Sequences curation model organism genes interfaces databases protein. Medical search. Frequent questions

Secondary databases are:[clarification needed] 23andMe's database HapMap OMIM (Online Mendelian Inheritance in Man): inherited diseases RefSeq 1000 Genomes Project: launched in January 2008. (wikipedia.org)
These databases may hold many species genomes, or a single model organism genome. (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)
Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. (biomedcentral.com)
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)
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)
In 1998, she and colleagues at other model organism databases (MODs) founded the Gene Ontology Consortium (GOC) as they recognized the need to create structured controlled vocabularies for molecular biology to allow comparison of data across different genomes and species. (biocuration.org)
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)
SynteView allows a fast and easy visualization of conservation of gene adjacency in many prokaryotic genomes for which orthology and neighbourhood data have been computed and stored in SynteBase, a dedicated relational database. (molbiol-tools.ca)
BugView - is a genome browser for comparing the arrangement of genes on a pair of related genomes, and can also be used to view individual genomes. (molbiol-tools.ca)
Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. (nature.com)
A phenomenon that has recently come to light via metagenomic studies is the prominence of phages with genomes that are much larger than the average size of ~55 kilobases (kb) predicted based on current genome databases 2 . (nature.com)
The recently reported phage genomes range up to 735 kb in length and encode a diversity of genes involved in transcription and translation, as well as genes that may augment host metabolism 2 . (nature.com)
Augmentation of bacterial energy generation by auxiliary metabolic genes has been reported for phages with smaller genomes. (nature.com)
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)
This interface allows the user to define a set of genomes and displays a tree showing the genomic similarity. (cns.fr)
This interface allows the user to search for common OR specific genes/regions between a query genome/replicon and other genomes/replicons chosen from the ones available in our PkGDB database (i.e, (re)annotation of bacterial genomes or complete proteome downloaded from the RefSeq/WGS sections). (cns.fr)
The RGP_Finder method first starts with the identification of synteny breaks between a query genome and other close genomes chosen from the ones available in our PkGDB database. (cns.fr)
The picture gives an overview of the conservation of synteny groups between the query genome and another genome chosen from the ones available in our PkGDB database (i.e, (re)annotation of bacterial genomes or complete proteome downloaded from the RefSeq/WGS sections). (cns.fr)
These events are computed from the synteny results obtained with the genomes available in the PkGDB database. (cns.fr)
This tool provides some statistics about the similarity results between the selected organism and all the genomes available in our PkGDB database. (cns.fr)
Among the computed values between two compared genomes are: the number and percentage of genes which are in BBH (Bidirectional Best Hit) and in synteny groups, the synteny groups number and size, etc. (cns.fr)
This tool provides some statistics about the similarity results between the selected organism and all the bacterial genomes available in RefSeq/WGS NCBI sections. (cns.fr)

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)
While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. (biomedcentral.com)
Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. (biomedcentral.com)
Starting in 1995, while working for the US Department of Defense, he began work on the the automatic generation of databases from computational ontologies, leading eventually to the founding of Knowledge Bus, Inc., in 1998 to commercialize the technology. (nationalacademies.org)
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)
The GOC is the primary resource for curation and standardization of functional information for all life forms, providing the ability to computational investigate molecular biology information. (biocuration.org)
In this work, a computational study is described to identify novel potential peptides designed by employing a database of non-natural amino acids. (mdpi.com)
Computational methods relying on protein structure strongly depend on the structure selected for investigation. (bvsalud.org)
To achieve such a goal, strategies that combine the different theoretical and computational methods to identify proteins and generate a set of plausible alternative network topologies for the process of interest are needed. (biomedcentral.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, we suggest several computational tools for studying the distribution of double mutants in the space of model phenotype probabilities. (researchgate.net)
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)
Her research group is recognized as one of the country's leading computational groups in atomic-scale modeling of materials and algorithm development. (jhu.edu)

Here, we demonstrate the PhenomeNET Variant Predictor (PVP) system that exploits semantic technologies and automated reasoning over genotype-phenotype relations to filter and prioritize variants in whole exome and whole genome sequencing datasets. (plos.org)
We find that PVP accurately identifies causative variants in whole exome and whole genome sequencing datasets and provides a powerful resource for the discovery of causal variants. (plos.org)
In a retrospective study, we apply PVP to the interpretation of whole exome sequencing data in patients suffering from congenital hypothyroidism, and find that PVP accurately identifies causative variants in whole exome and whole genome sequencing datasets and provides a powerful resource for the discovery of causal variants. (plos.org)
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)
Datasets available for such tasks include the primary literature, large scale micro array experiments, whole genome two hybrid screenings, full genome sequences, and the patterns of conserved/non-conserved homologues and orthologues in them. (biomedcentral.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)

It provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. (wikipedia.org)
FASSO: An AlphaFold based method to assign functional annotations by combining sequence and structure orthology. (usda.gov)
Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. (biomedcentral.com)
In addition, we studied all DPP4 mutations and found the functional substitution R336T weakens both DPP4 protein stability and S-DPP4 binding affinity. (frontiersin.org)
The methods described have application for functional genomics studies, particularly among non-model organisms. (biomedcentral.com)
These and many other functional genomics studies rely on full genomic sequence to establish well-annotated databases. (biomedcentral.com)
Tools like the TIGR Gene index [ 35 ] and Unigene [ 36 ] provide significant information on many species, yet these databases do not meet the needs of functional genomics projects for many non-model species. (biomedcentral.com)
Many methods are currently available to help with the problem of determining causative variant, using information about evolutionary conservation and prediction of the functional consequences of the sequence variant. (plos.org)
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)
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)
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)
Dr. Blake spent most of her career at the Jackson Laboratory (JAX) in Bar Harbor, Maine, where she was a Principal Investigator for the Mouse Genome Informatics project that includes the Mouse Genome Database for the laboratory mouse providing integrated genetic, genomic, and functional data for the study of human diseases. (biocuration.org)
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. (biocuration.org)
Gene-based association testing identified increased risk for iHLHS associated with variation in CAPN2 (p= 1.810(-5)), encoding a protein involved in functional adhesion. (cdc.gov)
AbstractMotivationMolecular-level classification of protein-protein interfaces can greatly assist in functional characterization and rational drug design. (edu.in)
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)

Other databases Nucleosome positioning region database These databases collect genome sequences, annotate and analyze them, and provide public access. (wikipedia.org)
We demonstrate the performance of PVP in identifying causative variants on a large number of synthetic whole exome and whole genome sequences, covering a wide range of diseases and syndromes. (plos.org)

AuReMe enables the reconstruction of metabolic networks from different sources based on sequence annotation, orthology, gap-filling and manual curation. (irisa.fr)
4) The manual curation assistance PADmet module allows the reported metabolic networks and their metadata to be curated. (irisa.fr)

Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction methods. (peerj.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)
AbstractMotivationIncreasing efforts are being made in the field of machine learning to advance the learning of robust and accurate models from experimentally measured data and enable more efficient drug discovery processes. (edu.in)
MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. (biokeanos.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)

Since the first successful identification of disease-causing variation From whole exome sequencing in 2010 [ 1 ], impressive advances have been made in the field of next generation sequencing and its related analysis, with the aim of fulfilling the promise of whole exome (WES) and whole genome (WGS) sequencing for personalized medicine. (plos.org)
The tools can perform powerful whole genome analyses such as prediction of replication origins and termini, estimation of gene expression from codon usage, and genome information visualization. (molbiol-tools.ca)

EggNOG Database: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. (wikipedia.org)
Working with the Quest for Orthologs group, orthology specialists from Harvard's DIOPT group, and representatives from numerous MODs, she helped spearhead the development of the Alliance orthology resources that are essential for data integration across organisms. (biocuration.org)

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)
Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. (biomedcentral.com)
We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. (biomedcentral.com)
PRO is a unique database resource for species-specific protein complexes. (biomedcentral.com)
PRO facilitates robust annotation of variations in composition and function contexts for protein complexes within and between species. (biomedcentral.com)
ProComp, the focus of this manuscript, represents multi-protein complexes, with an initial (but not exclusive) emphasis on protein components of complexes in mouse and human. (biomedcentral.com)
Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules. (biomedcentral.com)
Protein complexes are distinguished from protein-protein interactions in that they are continuant entities, i.e. they endure or continue to exist through time. (biomedcentral.com)
The explicit representation of protein complexes in PRO--defining each member of the complex at the level of its isoform, variant, or modified form--provides the ability to represent complex biological knowledge as it is emerging in the experimental research community in structures that are both human readable and accessible to algorithmic approaches. (biomedcentral.com)
ProComp leverages, and cross references, entries in existing protein-centric informatics resources, including the protein complexes that are represented in the Cellular Component branch of the Gene Ontology. (biomedcentral.com)
In the GO, types of protein complexes are defined in terms of constituent macromolecule classes and the function(s) that the complexes carry out. (biomedcentral.com)
A major contribution of PRO as a protein biology community informatics resource is that it provides a formal ontological structure with foundation in Basic Formal Ontology http://www.ifomis.org/bfo/ to describe types of protein complexes and gives these types unique, permanent identifiers http://www.obofoundry.org/id-policy.shtml . (biomedcentral.com)
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)

Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. (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)
We describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus . (biomedcentral.com)

Human Protein Atlas (HPA): a public database with expression profiles of human protein coding genes both on mRNA and protein level in tissues, cells, subcellular compartments, and cancer tumors. (wikipedia.org)
Predicting tissue-specific mRNA and protein abundance in maize: A machine learning approach. (usda.gov)

Data Sharing and Ontology use among Agricultural Genetics, Genomics and Breeding Databases and Resources of the AgBioData Consortium. (usda.gov)
The web interface for FunnyBase can be accessed at http://genomics.rsmas.miami.edu/funnybase/super_craw4/ . (biomedcentral.com)
Genes Genomics, 2020 Jun. (nih.gov)
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)
View Evolutionary Genomics of Environmental Pollution Several months after the KEGG project was initiated in 1995, the first report of the completely sequenced bacterial genome was published. (opensourcebiology.eu)
HGFDB: a collective database of helmeted guinea fowl genomics. (opensourcebiology.eu)

For this purpose, we developed and validated an annotation method (called pairwise comparative modelling) on the basis of a three-dimensional structure (homology comparative modelling), leading to the prediction of 6,095 ARDs in a catalogue of 3.9 million proteins from the human intestinal microbiota. (nature.com)
Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA) is a fundamental task in microbiology. (peerj.com)
Prediction of driver genes (tumor suppressors and oncogenes) is an essential step in understanding cancer development and discovering potential novel treatments. (bvsalud.org)
Once clustered, a subset of the most closely related templates is selected, and an interface prediction is made. (edu.in)
The prediction of binding affinity is one of the most frequent tasks of compound bioactivity modelling. (edu.in)
Learned models for binding affinity prediction are assessed by their average performance on unseen samples, but point predictions are typically not provided with a rigorous confidence assessment. (edu.in)
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)

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)
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)
We applied RNAi in Drosophila to 260 unknown genes that are conserved between flies and humans. (biorxiv.org)

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)
The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. (biomedcentral.com)
The Gene Ontology Consortium. (biocuration.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)

We have developed a novel algorithm (PVP) which augments existing strategies by using the similarity of the patients phenotype to known phenotype-genotype data in human and model organism databases to further rank potential candidate genes. (plos.org)
Next, based on the similarity of residue level conservation scores derived from the evolutionary profiles, a query protein is hierarchically clustered with all available template proteins in its superfamily with known interface definitions. (edu.in)
Computer-aided strategies are efficient tools for the high-throughput screening of AMPs.ResultsThis report highlights StarPep Toolbox, an open-source and user-friendly software to study the bioactive chemical space of AMPs using complex network-based representations, clustering, and similarity-searching models. (edu.in)
It allows researchers to do nucleotide or amino acid sequence similarity searches against public (or user-customized) databases locally stored. (molbiol-tools.ca)
Ultra-fast sequence clustering from similarity networks with SiLiX. (cns.fr)

Underlying the PATHWAY database is a set of manually drawn images, very similar to classical metabolic pathways charts. (opensourcebiology.eu)
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)

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)

The include: DNA Data Bank of Japan (National Institute of Genetics) EMBL (European Bioinformatics Institute) GenBank (National Center for Biotechnology Information) DDBJ (Japan), GenBank (USA) and European Nucleotide Archive (Europe) are repositories for nucleotide sequence data from all organisms. (wikipedia.org)
Logical and semantic access to related protein forms is critical for advancing bioinformatics approaches to representing, modeling, and reasoning about complex biological systems at the genomic and cellular level [ 1 ]. (biomedcentral.com)
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)
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)
The procedure combines structural bioinformatics tools and mathematical modeling techniques that allow the reconstruction of biochemical networks. (biomedcentral.com)
FastQC (Simon Andrews, Bioinformatics Group, Babraham Institute, UK) - aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. (molbiol-tools.ca)

To predict ARDs in the intestinal microbiota, we developed a method based on protein homology modelling (see Methods) that we termed pairwise comparative modelling (PCM). (nature.com)
Homology modelling revealed 65% identity between rFg14-3-3e and human 14-3-3 protein YWHAE. (biomedcentral.com)
Choosing the right templates in the immunoglobulin superfamily (IgSF) is challenging because its members share low sequence identity and display a wide range of alternative binding sites despite structural homology.ResultsWe present a new approach to predict protein interfaces. (edu.in)

Additionally, an online database will be created to store and analyze the variant data. (bu.edu)
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)
We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. (researchgate.net)

ProForm represents species-specific and species-independent classes of protein isoforms, co- and post-translationally modified forms, and variant forms. (biomedcentral.com)
These characteristics make F. heteroclitus an ideal species to investigate adaptive variation in gene expression. (biomedcentral.com)
Currently, TIGR and NCBI provide gene indices for 28 and 23 animal species, respectively. (biomedcentral.com)
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)
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)
Her background in evolutionary biology motivated her work to represent the relationships between genes across species whenever possible. (biocuration.org)

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)
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)
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)
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)

Biological databases are stores of biological information. (wikipedia.org)
The journal Nucleic Acids Research regularly publishes special issues on biological databases and has a list of such databases. (wikipedia.org)
Omics Discovery Index can be used to browse and search several biological databases. (wikipedia.org)
Database: The Journal of Biological Databases and Curation. (usda.gov)

Some add curation of experimental literature to improve computed annotations. (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)
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)
Predictions regarding how proteins act in ISC biogenesis are validated by comparison with published experimental results. (biomedcentral.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)
MetaboLights is a database for metabolomics studies, their raw experimental data and associated metadata. (biokeanos.com)
The use of this methodology for validating mathematical models from experimental data and designing new experiments is discussed. (researchgate.net)
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)
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)
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)

2) The meneco python package allows the gaps of a metabolic network to be filled by using a topological approach that implements a logical programming approach to solve a combinatorial problem 3) The shogen python package allows genome and metabolic network to be aligned in order to identify genome units which contain a large density of genes coding for enzymes, it also implements a logical programming approach. (irisa.fr)
The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. (biokeanos.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)
In prokaryotes, SecYEG associates with the motor ATPase SecA to carry out translocation for pre-protein secretion. (elifesciences.org)
The encapsulation and compartmentalisation of cells has necessitated the evolution of machineries that conduct proteins across membranes, including for protein secretion and organellar import. (elifesciences.org)
The bulk of protein secretion and membrane protein insertion is conducted by the ubiquitous Sec translocon. (elifesciences.org)
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)

PomBase: the knowledgebase for the fission yeast Schizosaccharomyces pombe SubtiWiki: integrated database for the model bacterium Bacillus subtilis The primary databases make up the International Nucleotide Sequence Database (INSD). (wikipedia.org)
Mouse Genome Database (MGD): Knowledgebase for mouse- human comparative biology. (biocuration.org)
BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. (biokeanos.com)

The goal of the present investigation is to examine the effects of missense mutations in the MERS-CoV S protein on protein stability and binding affinity with DPP4 to provide insight that is useful in developing vaccines to prevent coronavirus infection. (frontiersin.org)
We investigated the effects of MERS-CoV S protein viral mutations on protein stability and binding affinity. (frontiersin.org)
These findings provide further information on how mutations in coronavirus S proteins effect protein function. (frontiersin.org)
A humanized yeast model reveals dominant-negative properties of neuropathy-associated alanyl-tRNA synthetase mutations. (nih.gov)
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)
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)
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)
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 tool provides a list of candidate genes of a query genome potentially involved in a fusion or a fission event. (cns.fr)

We address the problem of how to distinguish which of the many thousands of DNA sequence variants carried by an individual with a rare disease is responsible for the disease phenotypes. (plos.org)
The Dupuis lab develops statistical approaches to identify specific genes or genetic variants that inﬂuence complex phenotypes through their associated quantitative traits, which are traits that can be measured numerically, such as height or blood pressure in humans, and seed size or oil content in plants. (bu.edu)

To assess circulating strains, we characterized the serotypes, sequence types, and antimicrobial susceptibility of 78 S. suis isolates from diseased farmed pigs in Italy during 2017-2019. (cdc.gov)
SSTAR , a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor - combines a locally executed BLASTN search against a customizable database with an intuitive graphical user interface for identifying antimicrobial resistance (AR) genes from genomic data. (molbiol-tools.ca)

JWS Online is One of the first resources offering curation of the models it distributes, and online simulation. (systems-biology.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)
A combination of molecular simulation with hydrogendeuterium-exchange mass spectrometry and electron paramagnetic resonance spectroscopy reveal an asymmetry across the membrane: ATP-induced conformational changes in the cytosolic cavity promote unfolded pre-protein structure, while the exterior cavity favours its formation. (elifesciences.org)

Altogether, our results indicate that the majority of intestinal microbiota ARDs can be considered intrinsic to the dominant commensal microbiota and that these genes are rarely shared with bacterial pathogens. (nature.com)
Bacteriophages (phages), viruses that infect and replicate within bacteria, are important in both natural and human microbiomes because they prey on bacterial hosts, mediate horizontal gene transfer, alter host metabolism and redistribute bacterially derived compounds via host cell lysis 1 . (nature.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)
Multiple representations of sequences include simple motif consensus sequence patterns, parametric representations, probabilistic techniques, graph theoretic approaches, and computer simulations. (nationalacademies.org)
Approaches such as the conformal predictor framework equip conventional models with a more rigorous assessment of confidence for individual point predictions. (edu.in)

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)
There are two types of user interface available in Noctua: 1) a form interface and 2) a graph interface. (geneontology.org)

Furthermore, the NIAID Data Ecosystem Discovery Portal developed by the National Institute of Allergy and Infectious Diseases (NIAID) enables searching across databases. (wikipedia.org)
Meta databases are databases of databases that collect data about data to generate new data. (wikipedia.org)
metadatabase is a database model for metadata management, global query of independent database, and distributed data processing. (wikipedia.org)
many are listed below Model organism databases provide in-depth biological data for intensively studied organisms. (wikipedia.org)
All three accept nucleotide sequence submissions, and then exchange new and updated data on a daily basis to achieve optimal synchronisation between them. (wikipedia.org)
These three databases are primary databases, as they house original sequence data. (wikipedia.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)
Pathway diagrams are interactive and include tools for visualizing gene expression data in the context of the diagrams. (systems-biology.org)
An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. (biomedcentral.com)
In a retrospective study, we further illustrate the application of PVP for the interpretation of whole exome sequencing data in patients suffering from congenital hypothyroidism. (plos.org)
AskOmics is made of three software blocks: (1) a web interface for data import, allowing the creation of a local triplestore from user's datasheets and standard data, (2) an interactive web interface allowing 'à la carte' query-building, (3) a server performing interactions with local and distant triplestores (queries execution, management of users parameters). (irisa.fr)
Five modules are composing AuReMe: 1) The Model-management PADmet module allows manipulating and traceing all metabolic data via a local database. (irisa.fr)
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)
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)
Harmonizing model organism data in the Alliance of Genome Resources. (biocuration.org)
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)
The lab has developed an analysis tool, VNTRseek, to identify VNTRs, using high-throughput sequencing data, but it is limited to those TRs that ﬁt within a sequencing read. (bu.edu)
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)
Options are available to focus on applied data study of neuronal gene expression, aquatic food-webs, or marine fishery management. (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)
This project involves the development of statistical tools and software for jointly analyzing microbial and host data from sequencing experiments, in order to determine community content, microbe-microbe interactions, and host-microbe relationships. (bu.edu)
Microbial DNA sequence data will be collected from soils obtained through a national sampling initiative - the National Ecological Observatory Network (NEON). (bu.edu)
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)
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)
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 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)
It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. (molbiol-tools.ca)
IntAct provides a database system and analysis tools for molecular interaction data. (biokeanos.com)
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)
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)
Transcriptomics data from Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ and, of interest, that the most rapidly growing methanotroph was infected by three pmoC-phages. (nature.com)
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)
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)
The database)Wikipedia of dominant equipment in the inhibiting data is the immigration of severity must- that is played. (cdseidel.de)

PANTHER Pathways consists of over 165, primarily signaling, pathways, each with subfamilies and protein sequences mapped to individual pathway components. (systems-biology.org)
The Database of Quantitative Cellular Signalling (DOQCS) is a repository of models of signalling pathways present in the neurons. (systems-biology.org)
Provides consolidation for 6,535 human-curated pathways across 12 databases using 7 types and 53 ontological categories. (toronto.edu)
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)
Pathways that include all genes in gene_ids. (opensourcebiology.eu)
Reactome is a free online database of biological pathways. (opensourcebiology.eu)
The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. (biokeanos.com)

Mathematical modeling of metabolic networks is a powerful approach to investigate the underlying principles of metabolism and growth. (mdpi.com)
0.001) enrichment in genes associated with amine metabolism. (biomedcentral.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)
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)

Tools for querying and downloading gene expression profiles are provided. (wikipedia.org)

We performed exome sequencing on 331 families with iHLHS aggregated from four independent cohorts. (cdc.gov)

Heterogeneous cDNAs can be amplified with PCR by appending known sequences to one or both ends of the cDNA so primers with known sequences can be used to amplify the heterogeneous cDNAs. (github.io)

They develop methods that can learn conserved structures, functions, features, and motifs from known protein and DNA sequences and use them to predict the function and structures of novel genes and proteins from the genomic efforts. (nationalacademies.org)
When the accuracy of genus predictions was averaged over a representative range of identities with the reference database (100%, 99%, 97%, 95% and 90%), all tested methods had ≤50% accuracy on the currently-popular V4 region of 16S rRNA. (peerj.com)
In these papers, accuracy is defined as the fraction of sequences that are correctly classified at each rank (see Acc RDP in Methods). (peerj.com)
This project will develop new algorithmic and statistical methods to permit detection of longer VNTR repeats and the use of longer read sequencing technologies. (bu.edu)
download malade et heureux huit attitudes and frontman methods for setting and streaming ecosystems of band-pass on, also, and over the emergency's s, and for continuing isolates to ask model magnitude and Systematic monocytogenes connected by right or such terms of accurate and serious policies. (ligaya-technologies.com)

Critical evaluation of the obtained results through this procedure allows devising new wet lab experiments to confirm its predictions or provide alternative explanations for further improving the models. (biomedcentral.com)
Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. (biokeanos.com)

Gene Ontology (GO) enrichment analysis was conducted using Funcassociate 3.0. (biomedcentral.com)

For organisms that live in interaction altogether (microbiotas), complementarity between these networks can be exploited to predict cooperation events. (irisa.fr)
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)

REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. (biokeanos.com)

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)
Due to the complex nature of noncovalent interactions and their long-range effects, analyzing protein conformations using network theory can be enlightening. (bvsalud.org)
STRING is a database of known and predicted protein interactions. (biokeanos.com)
All interactions are derived from literature curation or direct user submissions. (biokeanos.com)
STITCH is a resource to explore known and predicted interactions of chemicals and proteins. (biokeanos.com)
In the present study, host-pathogen interactions at the transcriptomic level were investigated in an in vitro macrophage infection model. (biomedcentral.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)

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)
eQuilibrator is a simple web interface designed to enable easy thermodynamic analysis of biochemical systems. (biokeanos.com)
Synopsis： COPASI is a widely used software tool for creating, simulating and analysing models of biochemical reaction networks. (aeplan.co.jp)

This is reflected by the fact that 498 of the 968-residue polypeptide human AARS shares 41% identity witht the E.coli protein. (nih.gov)
The human genome encodes ∼20,000 proteins, many still uncharacterised. (biorxiv.org)
Besides sequence type (ST) 1, the serotype 2 cluster included ST7, which caused severe human infections in China in 1998 and 2005. (cdc.gov)

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)

Alanyl-tRNA synthetase 1 (AARS1) gene mutation in a family with intermediate Charcot-Marie-Tooth neuropathy. (nih.gov)
Then it searches for HGT features (tRNA hotspot, mobility genes), and for compositional bias (AlienHunter (Vernikos and Parkhill, 2006), SIGI-HMM (Waack et al. (cns.fr)

10,000) and affected by historical, demographic and selective constraints, providing a framework for the partitioning of variation in gene expression within and among populations. (biomedcentral.com)
The Cadbiom software provides a formal framework to help the modeling of biological systems such as cell signaling network with Guarder Transition Semantics. (irisa.fr)
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)
This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. (biokeanos.com)

On the host side, upregulation of inflammatory cytokine genes was observed along with pattern recognition receptor genes. (biomedcentral.com)

Finally, we found that the relative abundance of pdARDs was positively associated with gene richness, but not when subjects were exposed to antibiotics. (nature.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)
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)
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)
The molecular structure of Fasciola gigantica 14-3-3 protein has been characterized. (biomedcentral.com)
Building a Molecular Platform for Understanding the Host-Pathogen Interface in Invertebrates. (exeter.ac.uk)

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)

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)

Co-expression pan-network reveals genes involved in complex traits within maize pan-genome. (usda.gov)
This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. (biomedcentral.com)
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)
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)

I assessed the accuracy of several algorithms using cross-validation by identity, a new benchmark strategy which explicitly models the variation in distances between query sequences and the closest entry in a reference database. (peerj.com)

This protein is 1,353 amino acids in length, and the monomers assemble to form a homotrimer. (frontiersin.org)

Anatomy2

Organisms36

Diseases3

Chemicals and Drugs29

Analytical, Diagnostic and Therapeutic Techniques and Equipment40

Psychiatry and Psychology2

Phenomena and Processes84

Disciplines and Occupations15

Anthropology, Education, Sociology and Social Phenomena2

Technology, Industry, Agriculture4

Humanities1

Information Science55

Health Care14

Genomes25

Computational13

Datasets6

Functional16

Genome sequences2

Manual curation2

Experimentally6

Whole genome2

Orthology2

Complexes14

Annotate3

MRNA and protein2

Genomics6

Prediction7

Drosophila3

Consortium5

Similarity5

Metabolic Pathways2

20001

Bioinformatics6

Homology3

Analyze3

Species6

KEGG8

Biological databases4

Experimental12

Enzymes2

Secretion5

Knowledgebase3

Mutations8

Candidate genes1

Phenotypes2

Antimicrobial2

Simulation3

Bacterial2

Approaches3

Noctua2

Data38

Pathways7

Metabolism4

Downloading gene expression1

Exome1

CDNA1

Methods5

Experiments2

Enrichment analysis1

Interaction2

Manually curated1

Interactions6

Pathway databases2

Biochemical3

Human3

Ligands1

TRNA2

Framework4

Cytokine1

Abundance1

Molecular6

Entities1

Variants1

Expression4

Variation1

Assemble1