutic Techniques and Equipment30

Psychiatry and Psychology2

Phenomena and Processes67

Disciplines and Occupations5

Anthropology, Education, Sociology and Social Phenomena1

Information Science22

Health Care11

Pathways5

20234

Regulation18

Differentiation12

Proliferation4

Progenitor cells3

20221

Embryonic development1

Regulate7

Transcriptional7

Target genes2

Proteins12

Mouse embryonic stem1

Neuronal3

20211

Regulates1

Genome-wide2

Binding to the promoter region1

Fate9

Signaling5

Lineage2

Biology4

Molecular3

Reveals2

Interactions6

Systematically2

Hematopoietic stem1

20191

Genetics1

Functional2

Stem cells8

Enhancers1

Morphogenesis1

Endogenous1

Multi-omic1

Epigenetic2

Structural5

GRNs1

Tumor1

Front Cell Dev Biol1

Apoptosis2

Transcription factor1

Progression3

Cancer3

Populations2

Knockout2

Genomic2

Chemical compounds1

Human7

Behavior2

Temporal1

Biological4

Survival3

Genetic network1

Nuclei1

Protein complexes1

Tissues2