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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GeneTrail Resource Report Resource Website 100+ mentions |
GeneTrail (RRID:SCR_006250) | GeneTrail | production service resource, data analysis service, service resource, analysis service resource | A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathway, microarray, enrichment, genomic, proteomic, function, transcription factor, genomic localization, protein-protein interaction, coiled-coil domain, granzyme-b clevage site, motif, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: TRANSPATH is related to: TRANSFAC is related to: Gene Ontology has parent organization: Saarland University; Saarbrucken; Germany |
PMID:17526521 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:genetrail, OMICS_02236 | https://bio.tools/genetrail | SCR_006250 | 2026-08-13 09:27:27 | 114 | ||||||
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Neurocritic Resource Report Resource Website 1+ mentions |
Neurocritic (RRID:SCR_006528) | Neurocritic | data or information resource, blog, narrative resource | The Neurocritic is a blog deconstructing the most sensationalistic recent findings in Human Brain Imaging, Cognitive Neuroscience, and Psychopharmacology. Born in West Virginia in 1980, The Neurocritic embarked upon a roadtrip across America at the age of thirteen with his mother. She abandoned him when they reached San Francisco and The Neurocritic descended into a spiral of drug abuse and prostitution. At fifteen, The Neurocritic''s psychiatrist encouraged him to start writing as a form of therapy. | human, brain imaging, cognitive neuroscience, psychopharmacology, brain, imaging, neuroimaging | nlx_144592 | SCR_006528 | The Neurocritic | 2026-08-13 09:27:31 | 2 | |||||||||
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PRED-TMR2 Resource Report Resource Website 1+ mentions |
PRED-TMR2 (RRID:SCR_006205) | PRED-TMR2 | production service resource, data analysis service, service resource, analysis service resource | A web server that classifies proteins into two classes from their sequences alone: the membrane protein class and the non-membrane protein class. This may be important in the functional assignment and analysis of open reading frames (ORF''s) identified in complete genomes and, especially, those ORF''s that correspond to proteins with unknown function. The network has a simple hierarchical feed-forward topology and a limited number of neurons which makes it very fast. By using only information contained in 11 protein sequences, the method was able to identify, with 100% accuracy, all membrane proteins with reliable topologies collected from several papers in the literature. Applied to a test set of 995 globular, water-soluble proteins, the neural network classified falsely 23 of them in the membrane protein class (97.7% of correct assignment). The method was also applied to the complete SWISS-PROT database with considerable success and on ORF''s of several complete genomes. The neural network developed was associated with the PRED-TMR algorithm (Pasquier,C., Promponas,V.J., Palaios,G.A., Hamodrakas,J.S. and Hamodrakas,S.J., 1999) in a new application package called PRED-TMR2. | prediction, transmembrane, protein, algorithm, neural network, classification, transmembrane protein, protein classification, membrane protein, protein structure |
is related to: DAM-Bio has parent organization: PRED-TMR |
European Union ERBFMRXCT960019 | PMID:10469822 | nlx_151766 | SCR_006205 | PRED-TMR2: Prediction of Transmembrane regions in proteins | 2026-08-13 09:27:36 | 1 | ||||||
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Musculoskeletal Transplant Foundation - MTF Resource Report Resource Website 1+ mentions |
Musculoskeletal Transplant Foundation - MTF (RRID:SCR_006684) | MTF | material resource, tissue bank, biomaterial supply resource | The Musculoskeletal Transplant Foundation is a non-profit service organization dedicated to providing quality allograft tissue through a commitment to excellence in education, research, recovery and care for recipients, donors and their families. We are a national consortium comprised of academic medical institutions, organ procurement organizations and tissue recovery organizations. MTF was created as a charitable organization with a mission that is dedicated to the needs of donors, donor families, patients and surgeons. We focus on respectful stewardship of the donated gift while advancing the science and practice of bone, ligament, cartilage and skin transplantation. Since our inception in 1987, MTF has recovered more than 60,000 donors and distributed more than 3 million grafts for transplantation. We also support research to expand the science of transplantation, and we encourage the efforts of our members and non-member clients to improve the understanding of donation and transplantation among the medical community and the public at large. Our policies are developed and implemented by MTF''''s Medical Board of Trustees, Donation Board of Trustees and Board of Directors, composed of physicians and recovery agency representatives who are dedicated to the mission of the Foundation. This fundamental commitment enables us to set and maintain the highest levels of safety assurance and quality control in all phases of our operations. |
is listed by: One Mind Biospecimen Bank Listing is parent organization of: International Institute for the Advancement of Medicine |
nlx_89982 | SCR_006684 | Musculoskeletal Transplant Foundation | 2026-08-13 09:27:33 | 1 | |||||||||
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Lists2Networks Resource Report Resource Website 1+ mentions |
Lists2Networks (RRID:SCR_006323) | L2N | production service resource, data analysis service, service resource, analysis service resource | A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system. | high-throughput sequencing, analysis, gene, protein |
is listed by: OMICtools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:20152038 | Free, Public, Account required | OMICS_02231 | http://www.lists2networks.org | SCR_006323 | Lists2Networks: Integrated analysis of gene/protein lists | 2026-08-13 09:27:28 | 3 | |||||
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PRED-TMR Resource Report Resource Website 1+ mentions |
PRED-TMR (RRID:SCR_006203) | PRED-TMR | production service resource, data analysis service, service resource, analysis service resource | A web server that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The algorithm refines a standard hydrophobicity analysis with a detection of potential termini (edges, starts and ends) of transmembrane regions. This allows both to discard highly hydrophobic regions not delimited by clear start and end configurations and to confirm putative transmembrane segments not distinguishable by their hydrophobic composition. The accuracy obtained on a test set of 101 non homologous transmembranes proteins with reliable topologies compares well with that of other popular existing methods. Only a slight decrease in prediction accuracy was observed when the algorithm was applied to all transmembrane proteins of the SwissProt database (release 35). | predict, transmembrane segment, protein, algorithm, sequence, membrane protein, protein structure, transmembrane region, hydrophobicity analysis |
is related to: waveTM is related to: DAM-Bio has parent organization: University of Athens Biophysics and Bioinformatics Laboratory is parent organization of: PRED-TMR2 |
European Union ERBFMRXCT960019 | PMID:10360978 | nlx_151765 | SCR_006203 | PRED-TMR: A novel method for predicting transmembrane segment in proteins based on a statistical analysis of the SwissProt database | 2026-08-13 09:27:26 | 7 | ||||||
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KI Biobank - Tissue Biobank Resource Report Resource Website 1+ mentions |
KI Biobank - Tissue Biobank (RRID:SCR_006043) | KI Biobank - Tissue Biobank | material resource, tissue bank, biomaterial supply resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 4, 2014. Tissue Biobank collects samples from different types of cancers patients prospectively. Blood samples are being sent to KI Biobank for DNA extraction and storage. Number of sample donors: 611 (June 2010) | blood, dna |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Karolisnka Biobank |
Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151440 | SCR_006043 | 2026-08-13 09:27:34 | 1 | |||||||
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AthaMap Resource Report Resource Website 50+ mentions |
AthaMap (RRID:SCR_006717) | data or information resource, database | Genome wide map of putative transcription factor binding sites in Arabidopsis thaliana genome.Data in AthaMap is based on published transcription factor (TF) binding specificities available as alignment matrices or experimentally determined single binding sites.Integrated transcriptional and post transcriptional data.Provides web tools for analysis and identification of co-regulated genes. Provides web tools for database assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. | gene, arabidopsis thaliana, binding site, genome, transcription factor, small rna binding site, small rna, rna, microrna, cis-regulatory element, post-transcriptional regulation, FASEB list |
is listed by: OMICtools is listed by: bio.tools has parent organization: Technical University of Braunschweig; Braunschweig; Germany |
PMID:22800758 PMID:21177332 PMID:18842622 PMID:17148485 PMID:16922688 PMID:15980498 PMID:14681436 |
Free, Freely available | nif-0000-02583, biotools:athamap, OMICS_00549, nif-0000-20814, SCR_013106 | https://bio.tools/athamap | SCR_006717 | Arabidopsis thaliana Map | 2026-08-13 09:27:40 | 50 | ||||||
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Phenomizer Resource Report Resource Website 10+ mentions |
Phenomizer (RRID:SCR_006157) | production service resource, data analysis service, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 31,2026. Phenomizer offers three different approaches to find the appropriate term for a phenotypic abnormality, indicated by the three tabs on the left hand side: Feature, Disease and Ontology. The Phenomizer is intended to be used by qualified and licensed physicians in order to provide assistance in reaching the correct diagnosis in patients with hereditary diseases and for use as a teaching aid. The Phenomizer does not make diagnoses. Rather, it produces a ranked list of possibilities that can be used by physicians as a part of the diagnostic workup. The Phenomizer does not contain information about all possible diagnoses or even all possible hereditary diseases. The Phenomizer should not be used to make medical decisions without the advice of a physician. | feature, disease, ontology, clinical, differential diagnoses |
is related to: Human Phenotype Ontology is related to: Human Phenotype Ontology has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
PMID:19800049 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151657 | SCR_006157 | Phenomizer - Clinical Diagnostics with Similarity Searches in Ontologies | 2026-08-13 09:27:35 | 32 | |||||||
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neuropathology blog Resource Report Resource Website 1+ mentions |
neuropathology blog (RRID:SCR_006825) | neuropathology blog | data or information resource, blog, narrative resource | Blog by Brian E. Moore, MD, discussing issues pertaining to the practice of neuropathology -- including nervous system tumors, neuroanatomy, neurodegenerative disease, muscle and nerve disorders, ophthalmologic pathology, neuro trivia, neuropathology gossip, job listings and anything else that might be of interest to a blue-collar neuropathologist. Brian E. Moore, MD: Neuropathologist, Memorial Medical Center in Springfield, Illinois. Co-Chair, Southern Illinois University School of Medicine Department of Pathology. | neuropathology, nervous system, tumor, neuroanatomy, neurodegenerative disease, muscle disorder, nerve disorder, ophthalmologic pathology, neuro trivia, job resource, neuropathologist, fellowship |
is used by: NIF Data Federation is used by: Integrated Blogs |
Nervous system tumor, Neurodegenerative disease, Muscle disorder, Nerve disorder, Ophthalmologic pathology | nlx_151652 | SCR_006825 | 2026-08-13 09:27:41 | 1 | ||||||||
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Aggrescan: The Hot Spot Finder Resource Report Resource Website 50+ mentions |
Aggrescan: The Hot Spot Finder (RRID:SCR_008403) | Aggrescan | production service resource, data analysis service, service resource, analysis service resource | Web-based tool for identifying hot spots of aggregation in polypeptides. Aggrescan uses an aggregation-propensity scale for natural amino acids derived from in vivo experiments and on the assumption that short and specific sequence stretches modulate protein aggregation. The algorithm is shown to identify a series of protein fragments involved in the aggregation of disease-related proteins and to predict the effect of genetic mutations on their deposition propensities. It also provides new insights into the differential aggregation properties displayed by globular proteins, natively unfolded polypeptides, amyloidogenic proteins and proteins found in bacterial inclusion bodies. | aggregation, amino acid, protein, mutation, polypeptide, amyloid, bacterial protein, protein aggregation, neurodegeneration |
is listed by: 3DVC has parent organization: Autonomous University of Barcelona; Barcelona; Spain |
Ministerio de Educacion y Ciencia BIO2004-05879; Ministerio de Educacion y Ciencia BIO2003-02848; Spain Generalitat de Catalunya SGR2005-00037; Spain Generalitat de Catalunya SGR2005-01037 |
PMID:17324296 | Free, Acknowledgement requested | nif-0000-30073 | SCR_008403 | 2026-08-13 09:27:53 | 65 | ||||||
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National Cell Repository for Alzheimer's Disease Resource Report Resource Website 10+ mentions |
National Cell Repository for Alzheimer's Disease (RRID:SCR_007313) | NCRAD | material resource, tissue bank, biomaterial supply resource | Cell repository for Alzheimer's disease that collects and maintains biological specimens and associated data. Its data is derived from large numbers of genetically informative, phenotypically well-characterized families with multiple individuals affected with Alzheimer's disease, as well as individuals for case-control studies. | gene, alzheimers disease, dementia, dna, late onset, memory loss, phenotypic data, research study, clinical data, plasma, serum, rna, brain tissue, family history, blood |
is listed by: One Mind Biospecimen Bank Listing is related to: DIAN - Dominantly Inherited Alzheimer Network is related to: Alzheimers Disease Genetics Consortium is related to: National Alzheimer's Coordinating Center has parent organization: Indiana University; Indiana; USA |
Alzheimer's disease, Late-onset Alzheimer's disease, Dementia, Memory loss | NIA ; NIH Blueprint for Neuroscience Research |
Public, Application required for genetic research | nif-0000-00178 | SCR_007313 | 2026-08-13 09:27:48 | 36 | ||||||
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Danubian Biobank Consortium Resource Report Resource Website 1+ mentions |
Danubian Biobank Consortium (RRID:SCR_010566) | material resource, tissue bank, biomaterial supply resource | Not yet vetted by NIF curator | nlx_39960 | SCR_010566 | 2026-08-13 09:28:18 | 1 | ||||||||||||
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Alpha Genesis Resource Report Resource Website 50+ mentions |
Alpha Genesis (RRID:SCR_010568) | AGI | material resource, tissue bank, biomaterial supply resource | A company which provides nonhuman primate products and bio-research services for the global scientific community. They provide serum, plasma, whole blood, and tissue samples from primates such as the Cynomolgus macaque, the Rhesus macaque, and the African Green. Products based on others species are available upon request. | commercial, supplier, nonhuman primate, macaque, african green | Commercial | nlx_40671 | http://www.alphagenesisinc.com/bioproducts.html | SCR_010568 | Alpha Genesis Inc, Alpha Genesis Incorporated | 2026-08-13 09:28:34 | 56 | |||||||
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Rhesus Monkey Breeding and Research Resource Report Resource Website 1+ mentions |
Rhesus Monkey Breeding and Research (RRID:SCR_008357) | RMBRR | material resource, tissue bank, biomaterial supply resource | This colony provides a national resource of rhesus monkeys and their tissues to carry out research benefiting the scientific community. The RMBRR maintains a colony of monkeys that have been derived to be specific pathogen free for members of both the herpes and retrovirus families. Over its history, the RMBRR has developed specialized management techniques, housing facilities and highly trained staff to avail these purposefully bred laboratory models, which are 93% genetically identical to humans, to researchers worldwide. Historically, this animal model has been instrumental in research involving blood classification, polio vaccine development, and drug safety and efficacy while currently they are the preferred model for studying the mechanisms of immunodeficiency diseases. Their susceptibility to Simian Immunodeficiency Virus and their homology to the human major histocompatibility complex (MHC) Class I, II and TCR genes make them valuable in HIV research. They are currently the models of choice for HIV/AIDS vaccine development and study. Other areas of research include atherosclerosis, myocarditis, alcoholism, diabetes, cancer and aging. The overall objectives of this resource are to improve the resources available at the RMBRR and to conduct resource-relevant research that improves both the health of the rhesus colony and its usefulness for studies of human disease. The Resource and Management Core is responsible for providing animal resources, tissues/biological fluids, cell lines, expert advice and research support to NIH extramural and intramural programs, other federal agencies and to private sponsors. The Resource-Related Research Core conducts research to improve the health of the animals maintained with special emphasis on studies that will enhance the usefulness of the rhesus as a model for studies of human disease. | animal model, tissue, live animal, cell line, bodily fluid, vaccine development, vaccine |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Texas MD Anderson Cancer Center |
Immunodeficiency disease, Human immunodeficiency virus, AIDS, Atherosclerosis, Myocarditis, Alcoholism, Diabetes, Cancer, Aging | Public: available to researchers worldwide | nif-0000-25893 | SCR_008357 | KCCMR Rhesus Monkey Breeding and Research, KCCMR RMBRR, Keeling Center for Comparative Medicine and Research Rhesus Monkey Breeding and Research | 2026-08-13 09:27:55 | 1 | ||||||
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MAP-O-MAT Resource Report Resource Website 1+ mentions |
MAP-O-MAT (RRID:SCR_008197) | production service resource, data analysis service, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. MAP-O-MAT is a web-based server for automated linkage mapping of human polymorphic DNA markers. The server uses publicly available genotype data for over 15,000 markers. It facilitates the verification of order and map distances for custom mapping sets using genotype data from the CEPH database, and from the Marshfield, SNP Consortium and Rutgers linkage maps. The CRI-MAP program is used for likelihood calculations and some mapping algorithms, and physical map positions are provided from the human genome assembly. | general human genetics databases, automated, distance, dna, genotype, human, linkage, map, mapping, marker, polymorphic, position, verification | has parent organization: Rutgers University; New Jersey; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21251 | http://compgen.rutgers.edu/mapomat/ | SCR_008197 | MAP-O-MAT | 2026-08-13 09:27:52 | 2 | |||||||
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Allen Mouse Spinal Cord Atlas Resource Report Resource Website 10+ mentions |
Allen Mouse Spinal Cord Atlas (RRID:SCR_007418) | Mouse Spinal Cord Atlas | data or information resource, database, atlas | Platform for exploring spinal cord at cellular and molecular levels. Map of gene expression for adult and juvenile mouse spinal cord. Provides map of normal mouse when used to compare gene expression in diseased or injury models. Interactive database of gene expression mapped across all anatomic segments of mouse spinal cord at postnatal days 4 and 56. Indexed set of images based on RNA in situ hybridization data, searchable and sortable by gene, age, expression, cervical, thoracic, lumbar, sacral, and coccygeal segments. | gene, expression, adult, diseased, injury, juvenile, models, mouse, postnatal, RNA, hybridization, spinal, cord, molecular, neuroanatomy, data |
has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Free, Freely available | nif-0000-00510 | http://mousespinal.brain-map.org/ | SCR_007418 | 2026-08-13 09:27:48 | 29 | |||||||
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Discover Magazine Resource Report Resource Website 10+ mentions |
Discover Magazine (RRID:SCR_008787) | Discover | data or information resource, blog, narrative resource | Popular science magazine which includes news and blogs on topics including Health & Medicine, Mind & Brain, Technology, Space, Human origins, Living World, Environment, and Physics & Math. NIF Indexes include: The Brain: DISCOVER blogger, columnist, and contributing editor Carl Zimmer''s monthly column will make your brain happy. Discover Interview: The magazine''s signature in-depth discussion with the leading lights of the world of science Vital Signs: A medical mystery, as written by the doctor involved. | health, medicine, mind, brain, technology, magazine |
is used by: NIF Data Federation is used by: Integrated Blogs is parent organization of: Neuroskeptic is parent organization of: The Loom |
nlx_144214 | SCR_008787 | 2026-08-13 09:27:56 | 15 | |||||||||
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OHSU Animal Model Support Core Facility Resource Report Resource Website 1+ mentions |
OHSU Animal Model Support Core Facility (RRID:SCR_009994) | OHSU TMM, TMM Core | core facility, service resource, access service resource | Core assists investigators with developing genetically engineered rodent models of human diseases for studying mutant genes and investigating molecular mechanisms underlying pathological processes. | ABRF, USEDit, developing genetically engineered rodent models, human diseases, mutant genes, pathological processes |
is listed by: Eagle I is related to: USEDit has parent organization: Oregon Health and Science University; Oregon; USA |
SciEx_9275, SCR_011002, nlx_156461 | http://ohsu.eagle-i.net/i/0000012a-2501-9822-d994-629180000000, http://www.scienceexchange.com/facilities/transgenic-mouse-models-ohsu | SCR_009994 | OHSU Transgenic Mouse Models Core Laboratory, Oregon Health & Science University Transgenic Mouse Models, Oregon Health and Science University Transgenic Mouse Models, OHSU Transgenic Mouse Model Shared Resource | 2026-08-13 09:28:07 | 2 | |||||||
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GC/GCF Resource Report Resource Website 1+ mentions |
GC/GCF (RRID:SCR_009075) | software resource, software application | Software application where GC implements the genomic control models. GCF implements the basic Genomic Control approach, but adjusts the p-values for uncertainty in the estimated effect of substructure. This approach is preferable if a large number of tests will be evaluated because it provides a more accurrate assessment of the significance level for small p-values. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, linux | is listed by: Genetic Analysis Software | nlx_154072, SCR_000846, nlx_154584 | SCR_009075 | R/GCF, R/GC, Genomic Control | 2026-08-13 09:28:02 | 1 |
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