Research and Faculty

Coming together from diverse backgrounds to advance mammalian genetics research.

Research Areas

We model and interpret genomic complexity, integrate basic research with clinical application and empower the global biomedical community by providing critical data, tools and services.

By Disease

By Research Type

Research Tools & Resources


  • Exome Sequencing Data

    Exome data on Mendelian mutations in mice for comparison to human mutations.

  • Mouse Tumor Biology Database

    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.

  • QTL Archive

    70+ QTL studies in a number of research areas, gathered and curated by the Churchill Group QTL Archive initiative.Each QTL study has phenotype and genotype data for members of a population derived from a specific cross.

Software Tools & Analysis

  • Gene Expression Miner

    This Strain Survey GEM holds data for a gene expression survey of 26 inbred mouse strains. Users can perform simple or advanced queries to find various locations of interest.

  • Genome Navigator

    Online tool used to find genes and transcripts in designated regions. Users can either enter a range manually or click and drag to select a region of interest.

  • HMM

    This software is used to fit Hidden Markov Models in Stochastic models for heterogeneous DNA sequences.

  • J/maanova

    J/maanova is an open sourced desktop application developed with the aim of simplifying the analysis of microarray experiments.

  • J/qtl

    J/qtl is a Java graphical user interface (GUI) for the popular QTL data analysis software R/qtl.

  • 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.

  • MAANOVA 2.0

    MAANOVA is a set of functions written in Matlab for the analysis of variance on microarray data.

  • Marker regression programs

    These programs are based on marker regression and are designed for detecting covariate effects and interactions from inbred line cross data.

  • MoDIS - Mouse Disease Information System

  • 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.

  • Pseudomarker programs

    Pseudomarker is a set of programs written in MATLAB for the analysis of QTL data from inbred line crosses.

  • PubArray

    PubArray is a desktop application that allows you to turn the analyzed results of your microarray experiment into a web application which is accessible via your browser.

  • R/maanova

    R/maanova is an extensible, interactive environment for Microarray analysis.

  • R/qtl

    R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.


  • Gene Ontology Consortium

    The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products across databases.

  • International Mouse Strain Resource

    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 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.

  • 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.