Computational BiologyGenomicsTarget genesGeneticsOrganism2023DrosophilaPatternsProtein-codinMetabolicInteractionsCell BiologyPromoterPhenotypesPathwaysBiological systemsEpigenetics20182022Signal transductionProteinsApproachesMicroRNALaboratoryEpigeneticInferenceCancerEnhancersModulateGenetic regulatoGenome-wideHigh-throughputMechanismsBiochemistryExperimentalAlgorithmsAnalysesEvolutionaryGenomicDifferentially expressed2021Certain genesSingle-nucleotideMethodsRNAsMicroarrayHuman genomeCandidate genesResistance genesEpidemiologyApproachBiophysicsDynamicsDataStructuralDevelopmentalTranscriptomeResearchersArabidopsisSusceptibilityMiRNA expression profilesClustersSynthetic biologyAnalysisTranscription factors
Computational Biology16
- His research links Computational biology with Gene. (research.com)
- His Computational biology study incorporates themes from HEK 293 cells, Cell culture, Gene expression, Automated reasoning and Chromosome conformation capture. (research.com)
- Computational biology, Cell biology, Signal transduction, MAPK/ERK pathway and Genetics are his primary areas of study. (research.com)
- His Computational biology study combines topics from a wide range of disciplines, such as Transcriptome, Regulation of gene expression, Gene, Drug and Gene regulatory network. (research.com)
- His primary areas of study are Cancer research, Transcriptome, Computational biology, Colorectal cancer and KRAS. (research.com)
- His Computational biology research incorporates themes from Serous ovarian cancer and Drug. (research.com)
- His main research concerns Transcriptome, Computational biology, Cell biology, MAPK/ERK pathway and Gene expression. (research.com)
- The study incorporates disciplines such as Pharmacogenomics, Cancer cell, Proteomics, Biomarker and Drug in addition to Computational biology. (research.com)
- Computational biology brings together approaches and methods from several fields, including computer science, mathematics, and statistics, to interpret this information and investigate biological and medical questions. (mpg.de)
- Michael Hiller heads the Computational Biology and Evolutionary Genomics group at the Max Planck Institute of Molecular Cell Biology and Genetics. (mpg.de)
- Thomas Lengauer is a Scientific Director at the Max Planck Institute for Informatics, where he also heads the Computational Biology & Applied Algorithmics Department. (mpg.de)
- She applies an interdisciplinary approach that combines genetics, genomics, and computational biology. (embl.de)
- ISMB 2018 invites submissions reporting theoretical , computational , and statistical advances in computational biology and its intersections with other fields. (iscb.org)
- 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)
- DNA bases ), i.e. it works on the small scale paying attention to details, computational biology is a subfield of computer science which builds large-scale general theoretical models of biological systems seeking to expand our understanding of them from an abstract point of view, just as mathematical biology does with mathematical models. (ind.in)
- With a background in computational biology, Raquel's research focuses on studying the role of transposable elements in the human brain. (lu.se)
Genomics6
- 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)
- We are rapidly entering an era of "personal genomics" wherein data on gene structure and expression will be available for large numbers of individuals. (ecmiindmath.org)
- 2023. Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives. (openwetware.org)
- Here we present a summary of the 2014 International Conference on Intelligent Biology and Medicine (ICIBM 2014) and the editorial report of the supplement to BMC Genomics and BMC Systems Biology that includes 20 research articles selected from ICIBM 2014. (biomedcentral.com)
- Four keynote speakers who are world-renowned leaders in bioinformatics, genomics, systems biology and computational medicine delivered lectures on their cutting-edge research and shared their views and perspectives of their research fields. (biomedcentral.com)
- Using a combination of chromatin biochemistry, computational modelling, atomic force microscopy (AFM), genetics, genomics and cell biology, Dr. Dalal and colleagues are investigating whether chromatin adopts alternate structural conformations in cancer cells, the functional consequences of large-scale chromosomal alterations upon the cancer epigenome, and identifying small molecules which can target these structures or processes. (elifesciences.org)
Target genes3
- In this paper, we predicted human and plant target genes using RNAhybrid and set some criteria to further filter them. (biomedcentral.com)
- We summarized the functions of these modules to three major categories: ion transport, metabolic process and stress response, and especially some target genes are highly related to ion transport, polysaccharides and the lipid metabolic process. (biomedcentral.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)
Genetics8
- His scientific interests lie mostly in Cell biology, Signal transduction, Genetics, Regulation of gene expression and Gene. (research.com)
- The group is interested in a central question in genetics and evolutionary biology: Which differences in the genome underlie differences in the phenotypes of species? (mpg.de)
- Florian Jug heads the Quantitative Bioimage Computation group at the Max Planck Institute of Molecular Cell Biology and Genetics. (mpg.de)
- Gene Myers is a director as well as a research group leader at the Max Planck Institute of Molecular Cell Biology and Genetics. (mpg.de)
- Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. (biomedcentral.com)
- In FlyBase (the Drosophila genetics database) we have therefore developed a pipeline to obtain such summaries from researchers who have worked extensively on each gene. (stanford.edu)
- NIEHS research uses state-of-the-art science and technology to investigate the interplay between environmental exposures, human biology, genetics, and common diseases to help prevent disease and improve human health. (nih.gov)
- An optimized reverse genetics system suitable for efficient recovery of simian, human and murine-like rotaviruses. (cdc.gov)
Organism8
- citation needed] The genome of an organism contains anywhere from a few hundred to thousands of different genes, all encoding a singular product or more. (wikipedia.org)
- The most efficient way for an organism to regulate gene expression is at the transcriptional level. (wikipedia.org)
- The development of high-throughput technologies provides numerous experimental data such as DNA sequences, protein sequence, and RNA expression profiles makes it possible to study interactions and regulations among genes or other substance in an organism. (tsinghua.edu.cn)
- Gene networks control organism phenotype in health and disease by dynamically processing information introduced by genotype and environment. (ecmiindmath.org)
- A largely studied class of biological systems is constituted by systems which regulate the expression of genes in an organism. (biomedcentral.com)
- There are several reasons for choosing Drosophila melanogaster as an organism for the global study of gene expression during embryonic development. (biomedcentral.com)
- However, writing such summaries is a daunting task, given the number of genes in each organism (e.g. 13,929 protein coding genes in Drosophila melanogaster). (stanford.edu)
- The ability of genes or alleles to affect the representation of the host organism in a biome is an operational definition for the "function" of the gene (in that context). (genomicglossaries.com)
20231
- 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)
Drosophila6
- We model transcriptional gene regulation by using a hybrid approach and applying it to the well characterized segmentation gene regulatory networks in Drosophila development. (ecmiindmath.org)
- As a model genetic system, we use the Drosophila gap genes, which is a class of segmentation genes controlling the body plan formation during the early embryo development. (ecmiindmath.org)
- Yad's group uses Drosophila embryogenesis as a model system to provide a unique view of the functionality of enhancer-promoter interactions in a developing embryo. (embl.de)
- We determined and documented embryonic expression patterns for 6,003 (44%) of the 13,659 protein-coding genes identified in the Drosophila melanogaster genome with over 70,000 images and controlled vocabulary annotations. (biomedcentral.com)
- the process that governs the early embryonic patterning of the Drosophila body plan is now the best understood example of a complex cascade of transcriptional regulation during development [ 14 , 15 ]. (biomedcentral.com)
- We have assembled an atlas of gene expression patterns during Drosophila embryogenesis. (biomedcentral.com)
Patterns12
- At the next level of the hybrid modelling approach, we use dynamical equations of the reaction-diffusion type to describe the spatiotemporal patterns of the target gene expression based on the calculated probability of its activation. (ecmiindmath.org)
- We use Statecharts for modeling small and recurring patterns of interactions in gene regulatory networks, called motifs . (biomedcentral.com)
- On the methodological side, their research includes work on analysis of biological sequences, analysis and prediction of protein structure and function, analysis of intermolecular interactions and interaction networks, gene and protein expression patterns, and computational drug screening and drug design. (mpg.de)
- Using a binary-coding system to identify unique concordant expression patterns among genes, the model resulted in a digital rendering of single-cell gene expression which enables non-invasive prognosis of prostate cancer patients. (biomedcentral.com)
- However, the range of gene expression patterns, the extent of the correlation of expression with function, and the classes of genes whose spatial expression are tightly regulated have been unclear due to the lack of an unbiased, genome-wide survey of gene expression patterns. (biomedcentral.com)
- Individual expression patterns are extraordinarily diverse, but by supplementing qualitative in situ hybridization data with quantitative microarray time-course data using a hybrid clustering strategy, we identify groups of genes with similar expression. (biomedcentral.com)
- Of 4,496 genes with detectable expression in the embryo, 2,549 (57%) fall into 10 clusters representing broad expression patterns. (biomedcentral.com)
- Nearly 60% of the genes with detectable expression exhibit broad patterns reflecting quantitative rather than qualitative differences between tissues. (biomedcentral.com)
- the expression patterns of over 1,500 of these genes are documented here for the first time. (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)
- This is where bioinformatics comes into play - enabling scientists to effectively manage and analyze complex datasets to unravel underlying patterns and potential therapeutic targets related to gene expression changes. (heartofamericanorthwest.org)
- Notably, circRNAs display cell-type, tissue-type and developmental-stage specific expression patterns in eukaryotic transcriptome, which reveals their significant regulatory functions in gene expression. (ijbs.com)
Protein-codin1
Metabolic4
- But there are specific regulatory elements in other strains that give those strains different metabolic capabilities. (frontiersin.org)
- F. Fontana, V. Manca, Discrete solutions to differential equations by metabolic P systems. (springer.com)
- 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)
- Integrated multi-omics analyses and genome-wide association studies reveal prime candidate genes of metabolic and vegetative growth variation in canola. (ipk-gatersleben.de)
Interactions12
- The study of specialized tissue domains and their interactions is essential for a comprehensive understanding of the function of biological systems, including the wide variety of plant species. (nature.com)
- Our goal is to understand in which situations genetic variability leads to alteration of molecular phenotype and in which it is buffered due to mutual interactions of network genes. (ecmiindmath.org)
- 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)
- a map is constructed that shows interactions among molecular entities (such as genes, proteins and RNAs), using information from literature and databases. (hindawi.com)
- The network combining putative targets of TF and miRNA regulation with experimentally proven molecular interactions was constructed and visualized. (hindawi.com)
- 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)
- These relationships may reflect gene co-expression/regulation, protein-protein interactions (PPIs) or information about production or consumption of metabolites [ 14 ]. (biomedcentral.com)
- It is impossible to fully understand biological systems without understanding the 3D structure of their constituting parts and their interactions. (iscb.org)
- By studying changes in gene expression levels, researchers can unravel the complex interactions between genes and their environment, leading to advancements in various fields such as medicine, agriculture, and biotechnology. (heartofamericanorthwest.org)
- 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)
- 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)
Cell Biology4
- Nils Blüthgen combines subjects such as Systems biology, Gene expression and Cell fate determination with his study of Cell biology. (research.com)
- He is researching MAPK/ERK pathway as part of the investigation of Cell biology and Signal transduction. (research.com)
- His studies deal with areas such as Epidermal growth factor and HRAS as well as Cell biology. (research.com)
- A.P. Arkin, Synthetic cell biology. (springer.com)
Promoter8
- The original definition presented cis-regulatory modules as enhancers of cis-acting DNA, which increased the rate of transcription from a linked promoter. (wikipedia.org)
- Thus gene-regulation functions (GRF) provide a unique characteristic of a cis-regulatory module (CRM), relating the concentrations of transcription factors (input) to the promoter activities (output). (wikipedia.org)
- 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)
- 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)
- 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)
- 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)
- Identification of suppressor genes in deleted regions, determination of promoter hypermethylation and their protein expression in tumor biopsies. (dry-lab.org)
- These dCas9-activator fusions targeted to the promoter region of endogenous genes can then modulate gene expression 7 - 11 . (cdc.gov)
Phenotypes8
- 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)
- Both circuits and gene expression phenotypes that are robust to genetic change are associated with a greater number of latent 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)
- lncHUB2 produces reports that contain the secondary structure fold of the lncRNA, related publications, the most correlated coding genes, the most correlated lncRNAs, a network that visualizes the most correlated genes, predicted mouse phenotypes, predicted membership in biological processes and pathways, predicted upstream transcription factor regulators, and predicted disease associations. (mssm.edu)
- These genes were selected based on their role in asthmatic inflammatory processes and History previously reported associations with asthma phenotypes. (cdc.gov)
- Of these mediators, cytokines play a single nucleotide polymorphisms (SNP) in pro-inflammatory cytokine genes and asthma phenotypes (Che et al. (cdc.gov)
Pathways6
- In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. (nature.com)
- This study will develop a new approach to reconstruct time delay Boolean networks as a tool for exploring biological pathways. (tsinghua.edu.cn)
- In addition, gene set enrichment analysis shows 6 pathways that differ between high- and low-risk group. (techscience.com)
- The function of Gene and potential pathways were researched by GO and KEGG pathway enrichment analysis. (researchsquare.com)
- The compounds-targets and targets-pathways network were constructed in an R and Cytosacpe software. (researchsquare.com)
- Resistance arises by mutation (influencing the target or efflux of the antimicrobial agent) or by the acquisition of resistance genes (encoding antimicrobial or target alter- ation, or alternate pathways) (2,3). (cdc.gov)
Biological systems7
- Understanding complex biological systems requires functional characterization of specialized tissue domains. (nature.com)
- We apply mathematical modeling and experimentation to study gene regulation, molecular transport and interplay between variability and robustness in biological systems. (ecmiindmath.org)
- However, experimental approaches have limitations when dealing with complex biological systems composed of multiple layers of regulation such as the transcriptional and post-transcriptional regulation by transcription factors (TFs) and miRNAs [ 2 ]. (hindawi.com)
- We present a Statecharts-based approach for the modeling of gene regulatory network motifs in biological systems. (biomedcentral.com)
- 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)
- 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)
- Achieving systematic, genome-scale perturbations within intact biological systems is important for elucidating gene function and epigenetic regulation. (cdc.gov)
Epigenetics1
- 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)
20181
- Immune escape is mainly caused by histocompatibility complex (MHC) class I, abnormal antigen signaling mechanism, immunosuppressive components (such as HLA-G), Fas and its ligands to activate apoptosis and overexpression of other immunosuppressive molecules, such as lymphocyte activation gene 3 (LAG-3), T cell immunoglobulin and mucin domain 3 (TIM-3) ( Steven and Seliger, 2018 ). (techscience.com)
20221
- 2022. Analysis of Carbohydrate-Active Enzymes and Sugar Transporters in Penicillium echinulatum: a Genome-wide Comparative Study of the Fungal Lignocellulolytic System. (openwetware.org)
Signal transduction2
- His Signal transduction research is multidisciplinary, incorporating perspectives in Stimulus, Neuroscience, Ultrasensitivity and Bioinformatics. (research.com)
- Plant/ crop productivity effected by the environmental strains such as water deficit condition (drought), Low temperature (cold), salt and High temperature (heat) these stresses disturb the signal transduction of gene regulatory systems of plants. (scielo.br)
Proteins5
- In particular, they work on mathematical models for analyzing large genomic sequences, especially in the context of next generation sequencing, and data derived from mass spectrometry experiments, for example to detect differential expression of proteins between normal and diseased samples. (mpg.de)
- In this process, mRNA molecules are guided by RNA-binding proteins that control their expression [ 6 ]. (biomedcentral.com)
- The potential proteins of DGP were acquired from TCMSP database, while the potential genes of ONFH were obtained from Gene Cards and Pubmed Gene databases. (researchsquare.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)
- Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)
Approaches11
- Most experimental approaches focus on the identification of miRNA targets and the investigation of physiological consequences when perturbing miRNA expressions but are unsuited to provide a system-level interpretation for observed phenomena. (hindawi.com)
- Editorial: Systems modeling: Approaches and applications-Volume II. (openwetware.org)
- To this end, 'big' biomedical data are integrated and curated using automated systems and disease-relevant information is extracted using statistical and machine learning approaches. (embl.de)
- 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)
- 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)
- Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. (biomedcentral.com)
- The rapid adoption of data-intensive biology approaches creates enormous challenges for computational visualization techniques, which are needed to enable researchers to gain insight from their large and highly complex data sets. (iscb.org)
- By deciphering how genes are regulated under various conditions, scientists can gain insights into biological processes and develop novel approaches for diagnostics, therapeutics, and precision medicine applications. (heartofamericanorthwest.org)
- To date, various genome-scale loss-of-function screening methods have been developed, including approaches employing RNA interference 1 , 2 and the RNA-guided endonuclease Cas9 from the microbial CRISPR (clustered regularly interspaced short palindromic repeat) adaptive immune system 3 , 4 . (cdc.gov)
- Genome-scale GOF screening approaches have largely remained limited to the use of cDNA library overexpression systems. (cdc.gov)
- Finally, we will invite speakers to talk about aspects of personalized or stratified medicine based on systems biology approaches for better care and future drug development. (lu.se)
MicroRNA3
- His studies in Regulation of gene expression integrate themes in fields like RNA, Protein biosynthesis, Three prime untranslated region, Messenger RNA and microRNA. (research.com)
- More importantly, circRNAs serve as microRNA (miRNA) sponges and crucial regulators of gene expression. (ijbs.com)
- microRNA (miRNA) expression level alterations between endometrial tissue and endometriotic lesions indicate their involvement in endometriosis pathogenesis. (mdpi.com)
Laboratory1
- The Ma'ayan Laboratory applies machine learning and other statistical mining techniques to study how intracellular regulatory systems function as networks to control cellular processes such as differentiation, dedifferentiation, apoptosis and proliferation. (mssm.edu)
Epigenetic3
- The design of cis-regulatory modules is such that transcription factors and epigenetic modifications serve as inputs, and the output of the module is the command given to the transcription machinery, which in turn determines the rate of gene transcription or whether it is turned on or off. (wikipedia.org)
- "Identifying All of Cancer's Manifestations through Integrated Pan Cancer Analysis" Dr. Josh Stuart presented the recent work of The Pan-Cancer Initiative of The Cancer Genome Atlas (TCGA) Research Network, including the analysis of thousands of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels in order to uncover data-driven tumor subtypes. (biomedcentral.com)
- My research questions have explored different aspects of transposable elements, including their transcription and epigenetic regulation. (lu.se)
Inference4
- However, it is crucial to make inference of genetic regulatory networks from gene expression profiles and protein interaction data for systems biology. (tsinghua.edu.cn)
- In the inference strategy, we will compare all pairs of input genes in those basic relationships by their corresponding -scores for every output gene. (tsinghua.edu.cn)
- Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum. (openwetware.org)
- 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)
Cancer15
- 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)
- MicroRNAs (miRNAs) are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. (hindawi.com)
- Prognostic models based on immune-related genes help to improve the prognosis prediction and clinical treatment of breast cancer patients. (techscience.com)
- The immune-related gene signature effectively predicts the survival and immune infiltration of breast cancer patients and is expected to provide more effective immunotherapy targets for the prognosis prediction of breast cancer. (techscience.com)
- By clicking the buttons in navigation bar of homepage, users can browse SEGs (Specifically expressed genes) by cancer types or tissues or regulators, as well as download datasets, search and get the statistical data. (hust.edu.cn)
- By clicking bar charts in "Tissue/Cancer" panel, users will see the barplot of highly/lowly expressed genes in different cancer types of TCGA or different tissues of other three datasets, and users can see detailed information of those genes by clicking pillars in the graph. (hust.edu.cn)
- In the "Synergistic Regulation" panel, users can build their own regulatory network by choosing data source and tissue/cancer type, as well as inputing miRNAs and TFs in the input boxes, by clicking the "Submit" button, the regulatory network will show in a new page. (hust.edu.cn)
- Browse by tissues or genes as mentioned above, users will get the informations of SEGs presented in table format, in which there is a column named "Tag", by clicking the content in this column, users will see highly/lowly expressions of that gene in various cancer types/tissues. (hust.edu.cn)
- While cancers are primarily classified on the basis of the body location where the disease originates, according to their new study, however, one in ten cancer patients would be classified differently using a new classification system based on molecular subtypes instead of the current tissue-of-origin system. (biomedcentral.com)
- Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapeutics effective in one cancer type to others with a matching genomic profile, and to construct personalized networks for use in developing combinatorial therapy. (biomedcentral.com)
- Pierre and his group's main focus is to understand principles of transcriptional regulation in development and cancer. (embl.de)
- To illustrate the importance of gene expression analysis, consider a hypothetical case study involving cancer research. (heartofamericanorthwest.org)
- Analyzing these data provides valuable information on which genes are upregulated or downregulated in lung cancer patients compared to healthy individuals. (heartofamericanorthwest.org)
- E7 from human papil omavirus type 16 cooperate to cancer: the European prospective investigation into doi:10.1093/carcin/bgp321 PMID:20047954 target the PDZ protein Na/H exchange regulatory cancer and nutrition study. (who.int)
- Travel times along a street network from all residential ZIP Codes to all cancer surgery facilities were calculated using a geographic information system. (cdc.gov)
Enhancers4
- However, this definition has changed to define cis-regulatory modules as a DNA sequence with transcription factor binding sites which are clustered into modular structures, including -but not limited to- locus control regions, promoters, enhancers, silencers, boundary control elements and other modulators. (wikipedia.org)
- In contrast, genome-wide comparative studies of steady-state systems showed that only a small fraction of active enhancers are conserved. (umassmed.edu)
- 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)
- This approach incorporates methods of statistical thermodynamics to calculate the activation probability of the target gene taking into account information about its regulatory genetic sequence (enhancers) and the transcription factors regulating the gene expression. (ecmiindmath.org)
Modulate1
- For instance, Pseudomonas aeruginosais, a symbiotic gram-negative bacterium, can produce HSL autoinducers to modulate gene expression in humans [ 2 ]. (biomedcentral.com)
Genetic regulato1
- CREs are vital components of genetic regulatory networks, which in turn control morphogenesis, the development of anatomy, and other aspects of embryonic development, studied in evolutionary developmental biology. (wikipedia.org)
Genome-wide3
- Genome wide association studies (GWAS) have identified mutations in non-coding regulatory regions as the most common features associated with human disease. (umassmed.edu)
- This study provides the first genome-wide captures of the dynamics of in vivo AmtR binding events and the regulatory network they define. (frontiersin.org)
- Brief summaries describing the function of each gene's product are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. (stanford.edu)
High-throughput5
- However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. (nature.com)
- Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. (nature.com)
- We built SEGreg database by identifying SEGs from high-throughput data of TCGA, BodyMap, CCLE and GTEx database, along with the corresponding miRNA and TF regulations collected from several databases. (hust.edu.cn)
- Next-generation sequencing (NGS) and other high-throughput experiments highlight one of the most significant advances in molecular biology over the past decade. (biomedcentral.com)
- Recent developments in high-throughput sequencing technologies and microarray techniques enable scientists to conduct comprehensive analyses on the abundance, composition, expression profile and molecular function of circRNAs [ 16 ]. (ijbs.com)
Mechanisms5
- Currently, an increasing number of studies are being carried out to deepen our understanding of miRNA regulatory mechanisms and functions. (hindawi.com)
- These regulatory mechanisms have strong connections with cellular metabolism. (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)
- Gene expression analysis plays a crucial role in understanding the intricate mechanisms underlying biological processes. (heartofamericanorthwest.org)
- Gene expression analysis is a crucial aspect of modern molecular biology research, enabling scientists to gain insights into the intricate mechanisms underlying gene regulation and cellular processes. (heartofamericanorthwest.org)
Biochemistry1
- Functional aspects such as growth, development, biochemistry and physiology ultimately derive from underlying gene expression programmes that are actively regulated in different organs and tissues. (nature.com)
Experimental6
- We emphasize close coupling between experiments, computations, and theory, and use the cell cultures as an experimental system for model validation. (ecmiindmath.org)
- Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. (hindawi.com)
- Next, the network was translated into a detailed mechanistic model, which was characterized and validated with experimental data. (hindawi.com)
- Although a number of experimental studies have demonstrated the discoveries of cross-species miRNA regulation, the effect of this event and the underlying mechanism are still unclear. (biomedcentral.com)
- In contrast, systems biologists have strong computational and analytical skills, but frequently lack hands-on experimental experience. (biomedcentral.com)
- We always welcome applications from students looking for experimental and/or bioinformatics master or bachelor projects. (lu.se)
Algorithms1
- 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)
Analyses2
- Furthermore, phylogenetic analyses identified molluscan-specific gene expansions of key enzymes involved in catecholamine biosynthesis. (exeter.ac.uk)
- RESULTS: in this work, we investigated the presence of caspase homologues using a combination of bioinformatics and phylogenetic analyses. (exeter.ac.uk)
Evolutionary2
- Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology. (nature.com)
- An important source of evolutionary adaptations are gene regulatory circuits. (biomedcentral.com)
Genomic3
- One great challenge of genomic research is to efficiently and accurately identify complex gene regulatory networks. (tsinghua.edu.cn)
- Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. (weizmann.ac.il)
- SARS-CoV-2 contextual data specification for open genomic epidemiology (podcast) Micro Binfie (Microbial Bioinformatics), Aug 12, 2020. (cdc.gov)
Differentially expressed2
- Estimation of genewise variance arises from two important applications in microarray data analysis: selecting significantly differentially expressed genes and validation tests for normalization of microarray data. (tsinghua.edu.cn)
- Our framework learns features for differentially expressed bio-molecules showing heat stress response. (biomedcentral.com)
20211
Certain genes2
- Plants respond to various stimuli under abiotic or biotic stress condition and express certain genes either structural or regulatory genes which maintain the plant integrity. (scielo.br)
- They suspect that certain genes involved in muscle development might be dysregulated in these individuals, leading to impaired muscle function. (heartofamericanorthwest.org)
Single-nucleotide1
- The ultimate goal of this approach is to formulate a quantitative map between the genotype (regulatory genetic sequence) and the corresponding molecular phenotype (gene expression level) with the single-nucleotide precision. (ecmiindmath.org)
Methods6
- In particulars, the book covers three important and rapidly advancing topics in biostatistics: analysis of survival and longitudinal data, statistical methods for epidemiology, and bioinformatics. (tsinghua.edu.cn)
- Sequencing technology is widely used with the updating of bioinformatics methods. (techscience.com)
- The performance of BRANEnet is compared to existing network integration methods. (biomedcentral.com)
- These methods, along with other emerging technologies, provide valuable tools for studying gene expression dynamics. (heartofamericanorthwest.org)
- Bioinformatics is an interdisciplinary scientific field that develops methods for storing, retrieving, organizing and analyzing biological data. (ind.in)
- 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)
RNAs3
- For example, food-derived plant miRNAs may pass through the gastrointestinal (GI) tract, enter into the plasma and serum of mammals, and interact with endogenous RNAs to regulate their expression. (biomedcentral.com)
- Certain Botrytis cinerea small RNAs (Bc-sRNA), like Bc-siR3.1, can silence Arabidopsis and tomato genes to inhibit their hosts' immunity [ 3 ]. (biomedcentral.com)
- Although the current generation of dCas9-based transcription activators is able to achieve up-regulation of some endogenous loci, the magnitude of transcriptional up-regulation achieved by individual single-guide RNAs (sgRNAs) 12 typically ranges from low to ineffective 8 - 11 . (cdc.gov)
Microarray1
- To investigate this hypothesis, they perform gene expression analysis using state-of-the-art techniques such as RNA-sequencing or microarray technologies. (heartofamericanorthwest.org)
Human genome2
- 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)
- Assembly of the human genome is one of the greatest achievements of bioinformatics. (ind.in)
Candidate genes1
- Pharmacogenomics provides an opportunity to identify candidate genes for studying disease progression and outcomes. (cambridge.org)
Resistance genes2
- 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)
Epidemiology1
Approach7
- Here we present the first available approach to generate and study high-resolution, spatially resolved functional profiles in a broad range of model plant systems. (nature.com)
- It is straightforward to use the systems biology approach to answer on these questions, as systems biology studies both structure and dynamical behavior of genetic networks. (ecmiindmath.org)
- 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)
- 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)
- 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)
- 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)
- This approach yielded 1,800 gene snapshots within a three month period. (stanford.edu)
Biophysics1
- 3DSIG focuses on structural bioinformatics and computational biophysics. (iscb.org)
Dynamics4
- A Bibliometric Analysis of Mexican Bioinformatics: A Portrait of Actors, Structure, and Dynamics. (openwetware.org)
- 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)
- Next, a stochastic simulation was performed to take inherent stochastic dynamics of gene expression into account. (igem.org)
- 2011). One reason for this is that model equations represent a significant simplification of actual biological dynamics of gene expression, which include a large number of reactions not explicitly considered in modeling, such as reactions describing chromosome opening and transcription initiation. (igem.org)
Data17
- Although these techniques can provide spatially resolved or cell-type-specific gene expression data, they each have inherent limitations. (nature.com)
- We also have implemented this method on simulated and empirical yeast gene expression data sets. (tsinghua.edu.cn)
- Based on the network structure, a detailed mechanistic model is established and its parameter values are determined using data. (hindawi.com)
- In order to study the cellular system and its functioning, omics data at each molecular level can be generated and efficiently integrated. (biomedcentral.com)
- Our goal is to efficiently integrate multi-omics data to study different regulatory aspects of multilayered processes that occur in organisms. (biomedcentral.com)
- The key challenges and bottlenecks of the modern-day molecular biology have shifted from simply gathering information to the analysis and interpretation of large quantities of data that can now be obtained. (biomedcentral.com)
- 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)
- In recent years, the advancement of bioinformatics has revolutionized gene expression analysis by providing powerful tools for data management, integration, and interpretation. (heartofamericanorthwest.org)
- The generated data contain information about which genes are actively transcribed in both healthy individuals and those affected by the disorder. (heartofamericanorthwest.org)
- Bioinformatics uses many areas of computer science , statistics , mathematics and engineering to process biological data. (ind.in)
- Databases and information systems are used to store and organize biological data. (ind.in)
- 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)
- In GWAS experiments, we integrate multi-omic data to identify the most likely gene-mechanism-phenotype paths. (ipk-gatersleben.de)
- An in-house algorithm predicts and ranks expert authors for each gene based on the data within FlyBase and extracts their email addresses from papers that we have curated. (stanford.edu)
- The signature of our top screening hits is significantly correlated with gene expression data from clinical melanoma samples. (cdc.gov)
- 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)
Structural2
- In this disturbance the maintenance involve the gene expression under the stress either in the form of structural gene or regulatory. (scielo.br)
- 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)
Developmental6
- Cis-regulatory modules perform a large amount of developmental information processing. (wikipedia.org)
- Within each of these categories, we identified clusters of genes associated with particular cellular and developmental functions. (biomedcentral.com)
- By deciphering how genes are turned on or off, scientists can gain valuable insights into various aspects of disease development, drug response, and developmental biology. (heartofamericanorthwest.org)
- Detlef Weigel received his PhD in 1988 from the Max Planck Institute for Developmental Biology. (elifesciences.org)
- Since 2002, he has been director of the Department of Molecular Biology at the Max Planck Institute for Developmental Biology. (elifesciences.org)
- He serves on the Editorial Boards of Annual Review of Cell and Developmental Biology and Genome Biology. (elifesciences.org)
Transcriptome1
- The Transcriptome study combines topics in areas such as Phenotype, Regulation of gene expression, Neuroepithelial cell and Gene expression profiling. (research.com)
Researchers2
- Written by active researchers in these emerging areas, it is intended to give graduate students and new researchers an idea of where the frontiers of biostatistics and bioinformatics are as well as a forum to learn common techniques in use, so that they can advance the fields via developing new techniques and new results. (tsinghua.edu.cn)
- More than one hundred researchers with diverse background spanning biology, medicine, computer science and engineering, statistics, and mathematics, among others attended the three-day event. (biomedcentral.com)
Arabidopsis1
- Hello darkness, my old friend: 3-KETOACYL-COENZYME A SYNTHASE4 is a branch point in the regulation of triacylglycerol synthesis in Arabidopsis thaliana. (ipk-gatersleben.de)
Susceptibility1
- These results suggest that genetic variations in TNF, TGFB1, PTGS1 and PTGS2 genes contribute to DA susceptibility. (cdc.gov)
MiRNA expression profiles1
- Finally, the calibrated model is used to study the effect of different miRNA expression profiles and cooperative target regulation on p21 expression levels in different biological contexts. (hindawi.com)
Clusters3
- Cis-regulatory modules are non-random clusters at their specified target site that contain transcription factor binding sites. (wikipedia.org)
- The remaining 1,947 (43%) genes fall into 29 clusters representing restricted expression, 20% patterned as early as blastoderm, with the majority restricted to differentiated cell types, such as epithelia, nervous system, or muscle. (biomedcentral.com)
- We investigate the relationship between expression clusters and known molecular and cellular-physiological functions. (biomedcentral.com)
Synthetic biology1
- These elements provide more options for synthetic biology by extending the scope of the AmtR regulon. (frontiersin.org)
Analysis9
- Construction and Analysis of Gene Co-Expression Network in the Pathogenic Fungus Ustilago maydis. (openwetware.org)
- Real-time quantitative PCR (RT-qPCR) analysis and sfGFP (superfolder green fluorescent protein) analysis reveal that AmtR directly and negatively regulates the transcription and expression of crn A, cre T, csh A, and hyu B. A growth test shows that C. glutamicum ATCC 14067 can use creatine or creatinine as a sole nitrogen source. (frontiersin.org)
- In the study, we used weighted gene co-expression network analysis to construct a co-expression network to screen out highly prognostic immune-related genes. (techscience.com)
- Subsequently, the prognostic immune-related gene signature was successfully constructed from highly immune-related genes through COX regression and LASSO COX analysis. (techscience.com)
- Combined the network analysis, molecular docking and in-vitro experiments, the results firstly demonstrated that the treatment effect of DGP on ONFH may be closely related to HIF-1α, VEGFA and HIF-1 signaling pathway. (researchsquare.com)
- This article aims to explore the significance of gene expression analysis in science and technology, with a particular focus on the role played by bioinformatics. (heartofamericanorthwest.org)
- Through gene expression analysis techniques, they compare the two groups' transcriptomes - that is, the complete set of RNA molecules produced by each individual's cells. (heartofamericanorthwest.org)
- Moving forward to the next section on Applications of Gene Expression Analysis, we will explore how these methodologies have revolutionized diverse areas of research and their potential implications in improving human health. (heartofamericanorthwest.org)
- 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)
Transcription factors7
- CREs typically regulate gene transcription by binding to transcription factors. (wikipedia.org)
- CRMs are stretches of DNA, usually 100-1000 DNA base pairs in length, where a number of transcription factors can bind and regulate expression of nearby genes and regulate their transcription rates. (wikipedia.org)
- They are labeled as cis because they are typically located on the same DNA strand as the genes they control as opposed to trans, which refers to effects on genes not located on the same strand or farther away, such as transcription factors. (wikipedia.org)
- Cis-regulatory modules carry out their function by integrating the active transcription factors and the associated co-factors at a specific time and place in the cell where this information is read and an output is given. (wikipedia.org)
- Regulatory elements are binding sites for transcription factors, which are involved in gene regulation. (wikipedia.org)
- The regulatory genes primarily the transcription factors that exert their activity by binding to certain cis DNA elements and consequently either up regulated or down regulate to target expression. (scielo.br)
- These transcription factors are known as masters regulators because its single transcript regulate more than one gene, in this context the regulon word is fascinating more in compass of transcription factors. (scielo.br)