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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
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Tetraodon Genome Browser Resource Report Resource Website 1+ mentions |
Tetraodon Genome Browser (RRID:SCR_007079) | data or information resource, database, portal, topical portal | The initial objective of Genoscope was to compare the genomic sequences of this fish to that of humans to help in the annotation of human genes and to estimate their number. This strategy is based on the common genetic heritage of the vertebrates: from one species of vertebrate to another, even for those as far apart as a fish and a mammal, the same genes are present for the most part. In the case of the compact genome of Tetraodon, this common complement of genes is contained in a genome eight times smaller than that of humans. Although the length of the exons is similar in these two species, the size of the introns and the intergenic sequences is greatly reduced in this fish. Furthermore, these regions, in contrast to the exons, have diverged completely since the separation of the lineages leading to humans and Tetraodon. The Exofish method, developed at Genoscope, exploits this contrast such that the conserved regions which can be identified by comparing genomic sequences of the two species, correspond only to coding regions. Using preliminary sequencing results of the genome of Tetraodon in the year 2000, Genoscope evaluated the number of human genes at about 30,000, whereas much higher estimations were current. The progress of the annotation of the human genome has since supported the Genoscope hypothesis, with values as low as 22,000 genes and a consensus of around 25,000 genes. The sequencing of the Tetraodon genome at a depth of about 8X, carried out as a collaboration between Genoscope and the Whitehead Institute Center for Genome Research (now the Broad Institute), was finished in 2002, with the production of an assembly covering 90 of the euchromatic region of the genome of the fish. This has permitted the application of Exofish at a larger scale in comparisons with the genome of humans, but also with those of the two other vertebrates sequenced at the time (Takifugu, a fish closely related to Tetraodon, and the mouse). The conserved regions detected in this way have been integrated into the annotation procedure, along with other resources (cDNA sequences from Tetraodon and ab initio predictions). Of the 28,000 genes annotated, some families were examined in detail: selenoproteins, and Type 1 cytokines and their receptors. The comparison of the proteome of Tetraodon with those of mammals has revealed some interesting differences, such as a major diversification of some hormone systems and of the collagen molecules in the fish. A search for transposable elements in the genomic sequences of Tetraodon has also revealed a high diversity (75 types), which contrasts with their scarcity; the small size of the Tetraodon genome is due to the low abundance of these elements, of which some appear to still be active. Another factor in the compactness of the Tetraodon genome, which has been confirmed by annotation, is the reduction in intron size, which approaches a lower limit of 50-60 bp, and which preferentially affects certain genes. The availability of the sequences from the genomes of humans and mice on one hand, and Takifugu and Tetraodon on the other, provide new opportunities for the study of vertebrate evolution. We have shown that the level of neutral evolution is higher in fish than in mammals. The protein sequences of fish also diverge more quickly than those of mammals. A key mechanism in evolution is gene duplication, which we have studied by taking advantage of the anchoring of the majority of the sequences from the assembly on the chromosomes. The result of this study speaks strongly in favor of a whole genome duplication event, very early in the line of ray-finned fish (Actinopterygians). An even stronger evidence came from synteny studies between the genomes of humans and Tetraodon. Using a high-resolution synteny map, we have reconstituted the genome of the vertebrate which predates this duplication - that is, the last common ancestor to all bony vertebrates (most of the vertebrates apart from cartilaginous fish and agnaths like lamprey). This ancestral karyotype contains 12 chromosomes, and the 21 Tetraodon chromosomes derive from it by the whole genome duplication and a surprisingly small number of interchromosomal rearrangements. On the contrary, exchanges between chromosomes have been much more frequent in the lineage that leads to humans. Sponsors: The project was supported by the Consortium National de Recherche en Genomique and the National Human Genome Research Institute. | duplication, element, euchromatic, evolution, exon, fish, gene, genetic, actinopterygians, aganth, ancestor, cartilaginous, cdna, chromosome, coding, collagen, cytokine, diversity, genome, genomic, heritage, hormone, human, interchromossomal, intergenic, intron, karyotype, lineage, mammal, molecule, mouse, nigroviridis, protein, proteome, pufferfish, receptor, region, selenoprotein, sequence, size, specie, synteny, system, takifugu, tetraodon, transposable, vertebrate | nif-0000-20997 | SCR_007079 | TGB | 2026-09-03 04:49:10 | 8 | ||||||||||
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Broad Institute Resource Report Resource Website 1000+ mentions |
Broad Institute (RRID:SCR_007073) | Broad | institution | Biomedical and genomic research center located in Cambridge, Massachusetts, United States. Nonprofit research organization under the name Broad Institute Inc., and is partners with Massachusetts Institute of Technology, Harvard University, and the five Harvard teaching hospitals. Dedicated to advance understanding of biology and treatment of human disease to improve human health. | biomedical, genomic, research, center, nonprofit, organization, human, biology, disease |
is affiliated with: Massachusetts Institute of Technology; Massachusetts; USA; is affiliated with: Harvard University; Cambridge; United States is affiliated with: Integrative Human Microbiome Project is affiliated with: MIT; Cambridge; Massachusetts; United States is related to: LINCS Information Framework is related to: HMS LINCS Database is related to: Cancer Cell Line Encyclopedia is related to: GO2MSIG is parent organization of: ARACHNE is parent organization of: MuTect is parent organization of: SiPhy is parent organization of: ContEst is parent organization of: Broad Minded is parent organization of: JBrowse is parent organization of: Birdseed is parent organization of: VAAL is parent organization of: SomaticCall is parent organization of: BIRDSUITE is parent organization of: GATK is parent organization of: SNAP - SNP Annotation and Proxy Search is parent organization of: SYZYGY is parent organization of: Genetic Maps of the Rat Genome is parent organization of: LINCS Connectivity Map is parent organization of: Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes is parent organization of: Haploview is parent organization of: Magnaporthe comparative Database is parent organization of: GeneCruiser is parent organization of: Fungal Genome Initiative is parent organization of: Gene Set Enrichment Analysis is parent organization of: GenePattern is parent organization of: MAGENTA is parent organization of: Multiple Myeloma Genomics Portal is parent organization of: ExAc is parent organization of: Ricopili is parent organization of: UnifiedGenotyper is parent organization of: SomaticIndelDetector is parent organization of: RNA-SeQC is parent organization of: Oncotator is parent organization of: ABSOLUTE is parent organization of: PathSeq is parent organization of: V-Phaser 2 is parent organization of: Indelocator is parent organization of: Scripture is parent organization of: VICUNA is parent organization of: Tuberculosis Database is parent organization of: HaploReg is parent organization of: CellProfiler Image Analysis Software is parent organization of: National Institute of Mental Health (NIMH) Human Genetics Initiative is parent organization of: ChemBank is parent organization of: GeneCluster 2: An Advanced Toolset for Bioarray Analysis is parent organization of: Ultrasome is parent organization of: Diabetes Genetics Initiative is parent organization of: Dog Genome Project is parent organization of: Gene Relationships Across Implicated Loci is parent organization of: InVEx is parent organization of: Broad Genetic Analysis Platform is parent organization of: CellProfiler Analyst is parent organization of: ALLPATHS-LG is parent organization of: MutSig is parent organization of: SegSeq is parent organization of: Argo Genome Browser is parent organization of: Integrative Genomics Viewer is parent organization of: MEDEA is parent organization of: Pathline is parent organization of: ASPGD is parent organization of: DGAP is parent organization of: BARD is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: Trinity is parent organization of: Genome Aggregation Database is parent organization of: GenomeSpace is parent organization of: Picard is parent organization of: Connectivity Map 02 is parent organization of: CMap is parent organization of: IndelGenotyper is parent organization of: Discovar assembler is parent organization of: Molecular Signatures Database is parent organization of: GSEA is parent organization of: Eagle is parent organization of: Morpheus by Broad Institute is parent organization of: Cancer Dependency Map Portal is parent organization of: LIGER is parent organization of: Drop-seq tools is parent organization of: scATAC Pipeline is parent organization of: Guide Design Resources is parent organization of: Smart-seq2 Single Sample Pipeline is parent organization of: Smart-seq2 Single Nucleus Multi Sample Pipeline is parent organization of: Broad Terra cloud commons for pathogen surveillance is parent organization of: Single Cell Portal is parent organization of: CEMBA MethylC Seq Pipeline is parent organization of: Pegasus is parent organization of: Cumulus is parent organization of: Cirrocumulus is parent organization of: BICCN Anatomy and Morphology Project is parent organization of: Terra is parent organization of: JUMP Cell Painting Consortium is parent organization of: Spectrum Mill is parent organization of: Polysolver is parent organization of: Brain Cell Data Viewer is parent organization of: Eagle is parent organization of: Broad Institute Imaging Platform Core Facility is parent organization of: ATAC Pipeline is parent organization of: ichorCNA is parent organization of: CRISPick is parent organization of: FireBrowse is parent organization of: Cellarium is parent organization of: multiVIB is parent organization of: SlideTags.wdl is parent organization of: Slide-seq Pipeline is parent organization of: BuildIndices is parent organization of: Broad Institute Genomics Platform has organization facet: GATK HaplotypeCaller has organization facet: GATK VariantFiltration |
Eli and Edythe Broad ; individual donors |
nif-0000-31438, grid.66859.34, Wikidata: Q4971893 | https://ror.org/05a0ya142 | SCR_007073 | Broad Institute of MIT and Harvard, Broad Institute Inc. | 2026-09-03 04:49:06 | 1931 | ||||||
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Chromosome 7 Annotation Project Resource Report Resource Website 10+ mentions |
Chromosome 7 Annotation Project (RRID:SCR_007134) | Chromosome 7 Annotation Project | data or information resource, data repository, database, service resource, storage service resource | Database containing the DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented; the most up to date collation of sequence, gene, and other annotations from all databases (eg. Celera published, NCBI, Ensembl, RIKEN, UCSC) as well as unpublished data. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. The objective of this project is to generate a comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications. There are over 360 disease-associated genes or loci on chromosome 7. A major challenge ahead will be to represent chromosome alterations, variants, and polymorphisms and their related phenotypes (or lack thereof), in an accessible way. In addition to being a primary data source, this site serves as a weighing station for testing community ideas and information to produce highly curated data to be submitted to other databases such as NCBI, Ensembl, and UCSC. Therefore, any useful data submitted will be curated and shown in this database. All Chromosome 7 genomic clones (cosmids, BACs, YACs) listed in GBrowser and in other data tables are freely distributed. | duplication, gene expression, family, fish, gene, gene annotation, genome, breakpoint, chromosome, chromosome 7, clinical, deletion, disease, dna sequence, human, insertion, inversion, polymorphism, rearrangement, segmental duplication, snp, translocation, annotation, data analysis service, blat, cosmid, bac, yac, biomaterial supply resource, malignant, non malignant, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: bio.tools |
PMID:12690205 | Free, (Genomic clones) | nif-0000-03550, biotools:chr7, r3d100012136 | https://bio.tools/chr7, https://doi.org/10.17616/R3VP9V | SCR_007134 | The Chromosome 7 Annotation Project, Chromosome 7 Annotation Project | 2026-09-03 04:49:08 | 13 | |||||
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Vision Public Information Network Resource Report Resource Website |
Vision Public Information Network (RRID:SCR_007340) | data or information resource, portal, topical portal | The National Eye Institute (NEI) created the VISION Public Information Network for the purpose of communicating with public information officers at NEI grantee institutions. The Network''s primary mission is to work with the NEI in disseminating research results to the national and local media. The Network also works to inform the public of the mission of the National Institutes of Health (NIH) to improve the health of America through medical research. The NEI is part of the NIH, U.S. Department of Health and Human Services (DHHS). General information portal for eye and vision related resources for the public. Sponsors: This resource is supported by the National Eye Institute. | eye, grant, health, human, information, media, medical, network, research, vision | has parent organization: National Eye Institute (NEI) Commons | nif-0000-00236 | SCR_007340 | Vision Network | 2026-09-03 04:49:19 | 0 | |||||||||
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NSR Physiome Project Resource Report Resource Website 1+ mentions |
NSR Physiome Project (RRID:SCR_007379) | NSR Physiome Project | data or information resource, portal, professional program, simulation software, software application, software resource, topical portal, training resource | Database of physiological, pharmacological, and pathological information on humans and other organisms and integration through computational modeling. Models include everything from diagrammatic schema, suggesting relationships among elements composing a system, to fully quantitative, computational models describing the behavior of physiological systems and an organism''s response to environmental change. Each mathematical model is an internally self-consistent summary of available information, and thereby defines a working hypothesis about how a system operates. Predictions from such models are subject to test, with new results leading to new models.BR /> A Tool developed for the NSR Physiome project is JSim, an open source, free software. JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim''s primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim''s model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also imports the SBML and CellML model archival formats. All JSim models are open source. Goals of the Physiome Project: - To develop and database observations of physiological phenomenon and interpret these in terms of mechanism (a fundamentally reductionist goal). - To integrate experimental information into quantitative descriptions of the functioning of humans and other organisms (modern integrative biology glued together via modeling). - To disseminate experimental data and integrative models for teaching and research. - To foster collaboration amongst investigators worldwide, to speed up the discovery of how biological systems work. - To determine the most effective targets (molecules or systems) for therapy, either pharmaceutic or genomic. - To provide information for the design of tissue-engineered, biocompatible implants. | physiome, computational modeling, cell, organ, organism, human, model, physiological, pharmacological, pathological, model repository, sbml, cellml, biophysics, biochemistry, database, proteome, jsim simulation analysis system, data analysis tool, parameter optimization tool, integrating biological system | has parent organization: University of Washington; Seattle; USA | NSF BE08407; NHLBI T15 HL88516-01; NSF BES-0506477; NHLBI R01HL073598; NIBIB R01EB001973 |
nif-0000-00532 | SCR_007379 | National Simulation Resource Physiome Project | 2026-09-03 04:49:11 | 3 | |||||||
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eMERGE Network: electronic Medical Records and Genomics Resource Report Resource Website 1+ mentions |
eMERGE Network: electronic Medical Records and Genomics (RRID:SCR_007428) | eMERGE | data or information resource, portal, topical portal | A national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. The consortium is composed of seven member sites exploring the ability and feasibility of using EMR systems to investigate gene-disease relationships. Themes of bioinformatics, genomic medicine, privacy and community engagement are of particular relevance to eMERGE. The consortium uses data from the EMR clinical systems that represent actual health care events and focuses on ethical issues such as privacy, confidentiality, and interactions with the broader community. | human, clinical, dna, alzheimer's disease, genome, genomics, gene, genetic, nervous system disease, nucleotide polymorphism, phenotype, bioinformatics, genomic medicine, privacy, community engagement, emr, electronic medical record |
is related to: PheKB is related to: NCBI database of Genotypes and Phenotypes (dbGap) is related to: PheWAS Catalog has parent organization: Vanderbilt University; Tennessee; USA |
Aging | NIGMS ; NHGRI |
Available to the research community | nif-0000-00539 | SCR_007428 | eMERGE Network: electronic Medical Records & Genomics - A consortium of biorepositories linked to electronic medical records data for conducting genomics studies, eMERGE Network: electronic Medical Records Genomics, eMERGE Network: electronic Medical Records & Genomics, eMERGE Network, electronic Medical Records & Genomics, The eMERGE Network: electronic Medical Records & Genomics | 2026-09-03 04:49:08 | 2 | |||||
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aneurIST Resource Report Resource Website 1+ mentions |
aneurIST (RRID:SCR_007427) | aneurIST | data or information resource, disease-related portal, portal, topical portal | Project focused on cerebral aneurysms and provides integrated decision support system to assess risk of aneurysm rupture in patients and to optimize their treatments. IT infrastructure has been developeded for management and processing of vast amount of heterogeneous data acquired during diagnosis. | gene, genetic, adult, cerebral aneurysm, cerebral brain hemorrhage, cerebral hemorrhage, cerebral parenchymal hemorrhage, cerebral hemorrhage, clinical, genomic, human, intracerebral hemorrhage, intracranial aneurysm, subarachnoid hemorrhage, risk, aneurysm rupture, patient, treatment, infrastructure, platform, genomics, disease, personalized risk assessment, bioinformatics, clinical, data management, data integration, data processing, software tool, cerebrum | has parent organization: Pompeu Fabra University; Barcelona; Spain | Cerebral aneurysm, Subarachnoid hemorrhage, Aging | European Union ; Sixth FPPriority 2 of the Information Society Technologies IST |
nif-0000-00538 | http://www.cilab.upf.edu/aneurist1/ | SCR_007427 | aneurIST - Integrated Biomedical Informatics for the Management of Cerebral Aneurysms, (at)neurIST, (at)neurIST - Integrated Biomedical Informatics for the Management of Cerebral Aneurysms | 2026-09-03 04:49:18 | 5 | |||||
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Allen Human Brain Atlas Resource Report Resource Website 100+ mentions |
Allen Human Brain Atlas (RRID:SCR_007416) | atlas, data or information resource, data processing software, data visualization software, database, software application, software resource | Multi modal atlas of human brain that integrates anatomic and genomic information, coupled with suite of visualization and mining tools to create open public resource for brain researchers and other scientists. Data include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is desktop software application for viewing human brain anatomy and gene expression data in 3D. | atlas, human, brain, anatomic, genomic, data, visualization, mining, tool, MRI, DTI, histology, gene, expression |
is related to: Speech Language Disorders Database has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Individual private donors ; U.S. Department of Health and Human Services 1C76HF15069; U.S. Department of Health and Human Services 1C76HF19619 |
PMID:23041053 | Free, Available for download, Freely available | nif-0000-00506 | http://humancortex.alleninstitute.org, http://human.brain-map.org/ | SCR_007416 | Human Cortex Study, Allen Institute for Brain Science Human Cortex Study, Allen Brain Atlas - Human Brain | 2026-09-03 04:49:35 | 135 | |||||
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VISTA Enhancer Browser Resource Report Resource Website 100+ mentions |
VISTA Enhancer Browser (RRID:SCR_007973) | VISTA Enhancer Browser | data or information resource, data repository, database, service resource, storage service resource | Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth. | human, noncoding fragment, mutant mouse strain, molecular neuroanatomy resource, image, telencephalon, development, genome, enhancer, dna fragment, embryo, embryonic mouse, brain, neural tube, eye, ear, heart, tail, limb, nose, cranial nerve, trigeminal, dorsal root ganglia, face, branchial arch, gene expression, annotation, vector, transgenic embryo, lacz reporter vector, lacz, biomaterial supply resource, in vivo, image collection, transcriptional enhancer, chip-seq, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: NIF Data Federation is related to: One Mind Biospecimen Bank Listing is related to: OMICtools has parent organization: Lawrence Berkeley National Laboratory |
American Heart Association ; DOE contract DE-AC02-05CH11231; DOE DE020060; NHGRI HG003988; NHLBI HL066681; NIDCR ; NINDS NS062859 |
PMID:17130149 | Free, Freely available | nif-0000-03637, OMICS_01568, biotools:vista_enhancer_browser | https://bio.tools/vista_enhancer_browser | SCR_007973 | 2026-09-03 04:49:31 | 249 | |||||
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VEGA Resource Report Resource Website 500+ mentions |
VEGA (RRID:SCR_007907) | VEGA | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Central repository for high quality frequently updated manual annotation of vertebrate finished genome sequence. Human, mouse and zebrafish are in the process of being completely annotated, whereas for other species the annotation is only of specific genomic regions of particular biological interest. The majority of the annotation is from the HAVANA group at the Welcome Trust Sanger Institute. Users can BLAST, search for specific text, export, and download data. Genomes and details of the projects for each species are available through the homepages for human mouse and zebrafish. The website is built upon code from the EnsEMBL (http://www.ensembl.org) project. Some Ensembl features are not available in Vega. From the users point of view perhaps the most significant of these is MartView. However due to their inclusion in Ensembl, Vega human and mouse data can be queried using Ensembl MartView. Vega contains annotation of the human MHC region in eight haplotypes, and the LRC region in three haplotypes. Vega also contains annotation on the Insulin Dependent Diabetes (IDD) regions on non-reference assemblies for mouse. | human, mouse, zebrafish, gorilla, wallaby, pig, dog, vertebrate, genome, orfs, FASEB list |
is listed by: Sequencing of Idd regions in the NOD mouse genome is related to: Consensus CDS has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:18003653 PMID:15975227 PMID:15608237 |
r3d100012575 | https://doi.org/10.17616/R3W77X | SCR_007907 | The Vertebrate Genome Annotation database (VEGA), Vertebrate Genome Annotation, Vertebrate Genome Annotation Database | 2026-09-03 04:49:30 | 765 | ||||||
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Multimodal Imaging Laboratory Resource Report Resource Website |
Multimodal Imaging Laboratory (RRID:SCR_008071) | MMIL | data or information resource, laboratory portal, organization portal, portal | An interdisciplinary group of scientists and clinicians who study the human brain using a variety of imaging, recording, and computational techniques. Their primary goal is to bridge non-invasive imaging technologies to the underlying neurophysiology of brain neuronal circuits for a better understanding of healthy human brain function, and mechanisms of disruption of this function in diseases such as Alzheimer's, epilepsy and stroke. The other goal of the MMIL is to develop and apply advanced imaging techniques to understanding the human brain and its disorders. In order to ground these methodological developments in their underlying neurobiology, invasive studies in humans and animals involving optical and micro physiological measures are also performed. These methodologies are applied to understanding normal function in sleep, memory and language, development and aging, and diseases such as dementia, epilepsy and autism. | dti, eeg, epilepsy, fmri, function, aging, alzheimer's, autism, brain, dementia, development, disease, disorder, human, mechanism, memory, microphysiological, neurobiology, neuronal circuit, neurophysiology, noninvasive methodology, pet, sleep, stroke, structural mri, language, meg, structural mri, meg |
has parent organization: University of California at San Diego; California; USA is parent organization of: Pediatric Imaging Neurocognition and Genetics |
Aging | nif-0000-10521 | SCR_008071 | 2026-09-03 04:49:32 | 0 | ||||||||
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Human Gut Microbiome Initiative Resource Report Resource Website |
Human Gut Microbiome Initiative (RRID:SCR_008137) | data or information resource, database, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2022. Human Gut Microbiome Initiative (HGMI) seeks to provide simply annotated, deep draft genome sequences for 100 cultured representatives of the phylogenetic diversity documented by 16S rRNA surveys of the human gut microbiota. Humans are supra-organisms, composed of 10 times more microbial cells than human cells. Therefore, it seems appropriate to consider ourselves as a composite of many species - human, bacterial, and archaeal - and our genome as an amalgamation of human genes and the genes in ''our'' microbial genomes (''microbiome''). In the same sense, our metabolome can be considered to be a synthesis of co-evolved human and microbial traits. The total number of genes present in the human microbiome likely exceeds the number of our H. sapiens genes by orders of magnitude. Thus, without an understanding of our microbiota and microbiome, it not possible to obtain a complete picture of our genetic diversity and of our normal physiology. Our intestine is home to our largest collections of microbes: bacterial densities in the colon (up to 1 trillion cells/ml of luminal contents) are the highest recorded for any known ecosystem. The vast majority of phylogenetic types in the distal gut microbiota belong to just two divisions (phyla) of the domain Bacteria - the Bacteroidetes and the Firmicutes. Members of eight other divisions have also been identified using culture-independent 16S rRNA gene-based surveys. Metagenomic studies of complex microbial communities residing in our various body habitats are limited by the availability of suitable reference genomes for confident assignment of short sequence reads generated by highly parallel DNA sequencers, and by knowledge of the professions (niches) of community members. Therefore, HGMI, which represents a collaboration between Washington University''s Genome Center and its Center for Genome Sciences, seeks to provide simply annotated, deep draft genome sequences for 100 cultured representatives of the phylogenetic diversity documented by 16S rRNA surveys of the human gut microbiota. | ecosystem, firmicutes, bacterial, bacteroidetes, body, cell, diversity, genome, gut, habitat, human, metabolom, microbial, microbiome, microbiota, phylogenetic, rrna, sequence, specie, synthesis | has parent organization: Washington University in St. Louis; Missouri; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20960 | http://genome.wustl.edu/projects/athaliana/ | SCR_008137 | HGMI | 2026-09-03 04:49:23 | 0 | |||||||
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Atlas of Medical Parasitology Resource Report Resource Website |
Atlas of Medical Parasitology (RRID:SCR_008163) | A.M.P., AMP | data or information resource, data repository, database, image repository, service resource, storage service resource |
Database of images on medical parasitology created to provide educational materials for medical students primarily, but professional workers in medical or paramedical fields may also refer to this site covering the significant parasites in the world. Each database of protozoans, nematodes, trematodes, cestodes and arthropods contains information on the morphology, life cycle, geographical distribution, symptoms, prevention, etc. Users who wish to contribute can send the editor unpublished images of human parasites (microscopical, clinical, radiological or epidemiological aspects of human parasitic infections) by mail or e-mail. Pathology specimens (slide, samples) are welcome too. The A.M.P. received the citation of reliable sources such as Parasitology today and The Lancet, and is now listed in the Internet Resources on Specific Infectious Diseases Topics of the Mandell, Douglas and Bennets Principles and Practice of Infectious Diseases Fifth Edition. This website was established with a great contribution of the PROJECT COLLABORATORS and many contributors of The Korean Society for Parasitology. |
epidemiological, clinical, disease, human, infection, medical, microscopical, parasite, parasitic, parasitology, pathology, radiological, specimen, morphology, life cycle, geographical distribution, symptom, prevention, human parasite, biospecimen repository, training material, image | has parent organization: Chungbuk National University; Cheongju; South Korea | Human parasitic infection | Ministry of Health and Welfare - Republic of Korea ; Korean Medical Research Information Center |
The community can contribute to this resource | nif-0000-21025 | http://www.cdfound.to.it/_atlas.htm | SCR_008163 | Web Atlas of Medical Parasitology | 2026-09-03 04:49:51 | 0 | ||||
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Gene Regulation Databases Resource Report Resource Website 100+ mentions |
Gene Regulation Databases (RRID:SCR_008033) | Gene Regulation Public Databases | data or information resource, portal, topical portal | In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers academic and non-profit organizations free access to reduced functionality versions of their products. TRANSFAC Professional provides gene regulation analysis solutions, offering the most comprehensive collection of eukaryotic gene regulation data. The professional paid subscription gives customers access to up-to-date data and tools not available in the free version. The public databases currently available for academic and non-profit organizations are: * TRANSFAC: contains data on transcription factors, their experimentally-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. * TRANSPATH: provides data about molecules participating in signal transduction pathways and the reactions they are involved in, resulting in a complex network of interconnected signaling components.TRANSPATH focuses on signaling cascades that change the activities of transcription factors and thus alter the gene expression profile of a given cell. * PathoDB: is a database on pathologically relevant mutated forms of transcription factors and their binding sites. It comprises numerous cases of defective transcription factors or mutated transcription factor binding sites, which are known to cause pathological defects. * S/MARt DB: presents data on scaffold or matrix attached regions (S/MARs) of eukaryotic genomes, as well as about the proteins that bind to them. S/MARs organize the chromatin in the form of functionally independent loop domains gained increasing support. Scaffold or Matrix Attached Regions (S/MARs) are genomic DNA sequences through which the chromatin is tightly attached to the proteinaceous scaffold of the nucleus. * TRANSCompel: is a database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signaling pathways. * PathoSign Public: is a database which collects information about defective cell signaling molecules causing human diseases. While constituting a useful data repository in itself, PathoSign is also aimed at being a foundational part of a platform for modeling human disease processes. | element, eukaryote, eukaryotic, expression, functionally, gene, genome, alignment, bind, binding site, cell, chromatin, collaborative, component, coupling, disease, dna, domain, human, matrix, molecular weight, molecule, mononucleotide, network, nucleotide, nucleus, pathological, protein, region, regulated, regulatory, scientific research, sequence, signaling, signal pathway, transcription factor, molecular neuroanatomy resource |
lists: TRANSFAC has parent organization: BIOBASE Corporation |
BIOBASE | nif-0000-10230 | SCR_008033 | gene-regulation.com: Public Databases for Academic and Non-profit Organizations | 2026-09-03 04:49:46 | 130 | |||||||
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HPV Sequence Database Resource Report Resource Website 1+ mentions |
HPV Sequence Database (RRID:SCR_008154) | data or information resource, database, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 23, 2016. The Human Papillomaviruses Database collects, curates, analyzes, and publishes genetic sequences of papillomaviruses and related cellular proteins. It includes molecular biologists, sequence analysts, computer technicians, post-docs and graduate research assistants. This Web site has two main branches. The first contains our four annual data books of papillomavirus information, called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. and the second contains papillomavirus genetic sequence data. There is also a New Items location where we store the latest changes to the database or any other current news of interest. Besides the compendium, we also provide genetic sequence information for papilloma viruses and related cellular proteins. Each year they publish a compendium of papillomavirus information called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. which can now be downloaded from this Web site. | gene, genetic, alignment, amino acid, biologist, cellular protein, genome, human, molecular, papilloma, papillomavirus, phylogenetic, sequence, virus | has parent organization: Los Alamos National Laboratory | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21000 | http://www.stdgen.lanl.gov/ | SCR_008154 | HPVSD | 2026-09-03 04:49:35 | 4 | |||||||
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U.S. Pig Genome Project Resource Report Resource Website |
U.S. Pig Genome Project (RRID:SCR_008151) | data or information resource, database, portal, topical portal | Database and resources on the pig genome. | embryo, embryonic, environmental, exercise, exposure, fat, feed, feeding, fibroblast, food, foot and mouth disease, function, genetic, acute, additive, alcohol, alcoholism, atherosclerosis, bed, behavior, biological, bone, breed, cancer, cell, chronic, clone, degenerative, density, deposition, dermal, developmental, diabetes, dietary, digestive, disease, genome, genomic, growth, habit, healing, human, hypertension, kidney, mammal, map, melanoma, metabolism, nephropathy, nuclear, nutrition, obesity, omnivore, organ, organism, parenteral, pathogen, pattern, phenotype, phenotypic, physiology, pig, pollutant, population, porcine, prenatal, pulmonary, reproductive, respiratory, retinal, sex, shock, size, social, somatic, structure, swine, taxon, technique, tissue, tobacco, transplantation, variation, vascular, warfare, xenobiotic, model | is listed by: 3DVC | nif-0000-20986 | SCR_008151 | U.S. Pig Genome Project | 2026-09-03 04:49:51 | 0 | |||||||||
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Department of Psychiatry, Turner Laboratory Resource Report Resource Website |
Department of Psychiatry, Turner Laboratory (RRID:SCR_008067) | Turner Lab | data or information resource, laboratory portal, organization portal, portal | Dr. Eric Turner''s laboratory studies the mechanisms underlying the development of the nervous system. The vertebrate brain is comprised of a tremendous variety of neurons, each class exhibiting a unique phenotype characterized by the expression of specific neurotransmitter receptors, ion channels, patterns of axonal growth, and synapse formation. The research we conduct focuses on the critical role transcription factors play in the specification of neuronal cell type during development. We are particularly interested in transcription factors of the homeodomain family that bind to DNA and in doing so activate or repress gene expression. One area of study is the role of POU-domain transciption factor Brn3a in axon growth and survival. The primary research areas are: * Neuronal cell fate determination: The expression of regulatory genes is manipulated in living chick embryos using microsurgery and electroporation and the effects on neural marker genes studied. * Molecular mechanisms of gene regulation: Target DNA binding sites of neural transcription factors are biochemically characterized and findings coordinated with sequence data from the mouse and human genomes. * Targeted misexpression of regulatory genes: Transgenic and knockout mouse technology is used to misexpress genes of interest, and the effects on neural marker genes, axonal growth, and cell survival studied. * Global analysis of neural gene expression: Micro-arrays (GeneChips) are employed in conjunction with other areas of study to understand the coordinated regulation of gene expression in the nervous system. Dr. Turner is a member of the University of California, San Diego''s Graduate Program in Neuroscience and Biomedical Sciences Program and accepts students from these two programs. Interesting rotation projects are available using methods ranging from biochemistry and molecular biology to embryology. Additionally, Dr. Turner is also the Director of this NIMH-funded training program for research-oriented psychiatrists, psychologists, and basic neuroscientists working in areas relevant to psychiatry. Typically Fellows spend two years in the program, during which they develop a research project under the close supervision of one of the highly productive members of the UCSD Department of Psychiatry, or another investigator in the La Jolla (UCSD/Salk/Scripps) research community. | electroporation, embryo, embryology, expression, gene, axon, biochemistry, biomedical science, cell, c hick, development, dna, dna binding site, homeodomain, human, knockout technology, microarray, microsurgery, misexpression, molecular biology, molecular mechanism, mouse, nervous system, neural gene, neural marker gene, neural transcription factor, neuronal cell, neuroscience, neuroscientist, psychiatrist, psychologist, regulation, regulatory gene, transcription factor, transgenic technology | has parent organization: University of California at San Diego Department of Psychiatry | nif-0000-10507 | SCR_008067 | UCSD Turner Laboratory, UCSD Psychiatry (Turner''s Lab), Turner Laboratory, Turner Laboratory Developmental Neurobiology Research | 2026-09-03 04:49:34 | 0 | ||||||||
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GeneWindow Resource Report Resource Website 1+ mentions |
GeneWindow (RRID:SCR_008183) | data analysis software, data processing software, software application, software resource | Software tool for pre- and post-genetic bioinformatics and analytical work, developed and used at the Core Genotyping Facility (CGF) at the National Cancer Institute. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro, or in novel genetic association studies. The Genewindow application and source code is publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions. Features of GeneWindow include: -Intuitive representation of genomic variation using advanced web-based graphics (SVG) -Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates -Gene-centric display (only when a gene of interest is in view) oriented 5 to 3 regardless of the reference strand and adjacent genes -Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview -Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5 or 3 direction (relative to the current gene) -Lists of available genomic features -Search for sequence matches in the Locus Overview -Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature -Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI -Integration with a Laboratory Information Management System (LIMS) or other databases is possible | gene, genetic, analysis, annotation, archive, bioinformatic, cancer, genome, genomic, genotype, genotyping, human, human genome databases, maps, polymorphism, position, variation, data set |
is listed by: 3DVC has parent organization: National Cancer Institute |
nif-0000-21173 | SCR_008183 | GeneWindow | 2026-09-03 04:49:37 | 1 | |||||||||
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University of Texas at San Antonio Laboratory of Professor Brenda Claiborne Resource Report Resource Website 1+ mentions |
University of Texas at San Antonio Laboratory of Professor Brenda Claiborne (RRID:SCR_008064) | UTSA Claiborne Lab | data or information resource, data set, laboratory portal, organization portal, portal | The long-term goals of my research are to understand the relationship between neuronal structure and function, and to elucidate the factors that affect neuronal morphology and function over the lifespan of the mammal. Currently we are examining 1) the effects of synaptic activity on neuronal development; 2) the effects of estrogen on neuronal morphology and on learning and memory; and, 3) the effects of aging on neuronal structure and function. We have focused our efforts on single neurons in the hippocampal formation, a region that is critical for certain forms of learning and memory in rodents and humans. From the portal, you may click on a cell in your region of interest to see the complete database of cells from that region. You may also explore the Neuron Database: * Comparative Electrotonic Analysis of Three Classes of Rat Hippocampal Neurons. (Raw data available) * Quantitative, three-dimensional analysis of granule cell dendrites in the rat dentate gyrus. * Dendritic Growth and Regression in Rat Dentate Granule Cells During Late Postnatal Development.(Raw data available) * A light and electron microscopic analysis of the mossy fibers of the rat dentate gyrus. | neuronal, structure, synaptic activity, rodent, human, neuron, neuronal morphology, synapse, neuronal development, learning, memory, estrogen, hippocampus, hippocampal formation, mammal, cell | has parent organization: University of Texas at San Antonio; Texas; USA | Aging | nif-0000-10481 | SCR_008064 | USTA Laboratory of Professor Brenda Claiborne | 2026-09-03 04:49:32 | 1 | |||||||
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RIKEN Omics Science Center Resource Report Resource Website |
RIKEN Omics Science Center (RRID:SCR_008241) | data or information resource, disease-related portal, portal, research forum portal, topical portal | Omics Science Center is aiming to develop a comprehensive system called Life Science Accelerator(LSA) for the advancement of omics research. The LSA is a comprehensive system consists of biological resources, human resources, technologies, know-how, and essential administrative ability. Ultimate goal of LSA is to support and accelerate the advancement in life science research. Omics is the comprehensive study of molecules in living organisms. The complete sequencing of genomes (the complete set of genes in an organism) has enabled rapid developments in the collection and analysis of various types of comprehensive molecular data such as transcriptomes (the complete set of gene expression data) and proteomes (the complete set of intracellular proteins). Fundamental omics research aims to link these omics data to molecular networks and pathways in order to advance the understanding of biological phenomena as systems at the molecular level. | expression, gene, genome, human, intracellular, life, living, model organisms and comparative genomics databases, molecule, omics, organism, pathway, protein, proteome, science, sequence, technology, transcriptome | is parent organization of: FANTOM DB | RIKEN Yokohama Institute Yokohama Research Promotion Division of Japan | nif-0000-21361 | SCR_008241 | RIKEN OSC | 2026-09-03 04:49:53 | 0 |
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