• There is evidence that this is so following whole genome duplication, or duplication at a single locus. (wikipedia.org)
  • From an experimental perspective, we have developed a whole-genome fitness profiling method using microarray-based genetic footprinting (Girgis et al. (columbia.edu)
  • The development of methods for whole-genome analysis of the regulatory regions of the gene transcription, combined with highly-productive DNA sequencing methods, creates qualitative new data available to study how genes work, genetic networks and regulatory circuits. (nsu.ru)
  • The catalog of driver genes involved in the development of several malignancies has grown in recent years, as a result of whole-exome and whole-genome analyses of cohorts of tumors, mainly within the framework of large international consortia [ 3 , 4 ]. (biomedcentral.com)
  • In this retrospective study, we used whole-genome sequencing (WGS) to delineate transmission dynamics, characterize drug-resistance markers, and identify risk factors of transmission among Papua New Guinea residents of the Torres Strait Protected Zone (TSPZ) who had tuberculosis diagnoses during 2010-2015. (cdc.gov)
  • The project will rely on published whole genome assemblies and gene annotations of various qualities. (lu.se)
  • We have extensive whole genome and RNA sequencing data taken from whole samples of flies at three life stages: larva, pupa and adult. (lu.se)
  • Towards this goal, we describe an automated procedure for prioritizing genetic perturbations in order to discriminate optimally between alternative models of a gene-regulatory network. (biomedcentral.com)
  • Genetic variations that lie outside of any known genes can lead to disease. (nih.gov)
  • These results give researchers a framework for uncovering genetic regulators that could be potential targets for drug development. (nih.gov)
  • The recent expansion of repeated HERV sequences has offered a framework for genetic and epigenetic innovation. (mdpi.com)
  • We have developed a powerful computational framework for revealing the genetic basis of bacterial traits by correlating the inheritance patterns of genes and phenotypes across all the sequenced bacterial genomes (Jim et al. (columbia.edu)
  • By applying this framework to mild resistance, we have identified a large number of loci whose genetic perturbations significantly affect antibiotic sensitivity. (columbia.edu)
  • DeRisi, J.L., Iyer, V.R. & Brown, P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. (nature.com)
  • Yeast microarrays for genome wide parallel genetic and gene expression analysis. (nature.com)
  • This leads to competition for resources by different genes, which alter a synthetic genetic circuit's behavior. (sontaglab.org)
  • While cellular resources are often limited, this results in a competition for resources by different genes and circuits, which affect the behaviors of synthetic genetic circuits. (sontaglab.org)
  • Harenza JL, Muldoon PP, De Biasi M, Damaj MI, Miles MF (2014) Genetic variation within the Chrna7 gene modulates nicotine reward-like phenotypes in mice. (genenetwork.org)
  • One focus of this research is on cancer genomes, with the goal of understanding the sources of genetic instability. (ucsc.edu)
  • Analyses of gene regulatory networks (GRNs) provide the ability to understand the underlying genetic and developmental mechanisms responsible for the origin of morphological structures both in the development of an individual and across entire evolutionary lineages. (echinobase.org)
  • 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)
  • Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model. (researchgate.net)
  • Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. (researchgate.net)
  • We describe a computational methodology allowing to systematically and quantitatively characterize a Boolean mathematical model of a biological network in terms of genetic interactions between all loss of function and gain of function mutations with respect to all model phenotypes or outputs. (researchgate.net)
  • We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. (researchgate.net)
  • In addition, it can be used to predict genetic interactions [3] by comparing the sensitivity value of a double gene mutation from the value predicted from single mutations, and reveal the network intervention [4] by applying the state-flip mutation subject to a single gene. (researchgate.net)
  • Altered islet cell CRE activity has been implicated in T2D genetic risk, but previous investigations have found altered gene expression levels or transcription accessibility at only about a quarter of the T2D-associated locations under steady-state conditions. (jax.org)
  • Via international collaborations and networks, we have established population-scale genetic and molecular data resources that allow us to unravel gene regulatory dependencies with unprecedented resolution in pluripotent cells and in cancer. (embl.org)
  • 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)
  • Genome-wide survival analysis for macular neovascularization development in central serous chorioretinopathy revealed shared genetic susceptibility with polypoidal choroidal vasculopathy , 129 (9): 1034-1042, 2022. (csml.org)
  • 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)
  • In addition to the approximately 2300 tests for individual genetic disorders, recent advances in technology have enabled the development of clinical tests which quickly and economically analyze the entire human genome. (cdc.gov)
  • 2022). Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons. (caltech.edu)
  • 2022). Harmonizing model organism data in the Alliance of Genome Resources. (caltech.edu)
  • Journal Article Genome Res · June 2022 Over a thousand different transcription factors (TFs) bind with varying occupancy across the human genome. (duke.edu)
  • Furthermore, we have developed a genome-wide epistasis analysis framework that efficiently reveals the organization of these genes within signaling and regulatory networks such as the Rcs phosphorelay pathway and the cyclic-di-GMP second-messenger system. (columbia.edu)
  • The vast majority of these, however, lie outside of known genes, as 98.5% of our genome doesn't code for proteins. (nih.gov)
  • Thus, common evolutionary rates could be forcing the genes for certain proteins to evolve together while preventing other genes from being co-opted unless there is a shift in evolutionary rate. (wikipedia.org)
  • Mitochondrial genes and proteins were induced upon pan-CD44 kd, as were OxPhos genes. (bvsalud.org)
  • a map is constructed that shows interactions among molecular entities (such as genes, proteins and RNAs), using information from literature and databases. (hindawi.com)
  • Counter-intuitively, a large majority (~90%) of those variants are found in non-coding regions, not the 1.5% of the genome that codes for the proteins that carry out functions within cells. (jax.org)
  • Chemically induced gene expression changes were characterized by qRT-PCR, global run-on sequencing (GRO-seq) and immunoblotting, and the network of cooperative proteins of GATA4 and NKX2-5 were further explored by the examination of the GATA4 and NKX2-5 interactome by BioID. (biomedcentral.com)
  • The new data support two out of three novel regulatory pathways predicted to mediate expression changes downstream of the yeast transcriptional regulator SWI4 . (biomedcentral.com)
  • Along with strong driver mutations and passenger mutations predicted to have neutral effects, the team's analysis pointed to a set of passenger mutations suspected of having intermediate effects on genes from immune, metabolic, and other pathways. (genomeweb.com)
  • Since cancer mutations are hypothesized to target a relatively small number of cellular signaling and regulatory pathways, a common practice is to assess whether known pathways are enriched for mutated genes. (princeton.edu)
  • CFH-CFHR1 hybrid genes in two cases of atypical hemolytic uremic syndrome , J Hum Genet, 68(6): 427-430 , 2023. (csml.org)
  • Design and implementation of hybrid cloud system for large-scale human genomic research , Hum Genome Var , 10: 6, 2023. (csml.org)
  • One of the central problems in biology is understanding how genomic variation affects genome function to influence phenotypes. (nih.gov)
  • That paper describes the Probabilistic Regulation of Metabolism (PROM), which provides a mechanism for integrating transcriptional regulatory networks and metabolic networks in a single in silico model and using it to make predictions about phenotypes such as flux and growth rate. (genomeweb.com)
  • On the other hand, we show that different networks can display mathematically equivalent competition phenotypes. (sontaglab.org)
  • Transcriptome analyses identify clusters of co-regulated genes during NC specification and migration that show high conservation across vertebrates but also identify transcription factors (TFs) and cell-adhesion molecules not previously implicated in NC migration. (ox.ac.uk)
  • As genome-scale measurements lead to increasingly complex models of gene regulation, systematic approaches are needed to validate and refine these models. (biomedcentral.com)
  • These relationships may reflect gene co-expression/regulation, protein-protein interactions (PPIs) or information about production or consumption of metabolites [ 14 ]. (biomedcentral.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)
  • Although microRNAs (miRNAs) are physically small, they have been shown to play an important role in gene regulation [ 1 ]. (hindawi.com)
  • The application of the systems biology approach to the analysis of a gene regulatory network is demonstrated with a case study of the regulation of p21 by multiple miRNAs [ 4 ]. (hindawi.com)
  • The network combining putative targets of TF and miRNA regulation with experimentally proven molecular interactions was constructed and visualized. (hindawi.com)
  • Non-coding regions are known to regulate gene expression, and the finding indicates that alterations in regulation networks play a larger role in disease risk than protein-coding variants. (jax.org)
  • The team used massively parallel reporter assays (MPRA) to assess the effects of variants on gene expression in cultured MIN6 mouse β cells, which have been found to accurately model the regulation networks found in human islet cells. (jax.org)
  • PRODORIC2: the bacterial gene regulation database in 2018. (uni-bielefeld.de)
  • 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)
  • 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)
  • With MPRA, the team was able to determine the transcription activity potential of thousands of sequences that represented 259 association signals from prior genome wide association studies (GWAS). (jax.org)
  • Noncoding RNA sequences can regulate gene expression via interactions with epigenetic and other control mechanisms. (stanford.edu)
  • Transcription factors (TFs) function by recognizing and binding specific sequences to regulate gene expression. (biomedcentral.com)
  • The availability of genome sequences for many living organisms has important implications for health improvement and it has been widely predicted that their elucidation will lead to a revolution in medical research and patient care. (who.int)
  • Recent advances in genomics and computational biology are enabling construction of large-scale models of gene-regulatory networks. (biomedcentral.com)
  • Paleogenomics unites the fossil record and all aspects of deep time, with modern genomics and developmental biology to understand the evolution of genomes in evolutionary time. (echinobase.org)
  • A general framework for association tests with multivariate traits in large-scale genomics studies. (unc.edu)
  • The unprecedented advances in the science of genomics, the study of the genome and its actions, have culminated in the announcement of the complete sequence of the human genome. (who.int)
  • Developmental gene regulatory network architecture across 500 million years of echinoderm evolution. (echinobase.org)
  • 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)
  • Researchers have identified numerous TFs essential to lens development in vertebrates, and each has its own set of TFBS, which integrate into a complex developmental regulatory gene network . (evolutionnews.org)
  • Pharmacological modulation of cell fate decisions and developmental gene regulatory networks holds promise for the treatment of heart failure. (biomedcentral.com)
  • 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 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)
  • We recently reported a procedure for inferring gene-regulatory network models by integrating gene-expression profiles with high-throughput measurements of protein interactions [ 18 ]. (biomedcentral.com)
  • Many of these models contain transcriptional interactions for which the regulatory effects (inducer versus repressor) are ambiguous and cannot be determined from publicly available expression profiles. (biomedcentral.com)
  • Stabilizing selection, if ubiquitously spread across the network, could then be a "wall" that makes the formation of novel interactions more difficult and maintains previously established interactions. (wikipedia.org)
  • coarse-grained and fine-grained models, where the former contain less detail on interactions between genes. (biomedcentral.com)
  • While these methods, they said, can be used to quickly reconstruct TRNs, "the overwhelming combinatorics of possible networks limits identification of mechanistic regulatory interactions. (genomeweb.com)
  • A third potential application would be to use GEMINI to study regulatory-metabolic interactions associated with disease-specific cancers, as well as metabolic and neurodegenerative diseases, he said. (genomeweb.com)
  • They cautioned that the additive effects model used in the current study "did not incorporate the effects of epistatic interactions," but noted that "our current framework can be extended by using more complex models that capture both additive and epistatic variance. (genomeweb.com)
  • T]he FunSeq tool assigns a molecular functional impact score to a mutation based on various features," the authors explained, such as "inter-species conservation, gain or break of transcription factor motifs, disruption of known enhancer-gene interactions, and centrality in the gene regulatory or protein-interaction network. (genomeweb.com)
  • They also explored potential passenger mutation interactions with transcription factor binding sites and other regulatory features in the genome and looked at the relationship between proposed passenger mutations and tumor features overall - from the apparent mutational processes at play to the mutation patterns in tumor sub-clones. (genomeweb.com)
  • We consider approaches for representing the role of protein complexes in the cell cycle, displaying modules of metabolism in a hierarchical format, integrating experimental interaction data with structured vocabularies such as Gene Ontology categories and representing conserved interactions among orthologous groups of genes. (nature.com)
  • We first construct a p21 regulatory network based on data from the literature and further expand it using algorithms that predict molecular interactions. (hindawi.com)
  • 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)
  • In addition, we will have regular interactions with the permanent staff at Physical Chemistry and will get to meet students in their fi nal studies thereby enlarging our network and creating possibilities for future recruitment. (lu.se)
  • This paper performs an analysis of several existing evolutionary algorithms for quantitative gene regulatory network modelling. (biomedcentral.com)
  • Algorithms are applied to both synthetic and real gene expression data from DNA microarrays, and ability to reproduce biological behaviour, scalability and robustness to noise are assessed and compared. (biomedcentral.com)
  • Presented is a comparison framework for assessment of evolutionary algorithms, used to infer gene regulatory networks. (biomedcentral.com)
  • He also said that they're exploring ways to integrate it with network inference algorithms with an eye toward creating a "model-guided platform for synthetic biology. (genomeweb.com)
  • BayesSuites solves the problems of scalability, extensibility and interpretability that massive networks bring by separating backend calculations from the frontend interface and using specialized learning algorithms for massive networks. (upm.es)
  • We test these algorithms on a large human protein-protein interaction network using somatic mutation data from glioblastoma and lung adenocarcinoma samples. (princeton.edu)
  • 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)
  • At the moment, several methods of discovering qualitative causal relationships between genes with high accuracy from microarray data exist, but large scale quantitative analysis on real biological datasets cannot be performed, to date, as existing approaches are not suitable for real microarray data which are noisy and insufficient. (biomedcentral.com)
  • We compiled these profiles by analyzing 11 632 datasets, including the GEUVADIS and The Cancer Genome Atlas (TCGA) repositories. (bvsalud.org)
  • These methods are available to the wider scientific community through the Immcantation framework , which provides a start-to-finish analytical ecosystem for high-throughput AIRR-seq datasets, with a focus on B cell receptor (BCR) repertoire profiling. (yale.edu)
  • We next introduce LPRI (Lung Cancer Prognostic Regulon Index), a precision oncology framework to identify new biomarkers associated with prognosis by leveraging the single cell regulon atlas and bulk RNA sequencing or microarray datasets. (biomedcentral.com)
  • To gain insights into these non-coding regions, a team of scientists partly supported by NIH's National Human Genome Research Institute (NHGRI) carried out a genome-wide survey of epigenetic marks - factors that change the way genes are read, or expressed, without changing the DNA sequence itself. (nih.gov)
  • The scientists assessed chromatin states across 9 different cell types by mapping the locations across the genome of several epigenetic modifications to DNA, such as methylation and acetylation. (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)
  • DNA Microarray technology enables us to measure mRNA concentrations in a cell for a large number of genes at the same time. (biomedcentral.com)
  • Recent genome sequencing studies have shown that the somatic mutations that drive cancer development are distributed across a large number of genes. (princeton.edu)
  • 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)
  • 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)
  • Both inference and analysis of this kind of model are difficult tasks, thus global, (high-level), analysis of the network, has its attractions. (biomedcentral.com)
  • ATAC-seq analysis uncovers an ensemble of cis-regulatory elements, including enhancers of Tfap2B, SoxE1 and Hox-α2 validated in the embryo. (ox.ac.uk)
  • With the help of a functionally informative sequencing method called FunSeq2, the researchers identified non-driver, somatic mutations and their predicted functional impact in 2,548 tumors profiled for the Pan Cancer Analysis of Whole Genomes (PCAWG). (genomeweb.com)
  • Subsequent transcriptomic analysis identified genes differentially regulated by MeJA+NaCl treatment and NaCl alone. (frontiersin.org)
  • Further weighted gene co-expression network analysis (WGCNA) uncovered that turquoise and yellow gene modules were tightly linked to antioxidant enzymes activity and ion content, respectively. (frontiersin.org)
  • Phylogenetic analysis of gene expression. (echinobase.org)
  • Then, the regulatory TFs for the mesenchymal signature genes were inferred from the use of master regulator analysis (MRA) together with or without stepwise linear regression method (SLR). (biomedcentral.com)
  • Meta-analysis of gene-level associations for rare variants based on single-variant statistics. (unc.edu)
  • Multi-omics factor analysis (MOFA) is a computational framework for unsupervised discovery of the principal axes of biological and technical variation when multiple omics assays are applied to the same samples or cells. (embl.org)
  • Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study. (oregonstate.edu)
  • CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. (uni-bielefeld.de)
  • There are two main reasons why the catalogs of cancer drivers produced by the aforementioned projects and others need to be broken down into related sets of genes for deeper analysis. (biomedcentral.com)
  • Finally, a multi-omics data analysis to characterize molecular alterations associated with LPRI was performed from The Cancer Genome Atlas (TCGA) dataset. (biomedcentral.com)
  • Including 4 multidrug-resistant tuberculosis isolates from Australia citizens epidemiologically linked to the TSPZ into the transmission network analysis revealed 2 probable cross-border transmission events. (cdc.gov)
  • Her lab focuses on mutations that cause changes in gene expression by affecting a process called alternative splicing of RNA. (ucsc.edu)
  • One in eight women in the United States will develop breast cancer in her lifetime, yet only about 15 percent of these cancers have been linked to inherited gene mutations. (ucsc.edu)
  • There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. (researchgate.net)
  • However, there are no proper tools to examine the network sensitivity against many different types of mutations, including user-defined ones. (researchgate.net)
  • To address this issue, we developed RMut, which is an R package to analyze the Boolean network-based sensitivity by efficiently employing not only many well-known node-based and edgetic mutations but also novel user-defined mutations. (researchgate.net)
  • In the first case study, we observed that the real biological networks were most sensitive to overexpression/state-flip and edge-addition/-reverse mutations among node-based and edgetic mutations, respectively. (researchgate.net)
  • Overall, we observed that the molecular functional impact has a multimodal distribution suggesting that the canonical dichotomy of drivers and passengers might not necessarily reflect the complex mutational landscape in cancer genomes," the authors wrote. (genomeweb.com)
  • Exploiting the aforementioned catalogs of driver genes, for example, we recently revealed the mutational landscape of chromatin regulatory factors (CRFs) in cancer [ 5 ]. (biomedcentral.com)
  • A new paper written by researchers from the Institute for Systems Biology describes a computational approach for studying regulatory activities in cells that relies on integrated networks of transcriptional and metabolic data. (genomeweb.com)
  • While PROM "solves the forward problem of combining disparate networks to predict phenotype" with GEMINI "we iteratively use PROM to aid in solving the more challenging inverse problem - guiding TRN structure prediction using the metabolic network and the emergent phenotype measurements," the researchers wrote. (genomeweb.com)
  • GEMINI says, [for example], 'I have a prediction that this transcription factor influences a gene that happens to code for a metabolic enzyme,'" Price said. (genomeweb.com)
  • The developers claim that theirs is the first approach that integrates regulatory and metabolic data in this way and use it to study cell's activities. (genomeweb.com)
  • Their findings, the researchers conclude, "suggest that a metabolic constraint-based approach can be successfully used to help reconstruct TRNs from high-throughput data, and highlights the potential of using a biochemically-detailed mechanistic framework to integrate and reconcile inconsistencies across different data-types. (genomeweb.com)
  • Metabolic networks are one of the better understood cellular systems, according to Price, making it the ideal starting point for studying at least those regulatory activities in which cell metabolism plays a role, such as growth rates. (genomeweb.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)
  • These data have spawned a variety of methods to infer the structure of gene-regulatory networks or to study their high-level properties, as recently reviewed [ 5 ]. (biomedcentral.com)
  • However, if we are to accurately model large gene networks in complex organisms, including fly, worm, mouse, and human, automated procedures will be essential for analyzing the network, choosing the best new experiments to test the model, conducting the experiments, and integrating the resulting data. (biomedcentral.com)
  • Data are available at the Gene Expression Omnibus under accession number GSE156478 . (nature.com)
  • that it improves on previous strategies that have used primarily "proximal data such as gene co-expression and transcription factor binding" to reconstruct and study TRNs. (genomeweb.com)
  • Our goal is to efficiently integrate multi-omics data to study different regulatory aspects of multilayered processes that occur in organisms. (biomedcentral.com)
  • We evaluate our framework using multi-omics data of Saccharomyces cerevisiae , a well-studied yeast model organism. (biomedcentral.com)
  • Omics technologies give access to these regulatory mechanisms and are thus able to provide large amounts of data at each molecular level. (biomedcentral.com)
  • Despite the efforts to perform whole-cell simulations of bacteria, recreating the vector field that indicates the temporal variations of a genome-wide expression state in mammalian cells from experimental data remains a significant challenge. (cbirt.net)
  • I will describe an overall framework for data integration that brings together different evidence to annotate features such as binding sites and ncRNAs. (gersteinlab.org)
  • In this work, we develop the novel embedded PINN (ePINN), which is composed of two nested loss-sharing neural networks to target and improve the unknown dynamics prediction from quantitative time series data. (sontaglab.org)
  • We demonstrate the tool by learning and visualizing a genome-wide gene regulatory network from human brain data with 20,708 nodes. (upm.es)
  • For a better understanding of the regulatory role of miRNAs in coordinating gene expression, we here present a systems biology approach combining data-driven modeling and model-driven experiments. (hindawi.com)
  • Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. (hindawi.com)
  • Based on the network structure, a detailed mechanistic model is established and its parameter values are determined using data. (hindawi.com)
  • The systems biology approach, combining data-driven modeling and model-driven experiments, provides a systematic and comprehensive perspective on the regulatory roles of miRNAs in gene regulatory networks [ 3 - 5 ]. (hindawi.com)
  • Next, the network was translated into a detailed mechanistic model, which was characterized and validated with experimental data. (hindawi.com)
  • We first constructed the regulatory networks from single-cell RNA sequencing data in human lung adenocarcinoma (LUAD). (biomedcentral.com)
  • 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)
  • 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)
  • 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)
  • These regulatory mechanisms have strong connections with cellular metabolism. (biomedcentral.com)
  • These regulatory processes are affected by specific bio-molecules potentially in separate cellular compartments with interconnected steps [ 1 ]. (biomedcentral.com)
  • Synthetic gene circuits require cellular resources, which are often limited. (sontaglab.org)
  • One step in this direction is thus to understand exactly which downstream genes and cellular processes become affected in the outcome of driver alterations. (biomedcentral.com)
  • Due to cellular heterogeneity in the heart, the activation of gene programs representing specific atrial and ventricular cardiomyocyte subtypes would be highly desirable. (biomedcentral.com)
  • Sunlight regulated the expression of genes involved in synthesis/accumulation of flavonoids and sugars and genes functioning in nutrient uptake and transport, leading to asymmetric distribution of these substances. (bvsalud.org)
  • To connect enhancer regions to likely target genes, the researchers compared patterns of chromatin activity with gene expression across the 9 cell types. (nih.gov)
  • The scientists were then able to piece together enhancer regulatory networks and their target genes. (nih.gov)
  • The combinations of TFs and their target genes can sometimes control gene expression which may determine cell identity. (biomedcentral.com)
  • The SCENIC algorithm infers the TFs and their potential target genes, which are jointly named a regulon. (biomedcentral.com)
  • Large tumor genome sequencing projects have now uncovered a few hundred genes involved in the onset of tumorigenesis, or drivers, in some two dozen malignancies. (biomedcentral.com)
  • 1997. The hardwiring of development: organization and function of genomic regulatory systems. (wikipedia.org)
  • A genomic regulatory network for development. (echinobase.org)
  • 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)
  • Towards recovering Allele-specific cancer genome graphs. (stanford.edu)
  • Much of her work is in collaboration with large national and international consortia, such as the Cancer Genome Atlas and the International Cancer Genome Consortium. (ucsc.edu)
  • Daniel Kim's lab studies the role of long noncoding RNA molecules (lncRNAs) in gene expression and cancer. (ucsc.edu)
  • There are tens of thousands of uncharacterized lncRNAs in our genome, many of which are misregulated in cancer. (ucsc.edu)
  • Gene expression signatures have been commonly used as diagnostic and prognostic markers for cancer subtyping. (biomedcentral.com)
  • In order to identify prognostic master regulators, we took the known 85 prognostic signature genes for colorectal cancer and inferred their upstream TFs. (biomedcentral.com)
  • With advances in genome-wide gene expression technologies, classification of cancer subtypes based on expression signatures is widespread and results in many biomarkers for various cancers. (biomedcentral.com)
  • The reason for this is that passengers frequently take the majority of the signature gene and an accurate discrimination of cancer drivers from passengers becomes a key subject in cancer genomic studies. (biomedcentral.com)
  • Regulatory network modeling has been widely used for a systematic understanding of disease progression at the molecular level, particularly for cancer (comprehensively reviewed by Peer and Hacohen) [ 7 ]. (biomedcentral.com)
  • MicroRNAs (miRNAs) are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. (hindawi.com)
  • We anticipate that our approach will find increasing use as cancer genome studies increase in size and scope. (princeton.edu)
  • Gene and cell therapies that improve cancer treatments. (lu.se)
  • Moreover, all three MYBs bind to several PAL, C4H, and 4CL genes, in addition to shikimate pathway genes, the WRKY03 stilbenoid co-regulator and resveratrol-modifying gene candidates among which ROMT2-3 were validated enzymatically. (nih.gov)
  • The refined networks support previously unknown regulatory mechanisms downstream of SOK2 and SWI4 . (biomedcentral.com)
  • Nevertheless, to date, the actual misregulation of genes or processes downstream these cliques has not been systematically proven or exploited with the purpose of identifying them. (biomedcentral.com)
  • The student will be responsible for improving the annotations, especially for the untranslated regions that lie up and downstream of protein coding genes. (lu.se)
  • Human endogenous retroviruses (HERVs) are a family of endogenous retroviruses that comprise the ~8.93% of the human genome sequence, with a high proportion being human specific. (mdpi.com)
  • NHGRI considered this problem in part through a workshop entitled "From Genome to Phenotype: Genomic Variation Identification, Association, and Function in Human Health and Disease" as part of its strategic planning efforts . (nih.gov)
  • For their next steps, Price and his colleague and co-author, Sriram Chandrasekaran, are trying to use GEMINI to study networks in cells other than yeast, such as human cell lines. (genomeweb.com)
  • Toward a proteome-scale map of the human protein-protein interaction network. (nature.com)
  • A gene expression map of human chromosome 21 orthologs in the mouse. (nature.com)
  • A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes. (gersteinlab.org)
  • Joint mouse-human phenome-wide association to test gene function and disease risk. (genenetwork.org)
  • Modern breakthroughs, such as the mapping of the human genome, the Nobel Prize-winning CRISPR gene editing scissors, the ability to rapidly map large amounts of DNA, and the Nobel Prize-winning discovery of how mature cells can be reprogrammed, have led to an increasing number of innovative biological therapies reaching patients. (lu.se)
  • Figure 7: Illustration of steps to determine a network in Homo sapiens using the metagraph concept, where each metanode represents a set of orthologous eukaryotic genes from the COG database 53 . (nature.com)
  • Journal Article Genome Res · June 2021 Though the sequence of the genome within each eukaryotic cell is essentially fixed, it exists within a complex and changing chromatin state. (duke.edu)
  • Journal Article · June 29, 2020 AbstractThough the sequence of the genome within each eukaryotic cell is essentially fixed, it exists within a complex and changing chromatin state. (duke.edu)
  • Doug Kellogg's lab is working to elucidate these mechanisms, using biochemistry, genetics, and mathematical modeling to understand signaling networks that are required for control of cell size and cell growth. (ucsc.edu)
  • Their upstream regulators such as transcription factors (TFs) may take a more critical role as drivers or master regulators to provide better clues on the underlying regulatory mechanisms and therapeutic applications. (biomedcentral.com)
  • Our network approach leads to the identification of the upstream transcription factors for prognostic signature genes to provide leads to their regulatory mechanisms. (biomedcentral.com)
  • Currently, an increasing number of studies are being carried out to deepen our understanding of miRNA regulatory mechanisms and functions. (hindawi.com)
  • This suggests that these DNA changes are disrupting important regulatory elements and thus play a role in disease biology. (nih.gov)
  • Integration of systems and synthetic biology provides a consolidated framework that draws system-level connections among biology, mathematics, engineering, and computer sciences. (sontaglab.org)
  • Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis. (genenetwork.org)
  • 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 aim is to present the techniques used and offer a comprehensive comparison of approaches, under a common framework. (biomedcentral.com)
  • applied a reverse engineering method for context-specific transcriptional regulatory networks to 176 gene expression profiles from high-grade glioblastoma (HGG) patients. (biomedcentral.com)
  • Figure 2: A metagraph of the network of protein complexes discovered through tandem affinity mass spectrometry tagging by Gavin et al . (nature.com)
  • The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. (duke.edu)
  • The disease is caused by a mutated gene that leads to a lack of the building blocks needed to form the cell's protein factories (known as ribosomes). (lu.se)
  • Sites associated with insulin transcription and secretion were prominent among those with decreased activity, and the findings reveal the specific regulatory elements that respond to ER stress conditions. (jax.org)
  • Using this procedure, we evaluate 38 candidate regulatory networks in yeast and perform four high-priority gene knockout experiments. (biomedcentral.com)
  • First, we use the previously described modeling procedure to generate a library of models corresponding to different gene-regulatory systems in yeast. (biomedcentral.com)
  • Because we can link these things together and make growth predictions, we can say, 'When we knock out that transcription factor in yeast, does it have the decrease in growth rate that we predict because of this regulatory interaction. (genomeweb.com)
  • Genome-wide association studies involve scanning the genomes of many people to link single differences in DNA sequence, called single nucleotide polymorphisms (SNPs), with specific diseases or traits. (nih.gov)
  • 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)
  • A Bayesian active learning experimental design for inferring signaling networks. (stanford.edu)
  • A Bayesian framework for estimating cell type composition from DNA methylation without the need for methylation reference. (stanford.edu)
  • BayesSuites 1 is the first web framework for learning, visualizing, and interpreting Bayesian networks that can scale to tens of thousands of nodes while providing fast and friendly user experience. (upm.es)
  • Modularity refers to the ability of a system to organize discrete, individual units that can overall increase the efficiency of network activity and, in a biological sense, facilitates selective forces upon the network. (wikipedia.org)
  • To this end, networks are widely used to represent individual bio-molecules (nodes) and their biological relationships (edges). (biomedcentral.com)
  • In turn, these hypotheses, which provide reasonable explanations for the biological phenomenon, lead to an enhanced understanding of the gene regulatory network. (hindawi.com)
  • One of our current research aims is to develop improved association tests for genome-wide association studies (GWAS) that scale to millions of samples while accounting for technical and biological confounding factors. (embl.org)
  • These medicines differ from 'ordinary' medicines because the active substance is produced in or purified from materials of biological origin such as living cells, genes or tissue," says Johan Flygare, researcher at the Lund Stem Cell Center and the Division of Molecular Medicine and Gene Therapy at Lund University. (lu.se)
  • To these ends his team is also developing methods to characterize gene function in this nontraditional model organism. (uni-goettingen.de)
  • We demonstrate that our approach could identify upstream biomarkers for a given set of signature genes with markedly smaller size and comparable performances. (biomedcentral.com)
  • How Reliable Are Gene Expression-Based and Immunohistochemical Biomarkers Assessed on a Core-Needle Biopsy? (lu.se)
  • Here, we present and study a computational framework, termed as LPRI, to help prognostic stratification of patients. (biomedcentral.com)
  • We demonstrate the applicability of the learned features for targeted omics inference tasks: transcription factor (TF)-target prediction, integrated omics network (ION) inference, and module identification. (biomedcentral.com)
  • Against such strong positive selection, other evolutionary forces acting on the network must exist, with gaps of relaxed selection, to allow focused reorganization to occur. (wikipedia.org)
  • Evolutionary rewiring of gene regulatory network linkages at divergence of the echinoid subclasses. (echinobase.org)
  • My research focuses on the study of macroevolutionary patterns of taxononomic diversity, morphological disparity and biogeographic distribution in a phylogenetic framework. (uni-goettingen.de)
  • In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms. (genomeweb.com)
  • Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks. (echinobase.org)
  • Comparative Study of Regulatory Circuits in Two Sea Urchin Species Reveals Tight Control of Timing and High Conservation of Expression Dynamics. (echinobase.org)
  • Genome-wide association study identifies five new schizophrenia loci. (unc.edu)
  • The study is carried out within the framework of an international collaboration with the Jackson Laboratory (USA), and Huazhong Agricultural University (China. (nsu.ru)
  • RMut can be used to analyze large-scale networks because it is implemented in a parallel algorithm using the OpenCL library. (researchgate.net)
  • Three chromatin states were associated with regulatory regions known as promoters, which sit close to genes and allow them to be read. (nih.gov)
  • Promoters active in both cells types were associated with general metabolism genes. (nih.gov)
  • A concurrent subtractive assembly approach for identification of disease associated sub-meta-genomes. (stanford.edu)
  • Since then, research into how genes affect our traits, health and disease has grown to include entirely new forms of medicines. (lu.se)
  • Instead of lifelong treatment of a disease caused by, for example, a defective gene, ATMP medicines have the potential to cure the patient by fixing the gene," says Johan Flygare. (lu.se)
  • In addition we will address important areas of modern epidemiology such as the influence of early life factors on adult health and disease, but also the importance of the gene-diet-microbiota interaction for body function and health. (lu.se)
  • K-mer Set Memory (KSM) motif representation enables accurate prediction of the impact of regulatory variants. (stanford.edu)
  • Common variants in psychiatric risk genes predict brain structure at birth. (unc.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)
  • Transcription factor GATA4-targeted compounds that have previously shown in vivo efficacy in cardiac injury models were tested for stage-specific activation of atrial and ventricular reporter genes in differentiating pluripotent stem cells using a dual reporter assay. (biomedcentral.com)
  • These are therapies based on cells, genes or tissues and fall under the umbrella term ATMP (Advanced Therapy Medicinal Products). (lu.se)