Research Tools and Resources

Name	Name (A-Z)	Research Area	Description
Seqfold Associated People Zhengqing Ouyang, Ph.D.	Seqfold	Resource Development and Dissemination\|Genetics and Genomics	SeqFold is a tool for RNA secondary structure prediction from experimental data.
Wormhole Associated People Ron Korstanje, Ph.D., FAHA	Wormhole	Genetics and Genomics\|Resource Development and Dissemination	A tool for novel Least Diverged Ortholog prediction through machine learning
Type 1 Diabetes Resource Associated People Edward H. Leiter, Ph.D.	Type 1 Diabetes Resource	Diabetes and Obesity	We collect, cryopreserve and distribute mouse strains important to research in type 1 diabetes.
Scientific Research Services for JAX Faculty Associated People Carolyn Paisie, Ph.D. Alan Sawyer Chia-Lin Wei, Ph.D. Honey Reddi, Ph.D., FACMG Stacey Sukoff Rizzo, Ph.D. Grace Stafford, Ph.D. Joshy George, Ph.D. Mark Adams, Ph.D.	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.
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.
The Nathan Shock Center of Excellence in the Basic Biology of Aging	Nathan Shock Center of Excellence in Basic Biology Aging	Aging\|Resource Development and Dissemination	Our goal is to focus our diverse expertise in biology and genomics on the problems and disorders associated with aging.
Biology of Beta Cell Consortium Associated People Lenny Shultz, Ph.D.	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.
The Jackson Laboratory Cre Repository Associated People Steve Murray, Ph.D. Janan Eppig, Ph.D. Lawrence Bechtel, B.S.	Jackson Laboratory Cre Repository	Resource Development and Dissemination	The JAX Cre Repository's aim is to provide the scientific community with a centralized, comprehensive set of well-characterized Cre-driver lines and related information resources.
The Jackson Laboratory Alzheimer's Disease Center	Jackson Laboratory Alzheimer's Disease Center		To understand disease mechanisms and ultimately develop effective therapies for AD, it is essential we apply state-of-the-art approaches to generate the next generation of more predictive animal models and make these models widely available to the AD research community.
MODEL-AD	MODEL-AD	Neurodegenerative and Neuromuscular Diseases	Alzheimer’s disease (AD) is a major cause of dementia, disability and death in the elderly. Despite recent advances in our understanding of basic biological mechanisms underlying AD, we do not yet know how to prevent AD or have an approved disease modifying intervention.
DO-AS cohort data Associated People Ron Korstanje, Ph.D., FAHA	DO-AS cohort data	Genetics and Genomics\|Computational Biology	Phenotype and RNAseq data from approx. 200 (B6-Col4a5 KO x DO)F1 mice
FusorSV	FusorSV	Computational Biology\|Genetics and Genomics	FusorSV is an open source framework that takes a data mining approach to assess performance and merge callsets from an ensemble of Structural Variant calling algorithms.
GeneWeaver Associated People Elissa J. Chesler, Ph.D.	GeneWeaver		GeneWeaver is a powerful web-based data and analysis software system designed to find a convergent signal in noisy functional genomics data.
Genetic Resource Science Associated People Laura Reinholdt, Ph.D. Cathleen (Cat) Lutz, Ph.D., M.B.A. Steve Murray, Ph.D. David E. Bergstrom, Ph.D. Judy Morgan Crystal Davis Chia-Yen Wu, Ph.D., M.B.A. Laure Case Krista Geister, Ph.D. Orsolya Kiraly, Ph.D.	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.
The JAX Center for Genetics of Fertility and Reproduction	JAX Center for Genetics of Fertility and Reproduction	Reproductive Disorders	Scientists in the JAX Center for Genetics of Fertility and Reproduction work on a variety of scientific problems of relevance to fertility and newborn health.
Black Bear Genome Associated People Ron Korstanje, Ph.D., FAHA	Black Bear Genome		Supplemental tables and figures,
The JAX Center for Genome Dynamics	JAX Center for Genome Dynamics		The goal of the CGD is to evaluate the role of genome-wide organization in mammalian biology by developing detailed maps of genetic interactions that encompass allelic diversity, functional categories, gene expression, recombination hotspots, and phenotype associations.
Roux Center for Genomics and Computational Biology	Roux Center for Genomics and Computational Biology	Computational Biology\|Genetics and Genomics	The center enables scientists to harness the full power of genomic technologies and computational strategies and use them to analyze the human genome to discover new and better ways of preventing and treating disease
Reproductive Genomics Program Associated People Mary Ann Handel, Ph.D. John Eppig, Ph.D. John Schimenti, Ph.D., Professor of Genetics, Cornell University	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.
GFR Calculator Associated People Ron Korstanje, Ph.D., FAHA	GFR Calculator	Genetics and Genomics\|Computational Biology	This tool calculates the glomerular filtration rate in mice using the FITC-inulin method
HSA Associated People Zhengqing Ouyang, Ph.D.	HSA	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
I-ATAC Associated People Duygu Ucar, Ph.D.	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.
JAX Genetic Diversity Initiative Associated People Carolyn Paisie, Ph.D. Chien-Yu Tung	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.
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!
The Jackson Laboratory Cancer Center	Jackson Laboratory Cancer Center	Resource Development and Dissemination\|Cancer\|Genetics and Genomics	The Jackson Laboratory Cancer Center (JAXCC) is a National Cancer Institute-designated Cancer Center complemented by institutional education, resource and service initiatives that support cancer research world-wide. The NCI designated JAXCC comprises approximately 50 members with multidisciplinary expertise who are united in research aimed at understanding and targeting the genomic complexity of cancer.
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.
JAX Colony Management System	JAX Colony Management System		The JAX Colony Management System (JCMS) is a free and supported multi-user relational database system for managing research mouse colonies.
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.
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.
Cytogenetic and Down Syndrome Models Resource Associated People Laura Reinholdt, Ph.D. Cathleen (Cat) Lutz, Ph.D., M.B.A.	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.
Special Mouse Strains Resource Associated People Laura Reinholdt, Ph.D. Cathleen (Cat) Lutz, Ph.D., M.B.A.	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.
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.
Mouse Resource for Craniofacial Research Associated People Steve Murray, Ph.D.	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.
Mouse Tumor Biology Database	Mouse Tumor Biology Database	Bioinformatics\|Genetics and Genomics	The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by electronic access to a variety of information.
International Mouse Strain Resource	International Mouse Strain Resource	Resource Development and Dissemination	The IMSR is a searchable online database of mouse strains, stocks, and mutant ES cell lines available worldwide, including inbred, mutant, and genetically engineered strains.
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.
MouseMine	MouseMine	Resource Development and Dissemination	MouseMine is a powerful new system for online access to mouse data from MGI (Mouse Genome Informatics).
Mouse Mutant Resource Associated People Laura Reinholdt, Ph.D. David E. Bergstrom, Ph.D.	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.
Eye Mutant Resource Associated People Patsy Nishina, Ph.D. Bo Chang, Ph.D.	Eye Mutant Resource	Resource Development and Dissemination\|Eye Research	Resource lists and describes mouse models for ocular research at JAX.
Mutant Mouse Resource and Research Center (MMRRC) Associated People Laura Reinholdt, Ph.D. Cathleen (Cat) Lutz, Ph.D., M.B.A.	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.
Center for Systems Neurogenetics of Addiction	Center for Systems Neurogenetics of Addiction	Behavioral Disorders\|Bioinformatics\|Complex Traits\|Computational Biology\|Genetics and Genomics\|Resource Development and Dissemination	The Center for Systems Neurogenetics of Addiction (CSNA) aims to identify the biological relationships between the stages and patterns of cocaine addiction and behaviors that predict drug abuse.
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.
OncoCL Associated People Mary Dolan, Ph.D.	OncoCL	Bioinformatics\|Cancer\|Computational Biology	OncoCL, an ontology to describe cancer cell types
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.
Optogenetics Resource Associated People Michael Sasner, Ph.D.	Optogenetics Resource	Resource Development and Dissemination	We offer a growing number of mouse lines expressing proteins that activate, inhibit or detect neuronal activity.
Parkinson's Disease Mouse Model Resource Associated People Michael Sasner, Ph.D.	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.
RFR-PEL Associated People Duygu Ucar, Ph.D.	RFR-PEL	Bioinformatics\|Computational Biology\|Genetics and Genomics	Random Forest Regression for Epigenetic Length prediction
Peripheral Neuropathy Resource Associated People Cathleen (Cat) Lutz, Ph.D., M.B.A. Robert Burgess, Ph.D.	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.
Mouse Phenome Database	Mouse Phenome Database	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.
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.
Digital Pathology Pipeline Associated People Ron Korstanje, Ph.D., FAHA	Digital Pathology Pipeline	Genetics and Genomics\|Computational Biology	Tools for automatic glomerulus identification and histological quantification from scanned PAS slides
JAX Center for Precision Genetics	JAX Center for Precision Genetics	Bioinformatics\|Genetics and Genomics\|Cancer	The Jackson Laboratory Center for Precision Genetics (JCPG) seeks to create and validate new, precise animal models of incurable and genetically complex human diseases. The JCPG was initiated in 2015 as one of three NIH-funded Pilot Centers for Precision Disease Modeling (NIH-1U54OD020351).
Knockout Mouse Project (KOMP) Associated People Steve Murray, Ph.D. Robert E. Braun, Ph.D. Robert Taft, Ph.D. Jacqui White, Ph.D.	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.
QuIN Associated People Duygu Ucar, Ph.D.	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.
The Rare and Orphan Disease Center	Rare and Orphan Disease Center		350 million people are affected by rare and orphan disease. The Rare and Orphan Disease Center conducts research to better treat these diseases.

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