| Name | Name (A-Z) | Research Area | Type | Description |
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Seqfold |
Seqfold | Resource Development and Dissemination|Genetics and Genomics|Data Science at JAX |
SeqFold is a tool for RNA secondary structure prediction from experimental data.
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WORMHOLEAccessOnline & Download Associated Individuals/GroupsContact |
WORMHOLE | Genetics and Genomics|Resource Development and Dissemination|Data Science at JAX |
The WORM Human OrthoLogy Explorer is a meta-tool that uses machine learning to predict novel least diverged orthologs (LDOs) by integrating ortholog predictions from 17 algorithms.
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SARNAclustAccessDownload Associated Individuals/GroupsContact |
SARNAclust | Data Science at JAX |
SARNAclust is a novel semi-automatic algorithm to identify RNA-protein binding motifs from immunoprecipitation data.
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aln ToolsAccessDownload Associated Individuals/GroupsContact |
aln Tools | Data Science at JAX |
Processes NGS alignments into a sparse compressed incidence matrix. Stores pre-defined binary format for efficient downstream analyses and storage.
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4D Nucleome Center |
4D Nucleome Center | Genetics and Genomics |
The ultimate goal of the JAX 4D Nucleome Center is to deliver a Nucleome Positioning System (NPS) for the generation of complex maps of chromatin interaction network in the context of 3D genome structures.
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CloudNeoAccessOnline & Download Associated Individuals/GroupsContact |
CloudNeo | Data Science at JAX |
CloudNeo is a cloud-based computational workflow for identifying patient-specific tumor neoantigens from next generation sequencing data.
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Computational Sciences |
Computational Sciences | Computational Biology|Bioinformatics |
Supports computational approaches to complex problems; develops software applications and platforms that facilitate access, visualization and sharing of data and algorithms and support JAX's research data and service products.
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Biology of Beta Cell ConsortiumAssociated Individuals/Groups |
Biology of Beta Cell Consortium | Resource Development and Dissemination|Immune Disorders|Diabetes and Obesity |
NOD-scid IL2rgnull (NSG) and NOD-Rag1null IL2rgnull (NRG) mice support heightened levels of engraftment with human cells and tissues. These engrafted mice allow research on human disease processes without putting individuals at risk.
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Data Science |
Data Science | Computational Biology|Bioinformatics |
Data science at JAX is a transdisciplinary research ecosystem that brings together scientists from the fields of computational biology, systems biology, bioinformatics, and statistics to develop tools and data resources for interpreting large, complex data sets.
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DO-AS cohort dataAssociated Individuals/Groups |
DO-AS cohort data | Genetics and Genomics|Computational Biology |
Phenotype and RNAseq data from approx. 200 (B6-Col4a5 KO x DO)F1 mice
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EMASEAccessDownload Associated Individuals/GroupsContact |
EMASE | Data Science at JAX |
An expectation maximization algorithm for allele specific expression. Primary author K. Choi of the Churchill Lab.
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Tumor FusionsAccessOnline Associated Individuals/GroupsContact |
Tumor Fusions | Data Science at JAX |
Based on integrated analysis of paired-end RNA sequencing and DNA copy number data from The Cancer Genome Atlas(TCGA), The Tumor Fusion Gene Data Portal provides a bona-fide fusion list across many tumor types.
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FusorSVAssociated Individuals/GroupsContact |
FusorSV | Computational Biology|Genetics and Genomics|Data Science at JAX |
FusorSV is a data mining-based framework that allows for comprehensive and robust detection of Structural Variations (SV) from next generation sequencing datasets. We built SV engine (SVE) that includes all tools including fusorSV that can be used for analysis of new datasets. SVE also includes data models built using 1000 Genomes SV callsets as ground truth.
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g2g ToolsAccessDownload Associated Individuals/GroupsContact |
g2g Tools | Data Science at JAX |
Genome Editing tools. Creates custom genomes by incorporating (phased) SNPs and indels into reference genome, extracts regions of interest, e.g., exons or transcripts, from custom genomes, and converts coordinates of files (bam, gtf, bed) between two genomes.
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gbrsAccessDownload Associated Individuals/GroupsContact |
gbrs | Data Science at JAX |
Genotype-free genome reconstruction and ASE quantification.
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GeneWeaverAccessOnline Associated Individuals/GroupsContact |
GeneWeaver | Data Science at JAX |
GeneWeaver is a platform for the integrative analysis of heterogeneous functional genomics data. It allows users to compare and contrast biological functions across multiple species based on the genes, gene products and variants associated with these functions in global functional genomics analyses.
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Gene Expression Database (GXD)AccessOnline Contact |
Gene Expression Database (GXD) | Data Science at JAX |
Gene Expression Database (GXD) is a database project that integrates different types of gene expression information from the mouse and provides a searchable index of published experiments on endogenous gene expression during development. GXD as a core component of the Mouse Genome Informatics (MGI) resource which is the international community database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.
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Black Bear GenomeAssociated Individuals/Groups |
Black Bear Genome |
Supplemental tables and figures,
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GFR CalculatorAssociated Individuals/Groups |
GFR Calculator | Genetics and Genomics|Computational Biology |
This tool calculates the glomerular filtration rate in mice using the FITC-inulin method
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HaploQAAccessOnline & Download Associated Individuals/GroupsContact |
HaploQA | Data Science at JAX |
A web application for performing haplotype analysis of genotype calls from the “MUGA” platform genotyping arrays
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HSA |
HSA | Data Science at JAX|Genetics and Genomics|Computational Biology|Aging|Cancer|Neurodegenerative and Neuromuscular Diseases |
Integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure
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I-ATACAssociated Individuals/Groups |
I-ATAC | Bioinformatics|Computational Biology |
ATAC-seq is a new protocol to capture open chromatin sites by performing adaptor ligation and fragmentation of open chromatin regions. Due to its efficiency in requirement of biological sample and in library preparation time, many scientists are generating ATAC-seq libraries to decipher the chromatin landscape of DNA in a given cell type and condition of interest.
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ImageEchelonAccessOnline & Download Associated Individuals/GroupsContact |
ImageEchelon | Data Science at JAX |
Tool to quantify images where meaningful differences are discernible by eye, but difficult to quantify using traditional methods.
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JAX Genetic Diversity InitiativeAssociated Individuals/Groups |
JAX Genetic Diversity Initiative |
The JAX Genetic Diversity Initiative is a strategic effort to increase the awareness and availability of diversity mouse populations and associated tools across the research community. These populations are powering a revolution in model organism research that will enable major advancements in the understanding of complex genetic traits.
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IntermediateAccessDownload Associated Individuals/GroupsContact |
Intermediate | Data Science at JAX |
An R package for eQTL/pQTL mediation analysis.
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Knockout Mouse Project (KOMP)Associated Individuals/Groups |
Knockout Mouse Project (KOMP) | Resource Development and Dissemination|Genetics and Genomics|Aging|Developmental Disorders |
Scientists around the world are working to generate a targeted knockout mutation for every gene in the mouse genome through the Knockout Mouse Project (KOMP) which is providing critical tools for understanding gene function and the genetic causes of human diseases.
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Clinical Knowledgebase (CKB)AccessOnline & Download Contact |
Clinical Knowledgebase (CKB) | Data Science at JAX |
CKB is a dynamic, digital encyclopedia for precision oncology that connects cancer variants to therapies, efficacy evidence, and clinical trials and aids interpretation of complex cancer genomic profiles.
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Joan Staats Library at The Jackson Laboratory |
Joan Staats Library at Jackson Laboratory | Resource Development and Dissemination |
Our specialized collection areas include: genetics, inbred mice, animal health and husbandry, development, embryology, complex traits, immunology, cancer, molecular biology, neuroscience and computational biology.
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MAV-seq |
MAV-seq | Computational Biology|Bioinformatics |
MAV-seq (Management, Analysis, Visualization of Sequence data) is an interactive, user friendly, cross platform, secure, encrypted, automated, customized, centralized, multi-roles based database application for the management of sample repertoires and automation of the data pre-processing of epigenomic and transcriptomic data.
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SNP Database |
SNP Database |
High quality single nucleotide polymorphism (SNP) database with more than 8 Million SNPs from 74 strains of laboratory mice, drawn from several sources.
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Model-AD Consortium |
Model-AD Consortium | Data Science at JAX |
Model organism development and evaluation for late-onset Alzheimer's Disease.
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MoDIS - Mouse Disease Information System |
MoDIS - Mouse Disease Information System |
MoDIS links to the Pathbase.net website to provide detailed information and annotated images of similar lesions in laboratory mice, making it a unique and useful training aid.
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Mouse Models of Human Cancer Database (MMHCdb)AccessOnline Associated Individuals/GroupsContact |
Mouse Models of Human Cancer Database (MMHCdb) | Bioinformatics|Genetics and Genomics|Data Science at JAX |
The Mouse Models of Human Cancer Database (formerly, the Mouse Tumor Biology database) integrates data on the frequency, incidence, genetics, and pathology of neoplastic disorders, emphasizing data on tumors that develop characteristically in different genetically defined strains of mice.
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Mouse Genome Database (MGD)AccessOnline Contact |
Mouse Genome Database (MGD) | Data Science at JAX |
Mouse Genome Database (MGD) is a core knowledgebase for the laboratory mouse and is focused on providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. MGD is a primary component of the Mouse Genome Informatics (MGI) Consortium.
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MouseCyc |
MouseCyc |
MouseCyc is a new, manually curated database of both known and predicted metabolic pathways for the laboratory mouse. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways, 1,790 enzymatic reactions, and 1,122 compounds in MouseCyc.
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MouseMineAccessOnline Contact |
MouseMine | Resource Development and Dissemination|Data Science at JAX |
MouseMine is a powerful data warehouse providing comprehensive API (application programming interface) access to MGI data, as well as a forms-based user interface.
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Multiple Genome ViewerAccessOnline Contact |
Multiple Genome Viewer | Data Science at JAX |
Explore and compare multiple annotated mouse genomes.
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Oak Ridge Collection at JAX |
Oak Ridge Collection at JAX |
For over half a century Oak Ridge National Laboratory generated and maintained a diverse collection of mouse stocks. A large part of this collection derived from induced mutagenesis programs using radiation or chemical mutagens. Many of these mutant stocks were cryopreserved at the Oak Ridge facility. In 2009 The Jackson Laboratory accepted and agreed to distribute the cryopreserved embryos and sperm in order that this resource would continue to be available to the worldwide research community.
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OncoCLAssociated Individuals/Groups |
OncoCL | Bioinformatics|Cancer|Computational Biology |
OncoCL, an ontology to describe cancer cell types
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Gene Ontology Consortium |
Gene Ontology Consortium | Genetics and Genomics|Resource Development and Dissemination|Bioinformatics |
The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products across databases.
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PDX Development and Trial Centers Research NetworkAccessOnline Associated Individuals/GroupsContact |
PDX Development and Trial Centers Research Network | Data Science at JAX |
PDXNet is an NCI-sponsored consortium that uses patient-derived xenografts to accelerate translational research for the broader research community. The Chuang lab has been co-leader of the Data Coordination Center for this consortium since 2017.
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PDX FinderAccessOnline Contact |
PDX Finder | Data Science at JAX |
PDX Finder is an open global cancer research portal to patient derived xenograft (PDX) models.
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RFR-PELAssociated Individuals/Groups |
RFR-PEL | Bioinformatics|Computational Biology|Genetics and Genomics |
Random Forest Regression for Epigenetic Length prediction
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Mouse Phenome DatabaseAssociated Individuals/Groups |
Mouse Phenome Database | Data Science at JAX|Bioinformatics|Complex Traits|Computational Biology|Genetics and Genomics |
This resource is a collaborative standardized collection of measured data on laboratory mouse strains and populations. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect. Also includes protocols, projects and publications, and SNP, variation and gene expression studies.
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Human Phenotype OntologyAccessOnline & Download Associated Individuals/GroupsContact |
Human Phenotype Ontology | Data Science at JAX |
The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease.
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Histological phenotyping and neural networksAssociated Individuals/Groups |
Histological phenotyping and neural networks |
Application of deep neural networks to rigorously and reproducibly quantify complex properties of histological images.
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Mouse Phylogeny Viewer |
Mouse Phylogeny Viewer |
Custom genome browser provides detailed answers to questions on the haplotype diversity and phylogenetic origin of the genetic variation underlying any genomic region of most laboratory strains.
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Digital Pathology PipelineAssociated Individuals/Groups |
Digital Pathology Pipeline | Genetics and Genomics|Computational Biology |
Tools for automatic glomerulus identification and histological quantification from scanned PAS slides
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Glaucoma Discovery PlatformAccessOnline Associated Individuals/GroupsContact |
Glaucoma Discovery Platform | Data Science at JAX |
Visualize and interrogate gene expression changes in glaucoma
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AMP-AD Knowledge PortalAccessOnline & Download Associated Individuals/GroupsContact |
AMP-AD Knowledge Portal | Data Science at JAX |
The AMP-AD Knowledge Portal is a platform to access data, analytical results and tools generated within the National Institute of Aging’s AD Translational Research Program. The majority of the content in the Portal is genomic data generated from human samples or experimental model systems. The Portal also contains analytical results and data summaries.
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QTL ViewerAccessOnline & Download Associated Individuals/GroupsContact |
QTL Viewer | Data Science at JAX |
Interactive web-based analysis tool that will allow users to replicate analyses reported for a study.
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QuINAssociated Individuals/Groups |
QuIN | Computational Biology|Bioinformatics|Genetics and Genomics |
QuIN (Query tool for Interaction Networks, available at quin.jax.org) is a tool for visualizing, annotating, and querying chromatin interactions derived from technologies such as ChIA-PET or HiC.
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R/DOQTLAccessDownload Associated Individuals/Groups
Contact |
R/DOQTL | Data Science at JAX |
DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations.
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Random Circuit Perturbation (sRACIPE)AccessDownload Associated Individuals/GroupsContact |
Random Circuit Perturbation (sRACIPE) | Data Science at JAX |
sRACIPE is a systems-biology modeling method which takes the gene regulatory circuit topology as the only input, and simulates an ensemble of models with random kinetic parameters at multiple noise levels. Statistical analysis of the generated gene expressions reveals the basin of attraction and stability of various phenotypic states and their changes associated with intrinsic and extrinsic noises yielding new insights on the structure and function of gene regulatory networks.
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Cre PortalAccessOnline Contact |
Cre Portal | Resource Development and Dissemination|Data Science at JAX |
The Cre Portal contains curated data about all recombinase-containing transgenes and knock-ins developed in mice to provide a comprehensive resource delineating known recombinase activity patterns and allowing users to find relevant mouse resources for their studies.
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Canines Helping to Cure Cancer |
Canines Helping to Cure Cancer |
Human cancers and dog cancers have a surprising amount in common. At The Jackson Laboratory, we believe that by studying canine cancers, we can gain important insights that may benefit both species!
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Scientific Research Services for JAX FacultyAssociated Individuals/Groups |
Scientific Research Services for JAX Faculty |
Interested in a career at The Jackson Laboratory? We empower and accelerate JAX research and discoveries with a broad array of shared scientific services and facilities.
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Mutant Mouse Resource and Research Center (MMRRC)Associated Individuals/Groups |
Mutant Mouse Resource and Research Center (MMRRC) | Resource Development and Dissemination |
The Mutant Mouse Resource and Research Center (MMRRC) distributes and cryopreserves scientifically valuable, genetically engineered mouse strains and mouse ES cell lines with potential value for the genetics and biomedical research community.
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Mouse Mutant ResourceAssociated Individuals/Groups |
Mouse Mutant Resource | Resource Development and Dissemination|Behavioral Disorders|Developmental Disorders|Eye Research|Genetics and Genomics|Immune Disorders|Neurodegenerative and Neuromuscular Diseases|Reproductive Disorders |
Mice harboring spontaneous mutations have long been a major source for animal models of human genetic disorders, particularly mendelian diseases. The Mouse Mutant Resource maintains over 700 established mutant strains.
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Special Mouse Strains ResourceAssociated Individuals/Groups |
Special Mouse Strains Resource | Resource Development and Dissemination|Complex Traits |
The SMSR maintains mice that are important tools for genetic analysis of complex diseases, including consomic strains.
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Cytogenetic and Down Syndrome Models ResourceAssociated Individuals/Groups |
Cytogenetic and Down Syndrome Models Resource | Developmental Disorders |
The Jackson Laboratory maintains and distributes chromosome-aberration stocks that provide mouse models for Down syndrome, as well as the study of chromosomal aneuploidy.
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Parkinson's Disease Mouse Model ResourceAssociated Individuals/Groups |
Parkinson's Disease Mouse Model Resource | Resource Development and Dissemination |
The Parkinson’s Disease Mouse Model Resource characterizes and distributes new mouse models of Parkinsonism and Parkinson’s disease.
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Optogenetics ResourceAssociated Individuals/Groups |
Optogenetics Resource | Resource Development and Dissemination |
We offer a growing number of mouse lines expressing proteins that activate, inhibit or detect neuronal activity.
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Mouse Resource for Craniofacial ResearchAssociated Individuals/Groups |
Mouse Resource for Craniofacial Research | Resource Development and Dissemination|Developmental Disorders |
This resource provides mouse models for facial, dental, eye, ear and skull development research, as well as mouse models of human craniofacial syndromes.
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Genetic Resource ScienceAssociated Individuals/Groups |
Genetic Resource Science | Resource Development and Dissemination |
Genetic Resource Science initiates and develops resource-generating research. Our team: identifies and implements innovative technologies for genetic research; makes and distributes new mouse models; and provides extensive genetic and phenotypic information on JAX mouse strains.
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Reproductive Genomics ProgramAssociated Individuals/Groups |
Reproductive Genomics Program |
Produce and distribute mutant models for infertility and to investigate underlying causes in order to identify new genes and pathways contributing to reproductive function.
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International Mouse Strain Resource (IMSR)AccessOnline Contact |
International Mouse Strain Resource (IMSR) | Resource Development and Dissemination|Data Science at JAX |
The International Mouse Strain Resource offers users a combined catalog of worldwide mouse resources (live, cryopreserved, and embryonic stem cells), with direct access to repository sites holding those resources of interest.
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Mouse Mutant Resource DatabaseAccessOnline Contact |
Mouse Mutant Resource Database | Data Science at JAX |
The MMR mouse variation database provides access to all genetic variants called from high-throughput exome and whole genome sequencing from mice exhibiting spontaneously arising Mendelian disease phenotypes. Phenotype, genetic mapping, and variant frequency metrics are also provided. Aggregated data analyses provide mutation candidate prioritization.
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Type 1 Diabetes Resource |
Type 1 Diabetes Resource | Diabetes and Obesity |
We collect, cryopreserve and distribute mouse strains important to research in type 1 diabetes.
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Peripheral Neuropathy ResourceAssociated Individuals/Groups |
Peripheral Neuropathy Resource | Neurodegenerative and Neuromuscular Diseases |
Serves as a centralized resource for mouse models and tools that have been validated for use in preclinical studies of peripheral neuropathy.
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Eye Mutant ResourceAssociated Individuals/Groups |
Eye Mutant Resource | Resource Development and Dissemination|Eye Research |
Describes mouse models for ocular research available at The Jackson Laboratory and provides a list of known mouse mutations that affect vision.
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