• All predicted or imported interactions are benchmarked against a common reference of functional partnership as annotated by KEGG (Kyoto Encyclopedia of Genes and Genomes). (wikipedia.org)
  • Fusion-fission events: Proteins that are fused in some genomes are very likely to be functionally linked (as in other genomes where the genes are not fused). (wikipedia.org)
  • All SBML files in this directory were converted from KEGG (Kyoto Encyclopedia on Genes and Genomes) by using our conversion script kegg2sbml with the permission of Professor Minoru Kanehisa (Kyoto University). (systems-biology.org)
  • PMC KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for understanding the functions and utilities of cells and organisms from both high-level and genomic perspectives. (opensourcebiology.eu)
  • Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (deepdyve.com)
  • We use experimental data to improve structural annotation of genomes and to functionally characterize gene products. (biomedcentral.com)
  • Livestock genomes will always have low build numbers compared with model organisms such as human and mouse and yet they have comparable numbers of genes (UniGene). (biomedcentral.com)
  • Students will help develop tools and workflows to compile annotated libraries of genes and genomes, curate functional associations between genes and microbes in metabolism, and link microbial abundance to host gene/pathway expression and other outcomes. (bu.edu)
  • The BioCyc collection of Pathway/Genome Databases (PGDBs) provides electronic reference sources on the pathways and genomes of many organisms. (sri.com)
  • BioCyc databases describe organisms with sequenced genomes. (sri.com)
  • Some genomes are not included in BioCyc because their data fail these quality checks, e.g., some genomes have such a small number of proteins with predicted functions that they are not included. (sri.com)
  • The Reactome project is a collaboration among Cold Spring Harbor Laboratory , The European Bioinformatics Institute , and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. (systems-biology.org)
  • As an example of such a curation form, we describe integration of TPC with the Noctua curation tool developed by the Gene Ontology (GO) Consortium. (biomedcentral.com)
  • We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO). (biomedcentral.com)
  • Standard annotations are defined as an association between a gene and a biological concept from one of the [http://geneontology.org/docs/ontology-documentation/ three GO aspects]: Molecular Function (MF), Biological Process (BP), and Cellular Component (CC). Standard annotations always contain a reference (either a published, peer-reviewed paper or internal GO reference) and an evidence code that indicates the type of experiment or method used to make the assertion. (geneontology.org)
  • Using RO relations, GO-CAMs link GO annotations together with biological entities and external ontology terms to model how a gene functions in the broader context of a biological process or pathway. (geneontology.org)
  • Noctua: the Gene Ontology's GO-CAM Annotation Tool == [http://noctua.geneontology.org/ Noctua] is a web-based, collaborative [http://geneontology.org/ Gene Ontology (GO)] annotation tool developed by the GO Consortium. (geneontology.org)
  • Bill Andersen is chief technology officer at Knowledge Bus, Inc. The company is working with the European Media Laboratory Scientific Databases and Visualization Group in Heidelberg, Germany, on the creation of an ontology comprising knowledge of biochemical pathways. (nationalacademies.org)
  • This ontology will be used to support multiple activities, including database generation, visualization, simulation, and natural-language processing of textual research reports. (nationalacademies.org)
  • Gene Ontology (GO) enrichment analysis was conducted using Funcassociate 3.0. (biomedcentral.com)
  • Protein ontology development supplemental grant funded to represent complexes. (geneontology.org)
  • Like many other databases that store protein association knowledge, STRING imports data from experimentally derived protein-protein interactions through literature curation. (wikipedia.org)
  • All interactions are derived from literature curation or direct user submissions. (biokeanos.com)
  • Occurrence: Proteins that have a similar function or an occurrence in the same metabolic pathway, must be expressed together and have similar phylogenetic profile. (wikipedia.org)
  • PANTHER Pathways consists of over 165, primarily signaling, pathways, each with subfamilies and protein sequences mapped to individual pathway components. (systems-biology.org)
  • Pathway diagrams are interactive and include tools for visualizing gene expression data in the context of the diagrams. (systems-biology.org)
  • Found insideA Focused, State-of-the-Art Overview of This Evolving FieldPresents Various Techniques for GlycoinformaticsThe development and use of informatics tools and databases for glycobiology and glycomics research have increased considerably in … In contrast, KEGG modules in the KEGG MODULE database are higher-resolution, localized wiring diagrams, representing tighter functional units within a pathway map, such as subpathways conserved among specific organism groups and molecular complexes. (opensourcebiology.eu)
  • Underlying the PATHWAY database is a set of manually drawn images, very similar to classical metabolic pathways charts. (opensourcebiology.eu)
  • KEGG Pathway Painter (KPP) performs batch painting of all relevant pathways in KEGG according to uploaded lists of upregulated and downregulated genes. (opensourcebiology.eu)
  • Privacy, Help Merge pathway name and pathway ID from KEGG database. (opensourcebiology.eu)
  • The KEGG PATHWAY database, the wiring diagram database, is the core of the KEGG resource. (opensourcebiology.eu)
  • 2021. The KEGG pathway database consists of two sections: the metabolic pathway section and the regulatory pathway section. (opensourcebiology.eu)
  • This document provides an overview of the BioCyc collection of Pathway/Genome Databases. (sri.com)
  • The information in this document pertains to all BioCyc databases (DBs), and to most other DBs created using the Pathway Tools software. (sri.com)
  • Most microbial PGDBs within BioCyc have been generated computationally by SRI and are regenerated every 6-12 months to take advantage of improvements in our pathway prediction algorithms and in the MetaCyc pathway database. (sri.com)
  • Tryptophan (TRP) is an essential dietary amino acid that, unless otherwise committed to protein synthesis, undergoes metabolism via the Tryptophan-Kynurenine (TRP-KYN) pathway in vertebrate organisms. (mdpi.com)
  • REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. (biokeanos.com)
  • Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. (biokeanos.com)
  • Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. (biokeanos.com)
  • The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. (biokeanos.com)
  • The more than likely absence of known mechanistic and kinetic data for each of the individual proteins in a novel pathway hinders the process of translating network topology into a mathematical model. (biomedcentral.com)
  • Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. (researchgate.net)
  • MetaCyc - experimentally elucidated enzymes and metabolic pathways from 3,400 organisms. (sri.com)
  • Western blot analysis showed that rFg14-3-3e protein is recognized by sera from goats experimentally infected with F. gigantica and immunofluorescence staining using rat anti-rFg14-3-3e antibodies demonstrated the specific binding of rFg14-3-3e protein to the surface of goat PBMCs. (biomedcentral.com)
  • MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. (biokeanos.com)
  • Our work demonstrates the importance of poorly understood genes, provides a resource for future research acceleration, and highlights a need for our awareness of ignorance to be protected from erosion by automated database annotation. (biorxiv.org)
  • However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. (biomedcentral.com)
  • The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes), return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. (biomedcentral.com)
  • For functional annotation, the GO is the de facto standard and its use for modeling microarray and other functional genomics data is growing exponentially [ 13 ]. (biomedcentral.com)
  • To provide more comprehensive annotation of genes and link their activities in a causal framework, the GO developed [http://geneontology.org/docs/gocam-overview/ GO-CAMs]. (geneontology.org)
  • 800px]] The basic unit of a GO-CAM model is the Activity Unit, outlined on the left, which represents a set of standard GO annotations with select annotation extensions, e.g. the inputs and outputs of a molecular function. (geneontology.org)
  • Angler, a companion program to the AceDB database that facilitates visualization of DIC (differential interference contrast) microscopy images coupled with lineage data and 3D cell positions [ 6 ], lacks the ability to edit annotation data as is possible in AceTree. (biomedcentral.com)
  • ACTION: Annotation groups need to get ISS annotations from PAINT into their databases this year. (geneontology.org)
  • Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. (biokeanos.com)
  • Annotation of biomedical documents with machine intelligible semantics facilitates advanced, semantics-based text management, curation, indexing, and search. (biomedcentral.com)
  • This process is widely known as semantic annotation, and the tools that perform it are known as semantic annotators. (biomedcentral.com)
  • Furthermore, STRING also store computationally predicted interactions from: (i) text mining of scientific texts, (ii) interactions computed from genomic features, and (iii) interactions transferred from model organisms based on orthology. (wikipedia.org)
  • Neighborhood: Similar genomic context in different species suggest a similar function of the proteins. (wikipedia.org)
  • Her research program in computational biology focusses on the integration, mathematical modeling and analysis of large-scale, longitudinal genomic, transcriptomic and immunological data from clinical studies to inform and address the mechanisms of immune-resistant cancer progression. (usc.edu)
  • The EMBL-EBI Complex Portal (www.ebi.ac.uk/intact/complex) is a central service that provides manually curated information on stable, on macromolecular complexes from model organisms. (stanford.edu)
  • The database currently holds approximately 2000 complexes with the majority from Saccharomyces cerevisiae, human and mouse. (stanford.edu)
  • The output table reports the coverage of the protein structures aligned to the UniProt sequence, overcoming numbering differences in PDB structures and providing information regarding model quality, protein complexes, ligands, and nucleic acid chain binding. (bvsalud.org)
  • David)some complexes defined by the proteins they containe, some by what the complex does. (geneontology.org)
  • Chris)GO should do complexes, PRO should do proteins which are then pointed to by GO components. (geneontology.org)
  • In molecular biology, STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a biological database and web resource of known and predicted protein-protein interactions. (wikipedia.org)
  • The data is weighted and integrated and a confidence score is calculated for all protein interactions. (wikipedia.org)
  • Predicted interactions are propagated to proteins in other organisms for which interaction has been described by inference of orthology. (wikipedia.org)
  • A web interface is available to access the data and to give a fast overview of the proteins and their interactions. (wikipedia.org)
  • To facilitate research on HD in a network-oriented manner, we have developed HDNetDB, a database that integrates molecular interactions with many HD-relevant datasets. (nature.com)
  • 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)
  • 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)
  • Due to the complex nature of noncovalent interactions and their long-range effects, analyzing protein conformations using network theory can be enlightening. (bvsalud.org)
  • They are also interested in predicting the interactions between ligands and proteins and between two interacting macromolecules and are actively studying the mechanisms of ligand-protein and protein-protein docking. (nationalacademies.org)
  • In this paper we present a radical upgrade to more than 2000 high-throughput datasets, processed to facilitate their comparison, introducing up-to-date collections of transcription termination sites, transcription units, as well as transcription factor binding interactions derived from ChIP-seq, ChIP-exo, gSELEX and DAP-seq experiments, besides expression profiles derived from RNA-seq experiments. (microbiologyresearch.org)
  • STRING is a database of known and predicted protein interactions. (biokeanos.com)
  • The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications. (biokeanos.com)
  • STITCH is a resource to explore known and predicted interactions of chemicals and proteins. (biokeanos.com)
  • VirHostNet 2.0 integrates an extensive and original literature-curated dataset of virus/virus and virus/host protein-protein interactions complemented with publicly available data. (biokeanos.com)
  • Thus, it is a challenge to transform the network of interactions inferred from the analysis of static data into a causal network that allows for the creation of mathematical models whose dynamic behavior can be analyzed and tested against experimental observations. (biomedcentral.com)
  • In the present study, host-pathogen interactions at the transcriptomic level were investigated in an in vitro macrophage infection model. (biomedcentral.com)
  • Mathematical modeling of metabolic networks is a powerful approach to investigate the underlying principles of metabolism and growth. (mdpi.com)
  • The use of this methodology for validating mathematical models from experimental data and designing new experiments is discussed. (researchgate.net)
  • In this approach, mathematical models play a central role for the evaluation of the alternative network structures that arise from literature data-mining, phylogenetic profiling, structural methods, and human curation. (biomedcentral.com)
  • The procedure combines structural bioinformatics tools and mathematical modeling techniques that allow the reconstruction of biochemical networks. (biomedcentral.com)
  • Such networks can then be translated into mathematical models whose dynamic behavior can be analyzed and compared to that of the real system, thus discriminating against some of the proposed topologies when they do not reproduce the expected behavior. (biomedcentral.com)
  • We use mathematical modelling, simulation and optimization to understand complex biological systems and processes. (fairdomhub.org)
  • The Database of Quantitative Cellular Signalling (DOQCS) is a repository of models of signalling pathways present in the neurons. (systems-biology.org)
  • These interacting partners play important roles in various biological processes such as transcriptional regulation, vesicular transport and apoptosis as well as in signaling pathways such as MAPK, mTOR signaling and NOD-like receptor signaling 22 , 23 . (nature.com)
  • Pathways that include all genes in gene_ids. (opensourcebiology.eu)
  • Reactome is a free online database of biological pathways. (opensourcebiology.eu)
  • Provides consolidation for 6,535 human-curated pathways across 12 databases using 7 types and 53 ontological categories. (toronto.edu)
  • MetaCyc does not seek to model the complete metabolic network of any one organism, but to provide a comprehensive collection of experimental pathways. (sri.com)
  • Characterization of signaling pathways immediately downstream of nerve injury could thus help understand the molecular and cellular changes that are critical for its development and uncover new targets for the treatment of chronic pain. (elifesciences.org)
  • Increasing amounts of data that can be mined for information about how proteins in cells assemble as metabolic pathways, signal transduction pathways, and gene circuits, are generated each day. (biomedcentral.com)
  • Such approaches include, among others, differential-equation-based modeling of metabolic systems, constraint-based modeling and metabolic network expansion of metabolic networks. (mdpi.com)
  • BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. (biokeanos.com)
  • It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. (systems-biology.org)
  • To facilitate biocuration efforts, TPC also allows users to select text spans from the full text and annotate them, create customized curation forms for any data type, and send resulting annotations to external curation databases. (biomedcentral.com)
  • It also allows users to create customized curation interfaces, use those interfaces to make annotations linked to supporting evidence statements, and then send those annotations to any database in the world. (biomedcentral.com)
  • It provides unique identifiers, names and synonyms, list of complex members with their unique identifiers (UniProt, ChEBI, RNAcentral), function, binding and stoichiometry annotations, descriptions of their topology, assembly structure, ligands and associated diseases as well as cross-references to the same complex in other databases (e.g. (stanford.edu)
  • The AgBase database includes a suite of computational tools to use GO annotations. (biomedcentral.com)
  • GO-CAMs and Noctua = *This documentation is presented in two parts: ** GO-CAM Principles ** Noctua Curation Tool == GO-CAM Principles == === Standard GO Annotations and GO-CAM Models === ==== Standard GO Annotations ==== [http://geneontology.org/docs/go-annotations/ GO annotations] have been a key component of GO since its inception. (geneontology.org)
  • GO-CAM Models ==== While standard GO annotations are very useful for discerning basic information about genes, they provide only a partial view of each gene's role in a larger biological context. (geneontology.org)
  • Thus, GO-CAM models use standard GO annotations as the foundation on which to build more comprehensive representations of biology. (geneontology.org)
  • Cellular Components in GO-CAMs ==== * Cellular component annotations are intended to capture where the MF enabled by a gene, gene product, or protein-containing complex occurs. (geneontology.org)
  • Cellular component annotations may be further qualified with cell, tissue, and organismal context if that information is germane to the process being modeled. (geneontology.org)
  • David)Automated annotations are too general, result in clustering at high level (like developmental process) which is not that valuable for new groups. (geneontology.org)
  • JWS Online is One of the first resources offering curation of the models it distributes, and online simulation. (systems-biology.org)
  • KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development. (opensourcebiology.eu)
  • Hands-on sessions, lectures and software demonstrations will be included, providing attendees with the necessary skills to access experimental kinetics data from available resources, to assemble computer models with these data, and finally to simulate the generated models using simulation tools. (aeplan.co.jp)
  • BioModels Database is a part of the international initiative BioModels.net, the resource provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. (systems-biology.org)
  • The advent of genome sequencing revealed in humans and other species thousands of genes encoding proteins that had not been identified by previous biochemical or genetic studies. (biorxiv.org)
  • Synopsis: COPASI is a widely used software tool for creating, simulating and analysing models of biochemical reaction networks. (aeplan.co.jp)
  • eQuilibrator is a simple web interface designed to enable easy thermodynamic analysis of biochemical systems. (biokeanos.com)
  • There are two types of user interface available in Noctua: 1) a form interface and 2) a graph interface. (geneontology.org)
  • We recently proposed Moonlight as a bioinformatics framework to predict driver genes and analyze them in a system-biology-oriented manner based on -omics integration. (bvsalud.org)
  • This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. (biokeanos.com)
  • So far I have been working on method development for stochastic models, a moment closure framework and a stochastic reachability method, to look into cell-to-cell-variability. (fairdomhub.org)
  • Integrative network models can provide powerful tools for this. (nature.com)
  • human gut microbiome, data repositories, large-scale and integrative computational tools, modelling, immunomodulation, drug screening Background The human gastrointestinal tract is a complex ecosystem in which eukaryotic cells continuously interact with nutrients and with the complex microbial population of the gut microbiota [1]. (deepdyve.com)
  • Also handling and exchange of biological models based on existing community standards will be demonstrated along with the basic principles of the underlying standard formats and how they support reproducible and FAIR computational modelling. (aeplan.co.jp)
  • The STRING database contains information from numerous sources, including experimental data, computational prediction methods and public text collections. (wikipedia.org)
  • Links are supplied to the originating data of the respective experimental repositories and database resources. (wikipedia.org)
  • Moreover, database models cannot always capture the richness of scientific information, and in some cases, experimental details crucial for reproducibility can only be found in the references used as evidence for the structured data. (biomedcentral.com)
  • KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. (opensourcebiology.eu)
  • Moreover, the experimental methods and bioinformatics tools we provide are widely applicable to many other species including model organisms. (biomedcentral.com)
  • Additional relations between MFs and BPs, e.g. 'causally upstream of or within', can be used to capture experimental information that, in the future, will be incorporated into a more complete model of that process. (geneontology.org)
  • Typical sources of protein structures include experimental structures available at the Protein Data Bank (PDB) and high-quality in silico model structures, such as those available at the AlphaFold Protein Structure Database. (bvsalud.org)
  • GO enrichment analysis of the interacting proteins identified terms related to apoptosis, protein binding, locomotion, hippo signalling and leukocyte and lymphocyte differentiation, supporting the experimental findings. (biomedcentral.com)
  • A particular effort was made to automatically extract detailed experimental growth conditions by implementing an assisted curation strategy applying Natural language processing and machine learning. (microbiologyresearch.org)
  • Synopsis: Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic data and how to simulate them in different systems biology platforms. (aeplan.co.jp)
  • MetaboLights is a database for metabolomics studies, their raw experimental data and associated metadata. (biokeanos.com)
  • Predictions regarding how proteins act in ISC biogenesis are validated by comparison with published experimental results. (biomedcentral.com)
  • Using the Iron Sulfur cluster biogenesis in S. cerevisiae as a test case we indicate how this procedure can be used to analyze and validate the network model against experimental results. (biomedcentral.com)
  • The resource also serves to highlight functional enrichments in user-provided lists of proteins, using a number of functional classification systems such as GO, Pfam and KEGG. (wikipedia.org)
  • Such networks can be used for filtering and assessing functional genomics data and for providing an intuitive platform for annotating structural, functional and evolutionary properties of proteins. (wikipedia.org)
  • MODULE - modules or functional units of genes, BRITE - hierarchical classifications of biological entities, This page was last edited on 22 October 2020, at 18:43. (opensourcebiology.eu)
  • About a quarter are required for viability, and functional screening of the rest revealed hits for fertility, development, locomotion, protein quality control and resilience to stress. (biorxiv.org)
  • The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. (biomedcentral.com)
  • The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. (biokeanos.com)
  • It allows users to obtain, visualize and prioritize molecular interaction networks using HD-relevant gene expression, phenotypic and other types of data obtained from human samples or model organisms. (nature.com)
  • Human HTT codes for a large protein of 3144 amino acids, which is ubiquitously expressed in various tissues and is present in several sub-cellular locations. (nature.com)
  • The human genome encodes ∼20,000 proteins, many still uncharacterised. (biorxiv.org)
  • Since the release of the first draft of the human genome sequence in 2000, the function of many of these new proteins has been identified. (biorxiv.org)
  • Processes such as host-microbe crosstalk, immune activation and inflammation, microbe-microbe signalling, microbial metabolism and antimicrobial activity are bioactive in the human gut [3]. (deepdyve.com)
  • Students will gain knowledge in human genetic variability and DNA repeats, and skills in analyzing high-throughput sequencing data, algorithm design and testing, and database development. (bu.edu)
  • Homology modelling revealed 65% identity between rFg14-3-3e and human 14-3-3 protein YWHAE. (biomedcentral.com)
  • Judy)Gene targets may want to be skewed towards genes known involved in Human disease. (geneontology.org)
  • Ruth)There are human genes which we know a lot about that are not annotated. (geneontology.org)
  • Integration of Evidence across Human and Model Organism Studies: A Meeting Report. (neurotree.org)
  • The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. (biokeanos.com)
  • When differentiated human THP-1 cells were infected with MAP, the expression of various genes associated with stress responses and metabolism was altered in both host and MAP at 3 h post-infection. (biomedcentral.com)
  • Also, this recombinant protein promoted the release of NO and cell apoptosis, and inhibited the proliferation and migration of goat PBMCs and suppressed monocyte phagocytosis. (biomedcentral.com)
  • The aim of my PhD is to understand how noise can be the driving force of decision-making processes (differentiation, self-renewal, apoptosis or tumorgenesis), and what are our chances to control them. (fairdomhub.org)
  • Another possibility to access data STRING is to use the application programming interface (API) by constructing a URL that contain the request. (wikipedia.org)
  • Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. (systems-biology.org)
  • 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)
  • We discuss the general utility of this approach for other databases that capture data from the research literature. (stanford.edu)
  • Web Application Programming Interfaces (APIs) are interfaces that data providers build to empower the outside world to interact with their business logic. (stanford.edu)
  • Hence, EmbedSeg is fully open source (https://github.com/juglab/EmbedSeg), offering (i) tutorial notebooks to train EmbedSeg models and use them to segment object instances in new data, and (ii) a napari plugin that can also be used for training and segmentation without requiring any programming experience. (mpi-cbg.de)
  • OpenSPIM is an Open Access platform for Selective Plane Illumination Microscopy (SPIM) and allows hundreds of laboratories around the world to generate and process light-sheet data in a cost-effective way due to open-source hardware and software. (mpi-cbg.de)
  • 2022). Harmonizing model organism data in the Alliance of Genome Resources. (caltech.edu)
  • Moonlight uses gene expression as a primary data source and combines it with patterns related to cancer hallmarks and regulatory networks to identify oncogenic mediators. (bvsalud.org)
  • As part of the GENESIS project, Dr. Bower's research group has been developing software tools to facilitate access of modelers to the data on which their models depend and access of nonmodelers to model-based analysis of their systems. (nationalacademies.org)
  • Overall, the GENESIS project is intended to provide a new mechanism for scientific communication and collaboration involving both models and data. (nationalacademies.org)
  • These data are critical for the evaluation of network models of nervous-system function. (nationalacademies.org)
  • The first lesions enjoy that the download results of the special politicians can, in Database, all answer voted from the installation Proceedings of the random data. (lightseed.com)
  • Additionally, an online database will be created to store and analyze the variant data. (bu.edu)
  • Options are available to focus on applied data study of neuronal gene expression, aquatic food-webs, or marine fishery management. (bu.edu)
  • Students will gain hands-on experience in data processing, non-parametric statistics, and time-series analysis using R or Python (based on preference). (bu.edu)
  • This project involves developing statistical analyses which combine genome wide association results with prior information from "omics" studies (gene variant functionality, gene expression, methylation, metabolomic data, and proteomic data) to determine regions with common or rare genetic variants that are potentially causally associated with traits of interest. (bu.edu)
  • The genome data source for a specific PGDB can be determined by selecting that PGDB as current database and then executing Tools → Analysis → Summary Statistics. (sri.com)
  • Our data suggest that rFg14-3-3e protein can influence various cellular and immunological functions of goat PBMCs in vitro and may be involved in mediating F. gigantica pathogenesis. (biomedcentral.com)
  • For ChIP-seq experiments we offer both the data as presented by the authors, as well as data uniformly processed in-house, enhancing their comparability, as well as the traceability of the methods and reproducibility of the results. (microbiologyresearch.org)
  • Participants are also encouraged to bring their own questions, models, data, simulations, and workflows that they would like to seek advice or assistance from the tutors during the afternoon session. (aeplan.co.jp)
  • IntAct provides a database system and analysis tools for molecular interaction data. (biokeanos.com)
  • Such an analytical process integrates omics data and provides testable predictions and information about systemic behavior. (biomedcentral.com)
  • The database)Wikipedia of dominant equipment in the inhibiting data is the immigration of severity must- that is played. (cdseidel.de)
  • In summary, a data hub should work in a centralized way, providing a Data Processing Agreement and a formal procedure to identify data providers, as well as data quality control, data integrity and anonymization methods. (bsc.es)
  • Here, we introduce PanDrugs2, a major upgrade of PanDrugs that, in addition to somatic variant analysis, supports a new integrated multi-omics analysis which simultaneously combines somatic and germline variants, copy number variation and gene expression data. (bsc.es)
  • In addition, we suggest several computational tools for studying the distribution of double mutants in the space of model phenotype probabilities. (researchgate.net)
  • The information in this database is authored by biological researchers with expertise in their fields, maintained by the Reactome editorial staff, and cross-referenced with the sequence databases at NCBI , Ensembl and UniProt, the UCSC Genome Browser , HapMap, KEGG ( Gene and Compound), ChEBI , PubMed and GO . (systems-biology.org)
  • The list can be found in the attribute bioservices.kegg.KEGG.databases. (opensourcebiology.eu)
  • Table 1: Main categories for KEGG databases. (opensourcebiology.eu)
  • In the beginning of the KEGG project, KEGG LIGAND consisted of three databases: KEGG COMPOUND for chemical compounds, KEGG REACTION for chemical reactions, and KEGG ENZYME for reactions in the enzyme nomenclature. (opensourcebiology.eu)
  • TRP and its metabolites have key roles in diverse physiological processes including cell growth and maintenance, immunity, disease states and the coordination of adaptive responses to environmental and dietary cues. (mdpi.com)
  • Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. (deepdyve.com)
  • Colonization of the gut starts just after birth when pioneering species interact, through surface receptors, with gut cells to promote the expression of a specific set of host genes and favour the colonization of commensal microorganisms [6]. (deepdyve.com)
  • A relatively large proportion of these genes in these species are electronically predicted. (biomedcentral.com)
  • 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)
  • There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. (researchgate.net)
  • This paper describes results on the association between protein kinase A and peptides corresponding to wild-type PLN (residues 8-22) and peptides bearing mutations (R9C and A11E) which in the context of full-length PLN (52 residues) result in dilated cardiomyopathy. (elifesciences.org)
  • There have been initiatives to develop new means to predict protein function or structure ( 9 - 13 ). (biorxiv.org)
  • Capabilities of bioinformatics tools for optimizing physicochemical features of proteins used in Nano biosensors: A short overview of the tools related to bioinformatics. (opensourcebiology.eu)
  • The large number of genes and the diversity of processes involved in the progression of neurological diseases in general, and HD in specific, emphasizes the need for comprehensive approaches in additional to studies of individual genes 14 . (nature.com)
  • Various assays were used to investigate the stimulatory effects of the purified rFg14-3-3e protein on specific functions of goat PBMCs, including cytokine secretion, proliferation, migration, nitric oxide (NO) production, phagocytosis, and apoptotic capabilities. (biomedcentral.com)
  • On the host side, upregulation of inflammatory cytokine genes was observed along with pattern recognition receptor genes. (biomedcentral.com)
  • In the last decades, HOX proteins have been extensively studied due to their pivotal role in transcriptional events. (mdpi.com)
  • These striking phenotypes result from the control by DLK of a transcriptional program in somatosensory neurons regulating the expression of numerous genes implicated in pain pathogenesis, including the immune gene Csf1 . (elifesciences.org)
  • We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. (researchgate.net)
  • Although HD is monogenic, its molecular manifestation appears highly complex and involves multiple cellular processes. (nature.com)
  • Use of GO in GO-CAMs === ==== Molecular Activities in GO-CAMs ==== * Wherever possible, curators should strive to select the single most granular GO Molecular Function (MF) term that best describes the overall activity of the gene, gene product, or protein-containing complex being annotated. (geneontology.org)
  • Biological Processes in GO-CAMs ==== * The ultimate aim of GO-CAMs is to create a suite of Biological Process (BP)-centric models that can be used to interrogate causal effects of molecular activities on one another as part of the execution of a larger BP. (geneontology.org)
  • Building a Molecular Platform for Understanding the Host-Pathogen Interface in Invertebrates. (exeter.ac.uk)
  • The molecular structure of Fasciola gigantica 14-3-3 protein has been characterized. (biomedcentral.com)
  • Finally, some genes may have roles that are not relevant to laboratory conditions ( Peña-Castillo and Hughes, 2007 ). (biorxiv.org)
  • However, the involvement of this protein in parasite pathogenesis remains elusive and its effect on the functions of innate immune cells is unknown. (biomedcentral.com)
  • 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)
  • In order to identify genes that may modify disease onset and progression, genome-wide association and gene expression studies have been performed 12 , 13 . (nature.com)
  • Current genome assemblies have several thousands of gaps, causing bad gene model predictions due to missing exons and splice sites. (biomedcentral.com)
  • The processing steps used to create BioCyc from an annotated genome are as follows. (sri.com)
  • We include comparisons against previously existing knowledge in RegulonDB from classic experiments, a nucleotide-resolution genome viewer, and an interface that enables users to browse datasets by querying their metadata. (microbiologyresearch.org)
  • BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs. (biokeanos.com)
  • We illustrated several HDNetDB functionalities through a case study and identified proteins that constitute potential cross-talk between HD and the unfolded protein response (UPR). (nature.com)
  • Here, we showcase the main functionalities of the package on the p53 tumor suppressor protein. (bvsalud.org)
  • The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. (biokeanos.com)
  • AceTree, a software application first released in 2006, facilitates exploration, curation and editing of tracked C. elegans nuclei in 4-dimensional (4D) fluorescence microscopy datasets. (biomedcentral.com)
  • Internal requirements have been changed that enable greater flexibility of use both in C. elegans contexts and in other model organisms. (biomedcentral.com)
  • The updates made to the codebase have extended AceTree's applicability beyond its initial use in C. elegans and enabled its usage with other model organisms. (biomedcentral.com)
  • The invariant lineage of the nematode C. elegans [ 1 ] makes the organism a powerful model for studying developmental processes. (biomedcentral.com)
  • Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. (biomedcentral.com)
  • A large-scale user-interface update adds new tools, removes obsolete ones and facilitates improved accessibility of key functionality. (biomedcentral.com)
  • PSNs can be defined according to very different principles, and the available tools have limitations in input formats, supported models, and version control. (bvsalud.org)
  • Notably, alterations in gene sets involved in arginine metabolism were observed in both the host and MAP, along with significant downregulation of NOS2 expression. (biomedcentral.com)
  • Downstream genes involved in type VII secretion systems, cell wall synthesis (polyketide biosynthesis proteins), and iron uptake were changed in response to the intracellular environment of macrophages. (biomedcentral.com)
  • These include the upregulation of immune gene Csf1 (colony stimulating factor 1) in primary sensory neurons. (elifesciences.org)
  • This paper presents the newest iteration of AceTree which contains extensive updates, demonstrates the new applicability of AceTree in other developmental contexts, and presents its evolutionary software development paradigm as a viable model for maintaining scientific software. (biomedcentral.com)
  • However, cancer immune dynamics have yet to be formally quantified and studied as an evolutionary process in the context of immunotherapy clinical trials. (usc.edu)
  • Moreover, PanDrugs2 now considers cancer genetic dependencies to extend tumor vulnerabilities providing therapeutic options for untargetable genes. (bsc.es)
  • Genomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying the different players that define gene regulation, particularly regulation of transcription initiation and operon organization. (microbiologyresearch.org)
  • We illustrate where such mechanisms of pattern formation arise in biological systems from cellular to tissue scales, with an emphasis on morphogenesis. (mpi-cbg.de)
  • Once the oncogenic mediators are identified, it is important to include extra levels of evidence, called mechanistic indicators, to identify driver genes and to link the observed gene expression changes to the underlying alteration that promotes them. (bvsalud.org)
  • Such a mechanistic indicator could be for example a mutation in the regulatory regions for the candidate gene. (bvsalud.org)
  • Coexpression: Predicted association between genes based on observed patterns of simultaneous expression of genes. (wikipedia.org)
  • This project will center on applying nonlinear causal inference to identify interaction between scales of complexity in natural systems (e.g. single fish populations and ecosystem functioning or single cell expression and organism physiology). (bu.edu)
  • We report on the cloning and expression of a recombinant F. gigantica 14-3-3 epsilon protein (rFg14-3-3e), and testing its effects on specific functions of goat peripheral blood mononuclear cells (PBMCs). (biomedcentral.com)
  • Here, we performed a meta-analysis of stroma-, and immune-related gene expression in the PDAC microenvironment to improve disease prognosis and therapeutic development. (bsc.es)
  • We selected 21 PDAC studies from the Gene Expression Omnibus and ArrayExpress databases, including 922 samples (320 controls and 602 cases). (bsc.es)
  • Students will become familiar with genetic studies and software for genetic analysis, and will explore publicly available databases to assign putative function to sets of variants. (bu.edu)
  • PLN interacts with sarco/endoplasmic reticulum Ca 2+ -ATPase (SERCA) and regulates calcium uptake, which is modulated by the protein kinase A (PKA)-dependent phosphorylation of PLN during the fight-or-flight response. (elifesciences.org)
  • Protein-protein interaction networks are an important ingredient for the system-level understanding of cellular processes. (wikipedia.org)
  • The CellML.org model repository is part of the international Physiome Project, and is a resource containing hundreds of computational biology models encoded in the CellML format. (systems-biology.org)
  • It is linked to journals such as Microbiology, FEBS Journal and IEE Proceedings in Systems Biology, that deposit the models upon submission of the manuscripts, so as to make them available to the reviewers. (systems-biology.org)
  • This is a long-awaited resource to make use of such wealth of knowledge and advance our understanding of the biology of the model bacterium E. coli K-12. (microbiologyresearch.org)
  • Because of its involvement in F. gigantica recognition by innate immune cells, rFg14-3-3e protein may have applications for development of diagnostics and therapeutic interventions. (biomedcentral.com)
  • During their migration and development, liver flukes encounter various host tissue types, distinct physiological microenvironments, and a combination of both humoral and cellular immune responses. (biomedcentral.com)
  • It originally went the immune Western League to process such download facing social class: how societal rank influences Secondary, and be some injunctions into NL st for brown ocean( Chicago, Boston, St. Louis, Philadelphia and Manhattan). (ournest.com)
  • Textpresso Central is an online literature search and curation platform that enables biocurators and biomedical researchers to search and mine the full text of literature by integrating keyword and category searches with viewing search results in the context of the full text. (biomedcentral.com)
  • Simi BioCell, a commercial product that enables tracking and documenting cellular divisions, is still aimed at manual lineaging [ 5 ], a significant disadvantage to the automated lineaging pipeline in AceTree. (biomedcentral.com)
  • I am an environmental biologist investigating how environmental stressors affect living organisms in aquatic systems, both within natural environments and in aquaculture. (exeter.ac.uk)
  • MAP upregulates stress-responsive global gene regulators, such as two-component systems and sigma factors, in response to oxidative and cell wall stress. (biomedcentral.com)