Scientific Research Services for JAX Faculty

Scientific Computing


The Mouse Mutant Database provides access to aggregated, annotated variant calls generated from high throughput sequencing of these strains with an emphasis on strains harboring recently acquired mutations that cause Mendelian disease phenotypes. Our V.2 dataset currently encompasses over 33.5 million SNP and INDEL variants and 11.6 million structural variants from ~450 samples representing more than 350 unique mouse strains. For more details visit



PI: Laura Reinholdt, Ph.D – Associate Professor

Co-Inv: Anuj Srivastava, Ph.D – Associate Director

David Bergstrom, Ph.D – Research Scientist – Program PI

Francisco Castellanos, M.S – Senior Scientific Software Engineer – SE Lead

Michael Lloyd, Ph.D – Assistant Computational Scientist

Oraya Zinder, B.S, Data Analyst

Song Yong Karst, Senior Biomedical Technician

Belinda Harris, Senior Research Technologist


Human Mouse Orthology DB

MVAR – Baha & Francisco

Metabolomics – Francisco & Georgi

PDX- Steve

Synteny Browser - Georgi

MPD – covered by Vivek

Gene Weaver




The Study Intake Platform (SIP) was created by the Mouse Phenome Database (MPD) team for phenomic data curation and has expanded to be an all-purpose data curation and study intake interface. SIP accepts quantitative trait baseline characterizations, diet studies, drug and alcohol studies, aging studies, challenge / pathogen studies, and more. Data from inbred strains and their derivatives are included such as recombinant inbred, F1 hybrid, and chromosome substitution strains, and also special panels such as Collaborative Cross and Hybrid Mouse Diversity Panel. Data from populations such as Diversity Outbred (DO) mice are also accepted.

Link :


Team :

  • Molly Bogue, PhD - Principal Investigator
  • Elissa Chesler, PhD - Co-Investigator
  • Vivek Philip, PhD - Co-Investigator and Analytic Lead
  • Robyn Ball, PhD - Computational Scientist
  • Dave Walton, BS - Software Technical Lead for MPD Functionality
  • Jake Emerson, MS - Software Technical Lead for Cube Functionality
  • Matt Dunn, BS - SIP Lead Developer
  • Stephen Grubb, MS - Developer
  • Georgi Kolishovski, MS - Developer
  • Alex Berger, BS - Developer
  • Abigail Ames, BS - Metadata Support Functionality
  • Anna Lamoureux, BS - User Experience and Interface Design
  • Beth Sundberg, MS - Software Quality Assurance
  • Gaurab Mukherjee, PhD - Biocuration Scientist
  • Beena Kadakkuzha, PhD – Project Manager



The Diversity Informatics Platform is powered by DiversityDB, a database with a dedicated API that provides access to genotype and phenotype data from experiments with Diversity Outbred mice. Data can be searched by publication, investigator, and data type and can be downloaded in zipped CSV or R/QTL2 formats. Users can download full datasets or a subset of samples, genotypes, clinical phenotypes and molecular phenotypes including transcript, proteomic, and metabolomic profiling data.

Link :


  • Dan Gatti, PhD – Program Owner , Senior Computational Scientist
  • Belinda Cornes, PhD – Data Analyst
  • Dave Walton, BS - Software Technical Lead
  • Alex Berger, BS - Developer
  • Anna Lamoureux, BS - User Experience and Interface Design
  • Matt Dunn, BS - SIP Lead Developer
  • Beth Sundberg, MS - Software Quality Assurance
  • Sejal Desai, BS – Software Quality Assurance Manager


HaploQA is a software platform that provides interpretation of genotype calls from the Mouse Universal Genotyping array platforms (including Mega-/Giga- MUGA) that are available from Neogen Genomics (Morgan et al., 2015). The software allows for direct upload of sample and genotype data, sample annotation, and organization by users. The software interprets genotype calls and uses established Hidden Markov Models that were generated by Dr. Gary Churchill’s laboratory to generate haplotypes with negative log likelihood scoring. There are additional options for interfacing with the data through a web-based graphics, links out to widely used genome browsers, data/image/report downloads, and options for making the data public.

Link :

Team :

PI: Laura Reinholdt, Ph.D – Associate Professor

EDOF tool - Imaging


Mouse Phenome Database (


Dave Walton, M.S. (Principal Scientific Software Engineer, Computational Sciences), Technical Lead

Matthew Dunn, B.S. (Software Engineer, Computational Sciences)

Matthew Gerring, M.S. (Software Engineer, Computational Sciences)

Georgi Kolishovski, B.S. (Software Engineer, Computational Sciences)

Sejal Desai, B.S. (QA, Computational Sciences)

Hao He, Ph.D. (Biostats, Computational Sciences)

Beena Kadakkuzha, Ph.D. (Project Management, Computational Sciences) 

PI: Molly Bogue, Ph.D. (Research Scientist, Chesler Lab)


Elissa Chesler, Ph.D. (Professor)

Vivek Philip, Ph.D. (Director, Computational Sciences)

The goal of the Mouse Phenome Project is to support biomedical research by delivering a widely accessed and highly functional data repository for well-documented disease relevant phenotypic data from heterogeneous mouse populations. The Mouse Phenome Database (MPD,, addresses the emerging needs of the biomedical research community by annotating data, making it available through a FAIR-compliant public repository, and provide tools that enable users to visualize, analyze, and download primary and summary data. Our objectives are to provide a central repository for data, documentation, and protocols, offering a unique and important venue for investigators needing to make their data public; to continually refine and develop tools and features to best locate, present, and analyze those datasets; and to maintain, enhance, and promote this resource to further enable quantitative, standardized and predictive phenotype studies and, in turn facilitate new scientific advances.

This services is only available to faculty and researchers at The Jackson Laboratory.