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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Sybil Resource Report Resource Website 10+ mentions |
Sybil (RRID:SCR_005593) | Sybil | software resource, database, data or information resource | A web-based software package for comparative genomics. | comparative genomics, genome, synteny, protein cluster, protein, gene, genomic region, synteny gradient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22121156 | OMICS_00945, biotools:sybil | https://bio.tools/sybil | SCR_005593 | Sybil: Web-based software for comparative genomics | 2026-08-04 09:41:23 | 37 | ||||||
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Human Adenovirus Type Classification Resource Report Resource Website 100+ mentions |
Human Adenovirus Type Classification (RRID:SCR_005753) | HAdV Type Classification | knowledge environment, analysis service resource, production service resource, service resource | The Human Adenovirus Type Classification coordinates the naming of candidate new types, prior to manuscript submission for peer review. This resource contains a method of submitting candidate HAdV, criteria for a new HAdV type, and a Serotyping tool, which displays all potential types corresponding to the query serotype entered by a user. The criteria are based on discussions at the International Adenovirus Meeting (Dobog��k, Hungary; 26-30 April, 2009) and the NIH Human Adenovirus Working Group Workshop (Bethesda, MD. USA; 3 February 2011), which are summarized in a Letter to the Editor. | hadv, human adenovirus, adenovirus, classification, serotyping, genotyping, genome, nucleotide sequence, human adenovirus working group, serotype | has parent organization: George Mason University; Virginia; USA | Adenovirus | nlx_149215 | SCR_005753 | 2026-08-04 09:41:26 | 121 | ||||||||
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CLIPZ Resource Report Resource Website 10+ mentions |
CLIPZ (RRID:SCR_005755) | CLIPZ | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets. | rna-binding protein, binding site, protein, functional annotation, cross-linking and immunoprecipitation, short read, mrna-seq, digital gene expression, small rna cloning, visualization, mining, analysis, post-transcriptional regulatory element, genome, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Basel; Basel; Switzerland |
PMID:21087992 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02256, biotools:clipz | https://bio.tools/clipz | SCR_005755 | 2026-08-04 09:41:26 | 20 | ||||||
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Honey Bee Genome Project Resource Report Resource Website 1+ mentions |
Honey Bee Genome Project (RRID:SCR_002890) | topical portal, portal, data or information resource | The HGSC has sequenced the honey bee, Apis mellifera. The version 4.0 assembly was released in March 2006 and published in October 2006. The genome sequence is being upgraded with additional sequence coverage. The honey bee is important in the agricultural community as a producer of honey and as a facilitator of pollination. It is a model organism for studying the following human health issues: immunity, allergic reaction, antibiotic resistance, development, mental health, longevity and diseases of the X chromosome. In addition, biologists are interested in the honey bee's social organization and behavioral traits. This project was proposed to the HGSC by a group of dedicated insect biologists, headed by Gene Robinson. Following a workshop at the HGSC and a honey bee white paper, the HGSC began the project in 2002. A 6-fold coverage WGS, BAC sequence from pooled arrays, and an initial genome assembly (Amel_v1.0) were released beginning in 2003. This has been a challenging project with difficulty in recovering AT-rich regions. The WGS data had lower coverage in AT-rich regions and BAC data from clones showed evidence of internal deletions. Additional reads from AT enriched DNA addressed these underrepresented regions. The current assembly Amel_4.0 was produced with Atlas and includes 2.7 million reads (1.8 Gb) or 7.5x coverage of the (clonable) genome. About 97% of STSs, 98% of ESTs, and 96% of cDNAs are represented in the 231 Mb assembly. About 2,500 reads were also produced from a strain of Africanized honey bee and SNPs were extracted. These were released in dbSNP and the NCBI Trace Archive. Analysis of the genome by a consortium of 20 labs has been completed. This produced a gene list derived from five different methods melded through the GLEAN software. Publications include a main paper in Nature and up to forty companion papers in Genome Research and Insect Molecular Biology. Sponsors: Sequencing of the honey bee is jointly funded by National Human Genome Research Institute (NHGRI) and the Department of Agriculture (USDA). Multiple drones from the same queen (strain DH4) were obtained from Danny Weaver of B. Weaver Apiaries. All libraries were made from DNA isolated from these drones. The honey bee BAC library (CHORI-224) was prepared by Pieter de Jong and Katzutoyo Osoegawa at the Children's Hospital Oakland Research Institute. | gene, agricultural, allergy, antibiotic, apis mellifera, array, behavioral, biologist, chromosome, development, disease, genome, heath, honey bee, human, immunity, insect, mental heath, organism, pollination, reaction, resistance, sequence, trait | has parent organization: Baylor University; Texas; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25604 | http://www.hgsc.bcm.tmc.edu/project-species-i-Apis%20mellifera.hgsc?pageLocation=Apis%20mellifera | SCR_002890 | Honey Bee | 2026-08-04 09:40:46 | 4 | |||||||
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Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis Resource Report Resource Website 50+ mentions |
Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) | CAMERA | data analysis service, portal, analysis service resource, storage service resource, organization portal, production service resource, service resource, data repository, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data. | ecology, energy, environment, gene, analysis, bioinformatics, biological, biology, community, cyberinfrastructure, data, dna, genome, genomics, health care, map, marine, metadata, metagenomic, microbial, microbiology, molecular biology, organism, research, scientific, sequence, sequencing, software, tool, training, viral |
is listed by: OMICtools is related to: VIROME has parent organization: University of California at San Diego; California; USA |
Gordon and Betty Moore Foundation | PMID:21045053 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_011924, OMICS_01476, nif-0000-23292 | SCR_002676 | 2026-08-04 09:40:42 | 83 | ||||||
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Gramene Resource Report Resource Website 500+ mentions |
Gramene (RRID:SCR_002829) | GR | database, data or information resource | Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site. | crop, plant genome, genetic, blast, gene, genome, genetic diversity, pathway, protein, marker, quantitative trait locus, comparative map, phenotype, genomics, physiology, comparative, grain, expressed sequence tag, trait, mutation, environment, taxonomy, web service, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Gene Ontology is related to: Plant Ontology is related to: Trait Ontology is related to: EnvO is related to: BioCyc has parent organization: Cold Spring Harbor Laboratory has parent organization: Cornell University; New York; USA is parent organization of: Trait Ontology is parent organization of: Plant Environmental Conditions is parent organization of: Plant Trait Ontology is parent organization of: Cereal Plant Development Ontology is parent organization of: Cereal Plant Gross Anatomy Ontology |
USDA IFAFS 00-52100-9622; USDA 58-1907-0-041; USDA 1907-21000-030; NSF 0321685; NSF 0703908; NSF 0851652 |
PMID:21076153 PMID:17984077 PMID:16381966 |
Free, Freely available | r3d100010856, nif-0000-02926, nlx_65829, biotools:gramene | https://bio.tools/gramene, https://doi.org/10.17616/R3GG7M | SCR_002829 | GR PROTEIN, RiceGenes, GR REF, GR GENE, Gramene: A Resource for Comparative Grass Genomics, GR QTL | 2026-08-04 09:40:45 | 778 | ||||
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Tribolium castaneum Genome Project Resource Report Resource Website 1+ mentions |
Tribolium castaneum Genome Project (RRID:SCR_002848) | topical portal, portal, database, data or information resource | This portal provides information about the Tribolium castabeum Genome Project. The Tribolium castaneum genome sequence and its analysis has been published in Nature, two companion journal issues (IBMB and DGE) and numerous other publications listed below. The red flour beetle, Tribolium castaneum, a common pest that is also a genetic model for the Coleoptera. The genome has been sequenced to 7-fold coverage using a whole genome shotgun approach and assembled using the HGSC's assembly engine, Atlas, with methods employed for the Drosophila pseudoobscura genome assembly. Approximately 90% of the genome sequence has been mapped to chromosomes in collaboration with Dick Beeman (USDA ARS) and Sue Brown (Kansas State University). Access to the Data :- Genome Assembly: The long term home of the Tribolium genome is Beetlebase. Tcas 3.0 is now available in GenBank and on our FTP site. Note there are no restrictions of any kind on the Tribolium data as it has been published. Version 2 of the assembly, Tcas_2.0 is available for download using the FTP Data link in the sidebar. The assembly is described in detail in the README in that directory. T.cas_1.0 was a preliminary genome assembly that did not include large insert paired end information and has been moved to a previous assemblies folder. A genboree browser of the Tcas2.0 sequence is available here: There are also links to the genboree browser from the blast results (at the bottom of each reported HSP) if you use the blast server on this page. The original linear scaffold file, Tcas2.0/linearScaffolds/Tcas20050914-genome, posted on the ftp site did not include singleton contigs from the assembly and thus did not fully reflect the tribolium genome sequence, missing ~4.4Mb of sequence in 1860 contigs and reptigs or approximately 2.5% of the assembled sequence. A corrected Tcas20051011-genome file containing these missing sequences is now available on the ftp site. The blast databases have also been updated to reflect this change. All other data is correct, and not affected by this change. :- BLAST Searches: The BLAST link is located in the sidebar. :* Linearized chromosome and unplaced scaffold sequences :* Assembled contigs :* Bin0 unassembled reads and Repeat reads Traces are available from the NCBI Trace Archive by using the link in the sidebar, or by using NCBI MegaBLAST with a same species or cross species query. Sponsors: Funding for this project has been provided by the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH), and the U.S. Department of Agriculture's Agricultural Research Service (USDA ARS Agreement No. 58-5430-3-338). | genetic, chromosome, coleoptera, drosophila, genome, model, pest, red flour beetle, sequence, tribolium castaneum | has parent organization: Baylor University; Texas; USA | Free, Freely available | nif-0000-25607 | http://www.hgsc.bcm.tmc.edu/project-species-i-Tribolium%20castaneum.hgsc?pageLocation=Tribolium%20castaneum | SCR_002848 | Tribolium | 2026-08-04 09:40:45 | 8 | |||||||
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International HapMap Project Resource Report Resource Website 5000+ mentions |
International HapMap Project (RRID:SCR_002846) | HapMap | experimental protocol, narrative resource, database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project. | genetic variant, disease, genetic sequence, genetic variation, single nucleotide polymorphism, genetic diversity, dna, sequence, catalog, genome, chromosome, bio.tools |
is used by: BioSample Database at EBI is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SNAP - SNP Annotation and Proxy Search is related to: Haploview is related to: NHGRI Sample Repository for Human Genetic Research is related to: DistiLD - Diseases and Traits in LD is related to: SNP at Ethnos is related to: GBrowse is related to: Broad Institute Genomics Platform has parent organization: NCBI |
Chinese Academy of Sciences ; Chinese Ministry of Science and Technology ; Delores Dore Eccles Foundation ; Genome Canada ; Genome Quebec ; Hong Kong Innovation and Technology Commission ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; National Natural Science Foundation of China ; SNP Consortium ; University Grants Committee of Hong Kong ; Wellcome Trust ; W. M. Keck Foundation ; NIH |
PMID:14685227 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02940, biotools:int_hapmap_project, r3d100011835, OMICS_00273 | http://www.hapmap.org/, https://bio.tools/int_hapmap_project, https://doi.org/10.17616/R3H06Q | http://snp.cshl.org | SCR_002846 | HapMap Project | 2026-08-04 09:40:45 | 6817 | |||
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HemBase Resource Report Resource Website 1+ mentions |
HemBase (RRID:SCR_002880) | resource, database, data or information resource | Database designed for web-based examination of the human erythroid transcriptome. The database is organized to provide a cytogenetic band position, a unique name as well as a concise annotation for each entry. Search queries may be performed by name, keyword or cytogenetic location. Search results are linked to primary sequence data and three major human genome browsers for access to information considered current at the time of each search. Hembase provides interested scientists and clinical hematologists with a genome-based approach toward the study of erythroid biology. Red blood cells in the circulation arise from hematopoietic stem cells that proliferate as erythroid progenitors and differentiate into erythroid precursor cells in response to the hormone erythropoietin. Messenger RNA was isolated from those cells and used to generate gene libraries. Sequencing several thousand expressed sequence tags (EST) from those libraries was then performed. Those EST and sequences encoding several hundred additional genes with known expression in erythroid cells are compiled here as a database of human erythroid gene activity. The database is organized and linked according to the location of these sequences within the human genome., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | erythroid, erythroid cell, erythroblast, expressed sequenced tag, transcriptome, gene, erythropoiesis, cytogenetic location, hematology, genome, red blood cell, progenitor cell, precursor cell, chromosome |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources has parent organization: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Anemia, Erythroleukemia, Malaria, Erythroid cell related disease | NIDDK 1ZIADK025098 | PMID:14681483 PMID:10409428 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02949 | SCR_002880 | Hembase | 2026-08-04 09:40:45 | 4 | |||||
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European Conditional Mouse Mutagenesis Program Resource Report Resource Website 50+ mentions |
European Conditional Mouse Mutagenesis Program (RRID:SCR_003104) | EUCOMM | production service resource, material service resource, service resource, biomaterial manufacture | Generate, archive, and distribute world-wide up to 12.000 conditional mutations across the mouse genome in mouse embryonic stem (ES) cells and Establish a limited number of mouse mutants from this resource. EUCOMM contributes the largest fraction of conditionally trapped and targeted genes in mouse C57BL/6N embryonic stem (ES) cells to the IKMC. EUCOMM vectors, mutant ES cells and mutant mice are distributed worldwide, enabling functional genomics research in a standardized and cost-effective manner by a much wider biomedical research community than has been possible previously. EUCOMM mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMM mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Mutagenesis Strategies * Conditional gene trapping - random approach for expressed genes * Conditional targeted trapping - directed approach, used for expressed genes * Conditional gene targeting - directed approach, used for non-expressed genes | mutant, c57bl/6n, embryonic stem cell, conditionally trapped, targeted gene, gene, functional genomics, vector, mutant embryonic stem cell, mutant mouse, mutagenesis, genome, gene trapping, gene targeting |
is related to: EuMMCR is related to: European Mouse Mutant Archive is related to: Europhenome Mouse Phenotyping Resource has parent organization: International Knockout Mouse Consortium |
European Union FP6 | Free, Freely available | nif-0000-30531 | SCR_003104 | 2026-08-04 09:40:49 | 54 | |||||||
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Assembly/Alignment/Annotation of 12 Related Drosophila Species Resource Report Resource Website 10+ mentions |
Assembly/Alignment/Annotation of 12 Related Drosophila Species (RRID:SCR_002921) | portal, data set, topical portal, organism-related portal, data or information resource | A single source for sequences, assemblies, annotations and analyses of the genomes of members of the fruitfly genus Drosophlia. It is meant as resource for Drosophilists and other researchers interested in comparative analysis of these species and their genomes. There are pages for each species, as well as pages for different types of multi-species resources (e.g. alignments). If you have a public resource that will help this project, please consider making it available through this page by emailing multiple_at_fruitfly.org. | sequence, annotation, analysis, genome, fruitfly, drosophila, research, comparative, alignment, assembly | has parent organization: Lawrence Berkeley National Laboratory | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30021 | SCR_002921 | AAA: 12 Drosophila Genomes | 2026-08-04 09:40:46 | 35 | ||||||||
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JASPAR Resource Report Resource Website 1000+ mentions |
JASPAR (RRID:SCR_003030) | JASPAR | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. | structural class, transcription factor binding site, profile, regulatory region, genome, genomic, matrix, transcription factor, binding site, dna, FASEB list |
is listed by: OMICtools is listed by: re3data.org is related to: Babelomics has parent organization: University of Copenhagen; Copenhagen; Denmark has parent organization: Karolinska Institute; Stockholm; Sweden |
Novo Nordisk Foundation ; European Union ; EMBRACEa Sixth Framework Network of Excellence ; Sars Centre ; Carlsberg Foundation |
PMID:18006571 PMID:16381983 PMID:14681366 |
Free, Freely available | r3d100010091, OMICS_00538, nif-0000-03061 | https://doi.org/10.17616/R3QC7R | http://129.177.120.189/cgi-bin/jaspar2010/jaspar_db.pl, http://jaspar.cgb.ki.se | SCR_003030 | JASPAR, JASPAR CORE, JASPAR CORE database, JASPAR database | 2026-08-04 09:40:48 | 4766 | |||
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ATGC: Montpellier bioinformatics platform Resource Report Resource Website 100+ mentions |
ATGC: Montpellier bioinformatics platform (RRID:SCR_002917) | ATGC | portal, topical portal, catalog, database, data or information resource | A bioinformatics platform that is a joint project of several South of France laboratories with available services based on their expertise, issued from their research activities which involve phylogenetics, population genetics, molecular evolution, genome dynamics, comparative and functional genomics, and transcriptome analysis. Most of the software and databases on ATGC are (co)authored by researchers from South of France teams. Some are widely used and highly cited. South of France laboratories: * CRBM (transcriptomes and stem cells). * IBC (computational biology). * MiVEGEC (evolution and phylogeny). * LGDP (plant genomics). * LIRMM (computer science). * South Green (plant genomics). | bioinformatics, genome, genetics, molecular evolution, comparative, functional, dynamics, transcriptome, analysis, database, data analysis service, software resource, data set, high-throughput sequencing, binary, phylogenetics, population genetics, genome dynamics, comparative genomics, functional genomics, transcriptome analysis, molecular, evolution, stem cell, computational biology, plant genomics, FASEB list |
is related to: ReNaBi has parent organization: Montpellier 2 University; Montpellier; France is parent organization of: MPscan |
nif-0000-30044 | SCR_002917 | ATGC - South of France bioinformatics platform | 2026-08-04 09:40:46 | 218 | ||||||||
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BRENDA Resource Report Resource Website 100+ mentions |
BRENDA (RRID:SCR_002997) | BRENDA | database, data or information resource | Database for functional enzyme and ligand-related information maintained as part of the German ELIXIR Node. Provides advanced query systems, evaluation tools, and various visualization options for the detailed assessment of enzyme properties. Enzyme data in BRENDA are classified according to the Enzyme Commission (EC) nomenclature of IUBMB. | enzyme, metabolic pathway, protein sequence, protein structure, genome, structure, function, annotation, kinetics, molecular property, occurrence, preparation, application, mutant, variant, pathway, ligand, web service, sequence, substructure, FASEB list |
is related to: ENZYME is parent organization of: BRENDA Tissue and Enzyme Source Ontology |
European Union SLING 226073; European Union FELICS 021902 (RII3) |
PMID:33211880 PMID:30395242 PMID:28438579 PMID:27924025 PMID:25378310 PMID:23203881 PMID:21062828 PMID:14681450 PMID:12850129 PMID:11796225 PMID:11752250 |
Free, Freely available, | r3d100010616, nif-0000-30222 | http://www.brenda-enzymes.info/, https://doi.org/10.17616/R39W42 | http://www.brenda.uni-koeln.de/ | SCR_002997 | Brenda: The Comprehensive Enzyme Information System, BRaunschweig ENzyme Database, Brenda: Enzyme Database, BRENDA: The Comprehensive Enzyme Information System | 2026-08-04 09:40:47 | 402 | |||
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Coriell Institute for Medical Research Resource Report Resource Website 100+ mentions |
Coriell Institute for Medical Research (RRID:SCR_003043) | Coriell | portal, topical portal, production service resource, service resource, data or information resource | Non-profit research center dedicated to the study of the human genome. Expert staff and pioneering programs in the fields of personalized medicine, cell biology, cytogenetics, genotyping, and biobanking drive our mission. The emerging field of personalized medicine draws upon a person's genomic information to tailor treatments and prescription drug dosing to optimize health outcomes. The Coriell Personalized Medicine Collaborative (CPMC) research study is seeking to understand the usefulness of genetic risk and pharmacogenomics in clinical decision-making and healthcare management. Coriell has a distinguished history in cell biology. We are building upon this expertise by playing an important role in induced pluripotent stem (iPS) cell research. These powerful cells, which can be made from skin cells or blood, are revolutionizing the way human disease is studied and how drugs are developed. The decline of neurons afflicted with Alzheimer's disease or pancreatic cells fighting diabetes can be studied in a Petri dish. By proving efficacy within the diseased environment prior to clinical trial, drugs can move through the pipeline quicker to reach patients sooner. In addition to pioneering cutting-edge research initiatives, Coriell offers custom research services including cell culture, cytogenetic analyses, and molecular biology to the scientific community. Furthermore, Coriell's Genotyping and Microarray Center is one of the nation's largest centers, with high-throughput DNA analysis systems from Illumina and Affymetrix. The Center is CLIA-certified in 48 states. | genome, induced pluripotent stem cell |
is used by: BioSample Database at EBI is related to: BioRep is parent organization of: Coriell Cell Repositories is parent organization of: Coriell Institute Stem Cell Biobank is parent organization of: Coriell Biobank is parent organization of: HuRef |
Free, Freely available | nif-0000-00169 | SCR_003043 | Coriell Institute | 2026-08-04 09:40:48 | 131 | |||||||
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BioPerl Resource Report Resource Website 100+ mentions |
BioPerl (RRID:SCR_002989) | BioPerl | source code, software resource, software repository, wiki, narrative resource, software toolkit, data or information resource | BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | perl, biology, ontology, library, sequence, analysis, computational, application, pipeline, bioinformatics, sequence, annotation, module, life science, python, java, genome, software library, parse, manipulate, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Gene Ontology is related to: OBO has parent organization: Duke University; North Carolina; USA has parent organization: European Bioinformatics Institute is required by: RelocaTE |
NIGMS T32 GM07754-22; NHGRI K22 HG00056; NHGRI K22 HG-00064-01; NHGRI HG00739; NHGRI P41HG02223 |
PMID:12368254 DOI:10.1101/gr.361602 |
Free, Available for download, Freely available | OMICS_04849, nif-0000-30188, biotools:bioperl | https://bio.tools/bioperl, https://sources.debian.org/src/bioperl/ | SCR_002989 | 2026-08-04 09:40:47 | 402 | |||||
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Gene Set Enrichment Analysis Resource Report Resource Website 10000+ mentions |
Gene Set Enrichment Analysis (RRID:SCR_003199) | GSEA | data processing software, data analysis software, software resource, software application, software toolkit | Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes. | gene, expression, profile, pathway, data, set, phenotype, genome, enrichment, RNA, analysis, bio.tools, bio.tools |
is used by: Molecular Signatures Database is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GoMapMan has parent organization: Broad Institute |
NCI ; NIH ; NIGMS |
PMID:16199517 | Free, Freely available | nif-0000-30629, SCR_016882, biotools:gsea, OMICS_02279 | http://www.broad.mit.edu/gsea, https://bio.tools/gsea | SCR_003199 | GSEA, Gene Set Enrichment Analysis, Gene Set Enrichment Analysis (GSEA) | 2026-08-04 09:40:50 | 18865 | ||||
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HuGE Navigator - Human Genome Epidemiology Navigator Resource Report Resource Website 100+ mentions |
HuGE Navigator - Human Genome Epidemiology Navigator (RRID:SCR_003172) | HuGE Navigator | data computation service, database, data or information resource, bibliography | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Knowledge base of genetic associations and human genome epidemiology including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. This tool explores HuGENet, the Human Genome Epidemiology Network, which is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. What does HuGE Navigator offer? *HuGEpedia - an encyclopedia of human genetic variation in health and disease, includes, Phenopedia and Genopedia. Phenopedia allows you to look up gene-disease association summaries by disease, and Genopedia allows you to look up gene-disease association summaries by gene. In general, HuGEpedia is a searchable database that summarizes published articles about human disease and genetic variation, including primary studies, reviews, and meta-analyses. It provides links to Pubmed abstracts, researcher contact info, trends, and more. *HuGEtools - searching and mining the literature in human genome epidemiology, includes, HuGE Literature Finder, HuGE Investigator Browser, Gene Prospector, HuGE Watch, Variant Name Mapper, and HuGE Risk Translator. *HuGE Literature Finder finds published articles in human genome epidemiology since 2001. The search query can include genes, disease, outcome, environmental factors, author, etc. Results can be filtered by these categories. It is also possible to see all articles in the database for a particular topic, such as genotype prevalence, pharmacogenomics, or clinical trial. *HuGE Investigator Browser finds investigators in a particular field of human genome epidemiology. This info is obtained using a behind-the-scenes tool that automatically parses PubMed affiliation data. *Gene Prospector is a gateway for evaluating genes in relation to disease and risk factors. This tool allows you to enter a disease or risk factor and then supplies you with a table of genes associated w/your query that are ranked based on strength of evidence from the literature. This evidence is culled from the HuGE Literature Finder and NCBI Entrez Gene - And you're given the scoring formula. The Gene Prospector results table provides access to the Genopedia entry for each gene in the list, general info including links to other resources, SNP info, and associated literature from HuGE, PubMed, GWAS, and more. It is a great place to locate a lot of info about your disease/gene of interest very quickly. *HuGE Watch tracks the evolution of published literature, HuGE investigators, genes studied, or diseases studied in human genome epidemiology. For example, if you search Trend/Pattern for Diseases Studied you'll initially get a graph and chart of the number of diseases studied per year since 1997. You can refine these results by limiting the temporal trend to a category or study type such as Gene-gene Interaction or HuGE Review. *Variant Name Mapper maps common names and rs numbers of genetic variants using information from SNP500Cancer, SNPedia, pharmGKB, ALFRED, AlzGene, PDGene, SZgene, HuGE Navigator, LSDBs, and user submissions. *HuGE Risk Translator calculates the predictive value of genetic markers for disease risk. To do so, users must enter the frequency of risk variant, the population disease risk, and the odds ratio between the gene and disease. This information is necessary in order to yield a useful predictive result. *HuGEmix - a series of HuGE related informatics utilities and projects, includes, GAPscreener, HuGE Track, Open Source. GAPscreener is a screening tool for published literature on human genetic associations; HuGE Track is a custom track built for HuGE data in the UCSC Genome Browser; and Open Source is infrastructure for managing knowledge and information from PubMed. | environment, epidemiology, gene, genetic, genetic associations, genetic markers, genome, disease, human, human disease, predictive value, prevalence, publications, risk factors, test evaluations, variance, FASEB list |
has parent organization: Centers for Disease Control and Prevention works with: Kinase Associated Neural Phospho Signaling |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00573 | http://hugenavigator.net/HuGENavigator/home.do | SCR_003172 | 2026-08-04 09:40:50 | 117 | |||||||
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Xenbase Resource Report Resource Website 100+ mentions |
Xenbase (RRID:SCR_003280) | XenBase | image repository, storage service resource, data repository, service resource, database, data or information resource | Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics. | molecular neuroanatomy resource, dna target, protein target, gene, genome, function, sequence, orthology, publication, gene expression, model organism, genomics, development, annotation, blast, development stage, publication, in situ hybridization, immunohistochemistry, video resource, organism-related portal, experimental protocol, organism supplier, data analysis service, developmental stage, gold standard, bio.tools, FASEB list, RRID Community Authority |
is listed by: OMICtools is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: University of Calgary; Alberta; Canada is parent organization of: Xenopus Anatomy Ontology |
NICHD R01 HD045776; NICHD P41 HD064556 |
PMID:23125366 PMID:19884130 PMID:36755307 |
Free, Available for download, Freely available | biotools:xenbase, OMICS_01665, nif-0000-01286, r3d100010279 | http://www.xenbase.org/entry/, https://bio.tools/xenbase, https://doi.org/10.17616/R3MP4S | SCR_003280 | Xenbase: Xenopus laevis and tropicalis biology and genomics resource | 2026-08-04 09:40:52 | 446 | ||||
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genomation Resource Report Resource Website 50+ mentions |
genomation (RRID:SCR_003435) | genomation | data processing software, data analysis software, software resource, software application, software toolkit | Software R package for simplfiying common tasks in genomic feature analysis. Toolkit to summarize, annotate and visualize genomic intervals. Provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. Can annotate given regions with other genomic features such as exons,introns and promoters. | genome, genomic interval, genomic feature analysis, GRanges objects, annotate given regions, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:25417204 | Free, Available for download, Freely available | biotools:genomation, OMICS_02306 | https://github.com/al2na/genomation, https://github.com/BIMSBbioinfo/genomation, https://bio.tools/genomation | http://al2na.github.io/genomation/ | SCR_003435 | 2026-08-04 09:40:54 | 58 |
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