Overview

Our research program bridges the fields of bioinformatics/computational biology and developmental genomics. As members of the Mouse Genome Informatics (MGI) consortium, we collaborate with other investigators at The Jackson Laboratory to build information systems that facilitate the use of the laboratory mouse as a model system for understanding the genetic basis of normative biology and disease processes in humans. We also use the well-curated and integrated information in MGI as the foundation for developing computational methods to predict novel functional relationships among genes (MouseMap).

We use genomics technologies to identify and study the genetic systems and pathways that are critical for normal lung development and, in turn, use the genomics of normal development as a natural framework for the discovery of the molecular genetic basis of diseases such as lung cancer and pulmonary fibrosis.

Scientific report

Bridging the digital biology divide

The Mouse Genome Sequences and Maps Group: Integrating sequence and biology in the Mouse Genome Informatics (MGI) database

The mission of the Mouse Genome Informatics (MGI) database consortium is to facilitate the use of the mouse as a model system for understanding human biological processes and disease. As part of the MGI consortium, the Mouse Genome Sequences and Maps group has as its mission to connect mouse sequence data with the wealth of biological knowledge about mouse genes available in the MGI database. We accomplish our mission by:
  • curating associations between sequences and genes;
  • building a complete and non-redundant catalog of mouse genes;
  • associating genes in MGI with relevant data in external databases;
  • supporting sequence-based queries of MGI using our customized MouseBLAST server; and
  • supporting the generation of customized data sets of sequences using biologically meaningful criteria (e.g., "Return all protein sequences for genes on Chromosome 2 that have been annotated as transcription factors").
Two highlights of the Mouse Genome Sequences and Maps group in the past year include the release of a unified gene catalog for the reference mouse genome assembly and the incorporation of microRNA genes into the MGI database. The goal of the unified gene catalog project was to generate a single list of all known and predicted mouse genes. This project was facilitated by an efficient computational algorithm developed by fellow MGI consortium member, Dr. Joel Richardson. Dr. Richardson's algorithm allowed us to compare tens of thousands of gene predictions for the mouse genome generated independently by three different external bioinformatics groups to determine which predictions represented the same gene and which predictions were unique to a particular annotation pipeline. The results of the unified gene catalog project are available from the MGI database. The increased recognition of the importance of non-coding genes such as microRNAs for transcription regulation and disease prompted us to incorporate what is known about more than 370 known mouse microRNAs into MGI. This project was done in collaboration with the microRNA database group (miRBase) at the Sanger Institute in the United Kingdom. See scientific reports by Drs. Janan Eppig, Martin Ringwald, and Judith Blake for information about additional projects related to the MGI database consortium (http://www.informatics.jax.org).

The Mouse Tumor Biology (MTB) database

The MTB database is the most comprehensive publicly accessible database on cancer characteristics in inbred and genetically-modified strains of mice. The data in MTB include strain characteristics for hyperplasias and neoplasias, histopathology reports and images, and tumor genetics. Data are obtained both from the primary literature and by direct submissions from cancer researchers. MTB is accessed via the Mouse Genome Informatics web site (http://www.informatics.jax.org). During the past year, the infrastructure for MTB was completely redesigned and upgraded. New query interfaces were implemented and a new pathology data submission tool was released.

Data management for large-scale animal husbandry and phenotyping

The JaxTrack laboratory information system supports workflow, data management, and data analysis associated with mutagenesis, animal husbandry, sample tracking, and phenotype analysis for the Heart, Lung, Blood and Sleep Disorders Center, the Nathan Shock Center of Excellence in Basic Biology of Aging, and the Center for Genome Dynamics. JaxTrack supports workflow management, data review, database queries, and project status reports. Much of the phenotyping data managed in the JaxTrack system is made available (after expert data review) to the scientific community via the Mouse Phenome Database (MPD). The JaxTrack project was recently integrated into the Computational Sciences Service to support optimal coordination with related software development projects at The Jackson Laboratory.

Mouse Phenome Database (MPD)

The Mouse Phenome Database (MPD) is a comprehensive resource for phenotypic information on commonly used inbred mouse strains. Through MPD, researchers can access and download measurement data for individual animals and details about the phenotyping protocols for each data set. The Web-based interfaces for MPD support basic statistical analyses and comparisons of data across or within strains and studies. The detailed phenotype information in MPD combined with increasingly dense maps of sequence variation for inbred lines of mice make this resource indispensable for in silico mapping experiments and for identifying appropriate mouse strains for drug testing, toxicology studies, complex trait analysis, and human disease models. The MPD database project is a collaborative effort involving academic and industry research labs from all over the world. See the scientific report by Dr. Molly Bogue for more information and recent updates about the Mouse Phenome Database project.

MouseCyc: A biochemical pathways database for the laboratory mouse

The availability of the complete genome sequence for the C57BL/6J strain of laboratory mouse provides a powerful platform for predicting genes and other genome features. However, building a catalog of genome annotations is just the beginning for biology in a "post-genome" era. To gain new insights into fundamental biological processes using complete genome sequences and related genome-scale data will require understanding how genome features interact in pathways and networks in the cell and how perturbations of these interactions contribute to normal biological and disease processes.

The MouseCyc database is a new resource for exploring the biology of the laboratory mouse in the context of biochemical pathways. MouseCyc represents a significant step forward in providing researchers with access to mouse genomic data in the context of physiological and cellular processes. The initial focus for the development of MouseCyc will be on metabolism that includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc is unique relative to other pathway databases because the resource incorporates the rich biological knowledge about mouse genes and phenotypes that is available from the Mouse Genome Informatics (MGI) database.

Lab staff

Principal Investigator
Carol J. Bult, Ph.D., Professor


Co-Principal Investigators

Janan T. Eppig, Ph.D., Professor
Judith A. Blake, Ph.D., Associate Professor
Joel E. Richardson, Ph.D., Senior Research Scientist
James A. Kadin, Ph.D., Senior Research Scientist

Research Scientist
Molly A. Bogue, Ph.D.
Julie Wells, Ph.D.

Senior Scientific Curators
Dale Bagley, Ph.D.
Debra M. Krupke, M.S.
Yunzia "Sophia" Zhu, Ph.D.

Scientific Curator Assistant
Deborah J. Reed

Bioinformatics Analyst
Paul Hale, M.S.
Jill Recla, Ph.D.

Software Engineers
Stephen C. Grubb, M.S.

Affiliated Scientist:
Connie Birkenmeier, Ph.D.

Research Administrative Assistant
Glenn Smallidge

Publication listings

Publications 2008-Present

2012

Bult CJ.  2012.  Bioinformatics resources for behavior studies in the laboratory mouse.  Rev Neurobiol. 104:71-90.

Bult CJ, Eppig JT, Blake JA, Kadin JA, Richardson JE; the Mouse Genome Database Group.  2012.  The Mouse Genome Database: Genotypes, Phenotypes, and Models of Human Disease.  Nucleic Acids Res. 2012 Nov 21. [Epub ahead of print]

Guan Y, Gorenshteyn D, Burmeister M, Wong AK, Schimenti JC, Handel MA, Bult CJ, Hibbs MA, Troyanskaya OG.  2012.  Tissue-specific functional networks for prioritizing phenotype and disease genes.  PLoS Comput Biol. 8(9):e1002694 PMCID:PMC3459891.

Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, Bürger A, Bult CJ, Bushell W, Collins FS, Desaintes C, Doe B, Economides A, Eppig JT, Finnell RH, Fletcher C, Fray M, Frendewey D, Friedel RH, Grosveld FG, Hansen J, Hérault Y, Hicks G, Hörlein A, Houghton R, Hrabé de Angelis M, Huylebroeck D, Iyer V, de Jong PJ, Kadin JA, Kaloff C, Kennedy K, Koutsourakis M, Lloyd KC, Marschall S, Mason J, McKerlie C, McLeod MP, von Melchner H, Moore M, Mujica AO, Nagy A, Nefedov M, Nutter LM, Pavlovic G, Peterson JL, Pollock J, Ramirez-Solis R, Rancourt DE, Raspa M, Remacle JE, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Schick JZ, Schnütgen F, Schofield P, Seisenberger C, Selloum M, Simpson EM, Skarnes WC, Smedley D, Stanford WL, Stewart AF, Stone K, Swan K, Tadepally H, Teboul L, Tocchini-Valentini GP, Valenzuela D, West AP, Yamamura K, Yoshinaga Y, Wurst W.  2012.  The mammalian gene function resource: the International Knockout Mouse Consortium.  Mamm Genome. 2012 Oct;23(9-10):580-6  PMCID:PMC3463800.

Russell MK, Longoni M, Wells J, Maalouf FI, Tracy AA, Loscertales M, Ackerman KG, Pober BR, Lage K, Bult CJ, Donahoe PK.  2012.  Congenital diaphragmatic hernia candidate genes derived from embryonic transcriptomes.  Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2978-83.  PMCID:PMC3286948.

Maddatu TP, Grubb SC, Bult CJ, Bogue MA.  2012.  Mouse Phenome Database (MPD).  Nucleic Acids Res. 2012 Jan;40(Database issue):D887-94.  PMCID:PMC3245053.

2011

Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE; Mouse Genome Database Group.  2012.  The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse.  Nucleic Acids Res.  Jan;40(Database issue):D881-6. doi: 10.1093/nar/gkr974. Epub 2011 Nov 10.  PMCID:PMC3245042.

Bult CJ, Drabkin HJ, Evsikov A, Natale D, Arighi C, Roberts N, Ruttenberg A, D'Eustachio P, Smith B, Blake JA, Wu C.  2011.  The representation of protein complexes in Protein Ontology (PRO). BMC Bioinformatics.  Sep 19;12:371. PMCID:PMC3189193

Meehan TF, Carr CJ, Jay JJ, Bult CJ, Chesler EJ, Blake JA.  2011.  Autism candidate genes via mouse phenomics.  J Biomed Inform.  Dec;44 Suppl 1:S5-11. PMCID:PMC3263820.

Begley DA, Krupke DM, Neuhauser SB, Richardson JE, Bult CJ, Eppig JT, Sundberg JP. 2011 The Mouse Tumor Biology Database (MTB): A Cental Electronic Resource for Locating and Integrating Mouse Tumor Pathology Data. Vet Pathol.  Jan;49(1):218-23. PMCID:PMC3130112

Blake JA, Bult CJ, Kadin JA, Richardson JE, Eppig JT. 2011. The Mouse Genome Database (MGD): Premier model organism resource for mammalian genomics and genetics. Nucleic Acids Research, 10.1093/nar/gkq1008.

Ringwald M, Iyer V, Mason J, Stone K, Tadepally H, Kadin J, Bult C, Eppig J, Oakley D, Briois S, Stupka E, Macelli V, Smedley D, Liu S, Handwen JM, Ballabio A, Baldock R, Wurst W, Hicks G, Skarnes B. 2011. The IKMC Web Portal: a central point of entry to data and resources from the International Knockout Mouse Consortium. Nucleic Acids Research, 10.1093/nar/gkq879.

Natale, DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, DÕEustachio P, Evsikov, AV, Huang H, Nchoutmboube J, Roberts NV, Smith B, Wu CH. 2011. The Protein Ontology (PRO): A structured representations of protein forms and complexes. Nucleic Acids Research, 10.1093/nar/gkq907.

2010

Gaudet P, Bairoch A, Field D, Sansone S-A, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, et al. 2010. Towards a BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Research doi.10.1093/nar/gkq1173.

Doore SA, Beard K, Bult CJ. An ontology based personal exposure history. 2010. Proceedings from the 1st ACM International Health Informatics Symposium, November 2010.

Bult CJ. The laboratory mouse as a model system for human biology and disease: an introduction to the Mouse Genome Informatics (MGI) Database. 2010. NCI-Nature Pathway Interaction Database, doi:10.1038/pid.2010.2.

Donnelly CJ, McFarland M, Ames A, Sundberg BA, Springer D, Blauth P, and Bult CJ. 2010. JAX Colony Management System (JCMS): An extensible colony and phenotype data management system. Mammalian Genome DOI: 10.1007/s00335-010-9250-1

Fijalkowska I, Shamrma D, Bult CJ, Danoff SK. 2010. Expression of the transcription factor, TFII-I, during post implantation mouse embryonic development. BMC Research Notes 3:203.

Bult CJ, Kadin, JA, Richardson, JE, Blake JA, Eppig JT, Mouse Genome Database Group. 2010. The Mouse Genome Database: enhancements and updates. Nucleic Acids Res. 38:D586-92.

2009

Evsikov AV, Dolan ME, Genrich MP, Patek E, Bult CJ. 2009. MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biol Aug14;10(8):R84.

Yuan R, Tsaih SW, Petkova SB, de Evsikova CM, Xing S, Marion MA, Bogue MA, Mills KD,Peters LL, Bult CJ, Rosen CJ, Sundberg JP, Harrison DE, Churchill GA, Paigen B. 2009. Aging in inbred strains of mice: study design and interim report on median lifespans and circulating IGF1 levels. Aging Cell 8(3):277-87.

Cox A, Ackert-Bicknell CL, Dumont BL, Ding Y, Bell JT, Brockmann GA, Wergedal JE, Bult C, Paigen B, Flint J, Tsaih SW, Churchill GA, Broman KW. 2009. A new standard genetic map for the laboratory mouse. Genetics 182(4):1335-44.

Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M, Hlavina W, Kapustin Y, Meric P, Maglott D, Birtle Z, Marques AC, Graves T, Zhou S, Teague B, Potamousis K, Churas C, Place M, Herschleb J, Runnheim R, Forrest D, Amos-Landgraf J, Schwartz DC, Cheng Z, Lindblad-Toh K, Eichler EE, Ponting CP; Mouse Genome Sequencing Consortium. 2009. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol 7(5).

2008

Guan Y, Myers CL, Bult CJ, Troyanskaya O. 2008. A genome-wide functional network for the laboratory mouse. PLOS Computational Biology, 4(9):e1000165.

Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles B, Kasif S, Kohane I. 2008. Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers. Genome Biology, 9:R108.

Evsikov AV, Dolan ME, Genrich MP, Patek E, Bult CJ.  2009.  MouseCyc: a curated biochemical pathways database for the laboratory mouse.  Genome Biol.  10(8):R84. Epub 2009 Aug 14.

Yuan R, Tsaih SW, Petkova SB, Marin de Evsikova C, Xing S, Marion MA, Bogue MA, Mills KD, Peters LL, Bult CJ, Rosen CJ, Sundberg JP, Harrison DE, Churchill GA, Paigen B.  2009.  Aging in inbred strains of mice: study design and interim report on median lifespans and circulating IGF1 levels.  Aging Cell. Jun;8(3):277-87. Epub 2009 Apr 9.

Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M, Hlavina W, Kapustin Y, Meric P, Maglott D, Birtle Z, Marques AC, Graves T, Zhou S, Teague B, Potamousis K, Churas C, Place M, Herschleb J, Runnheim R, Forrest D, Amos-Landgraf J, Schwartz DC, Cheng Z, Lindblad-Toh K, Eichler EE, Ponting CP; Mouse Genome Sequencing Consortium.  2009. Lineage-specific biology revealed by a finished genome assembly of the mouse.  PLoS Biol. May 5;7(5):e1000112. Epub 2009 May 26.

Blake JA, Bult CJ, Eppig JT, Kadin JA, Richardson JE; The Mouse Genome Database Group. 2009. The Mouse Genome Database genotypes::phenotypes. Nucleic Acids Res.37 37(Database):D712-9.

Grubb SC, Maddatu TP, Bult CJ, Bogue MA. 2009. Mouse phenome database. Nucleic Acids Res. 37(Database):D720-30.

2008

Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA; Mouse Genome Database Group. 2008. The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res. 36(Database):D724-8.

Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG. 2008. A genomewide functional network for the laboratory mouse. PLoS Comput Biol. 4(9):e1000165.

Krupke DM, Begley DA, Sundberg JP, Bult CJ, Eppig JT. 2008. The Mouse Tumor Biology database. Nat Rev Cancer 8(6):459-65.

Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB, Kasif S, Kohane IS. 2008. Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers. Genome Biology 9(R108):R108.


Books, Book Chapters, and Reviews

Sundberg JP and Bult CJ. 2006.  Professional use of mutant laboratory mice in research. In:  Handbook on Genetically Engineered Mice. JP Sundberg and T Ichiki(eds.). CRC Press Taylor and Francis Group. pp. 185-209.

Bult CJ, Krupke DM, Vincent MJ, Allio T, Sundberg JP, Mikaelian I, and Eppig JT. 2006.  The Mouse Tumor Biology Database: An online resource for mouse models of human cancer. In: Cancer Bioinformatics: From therap  Design to Treatment(S. Nagl, ed.) John Wiley and Sons. pp 143-153.

Woychik R and Bult CJ. 2005.  Functional analysis of genes. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. LB Jorde, PFR Little, MJ Dunn and S. Subramaniam(eds.)John Wiley and Sons LTD. 1135-41.

Blake J, Eppig JT, Bult CJ. 2006. Mouse and Rat Genome Informatics.  In:  Bioinformatics for Geneticists, Barnes MR, Gray IC, [eds], John Wiley and Sons, London

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