Our research program focuses on two major areas: bioinformatics and developmental genomics. In the area of bioinformatics we focus on building information systems that can facilitate the use of the laboratory mouse as a model system for understanding normative biology and disease processes in humans. We are members of the Mouse Genome Informatics (MGI) consortium and work collaboratively with other investigators at The Jackson Laboratory to build and maintain databases that contain the most comprehensive collection of integrated functional genetic and genomic data for the laboratory mouse available in the public domain. In addition to the MGI information system, we also maintain the Mouse Phenome Database, which contains baseline phenotype measurement for hundreds of traits across scores of inbred lines of mice. Recent projects include the release of a comprehensive gene catalog for the reference mouse genome assembly and the release of MouseCyc, a database of curated biochemical pathways in the laboratory mouse.
In the area of developmental genomics, we are working in collaboration with Dr. Isaac Kohane (Children’s Hospital Boston) to use an understanding of the molecular genetics of normal lung development in mouse as a framework for identifying key genes and pathways in lung diseases such as cancer and pulmonary fibrosis. Recent projects include generating an integrated data set of mRNA and microRNA profiles over several key developmental time points in murine lung development.
My research group focuses on two major areas: bioinformatics and developmental genomics.
In the area of bioinformatics we build information systems that integrate diverse genetic and genomic data to facilitate the use of the laboratory mouse as a model system for understanding normative biology and disease processes in humans. My group is a member of the Mouse Genome Informatics consortium at The Jackson Laboratory which hosts the Mouse Genome Informatics database (http://www.informatics.jax.org).
In the area of developmental genomics, our goal is to use molecular genetics of normal lung development in mouse as a framework for identifying key genes and pathways in lung diseases such as cancer and pulmonary fibrosis.
- 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.
- 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.
- Krupke DM, Begley DA, Sundberg JP, Bult CJ, Eppig JT. 2008. The Mouse Tumor Biology Database. Nature Rev Cancer 8:459-65.
- Bogue MA, Grubb SC, Maddatu TP, Bult CJ. 2007. Mouse Phenome Database (MPD). Nucleic Acids Res. 35(Database ):D643-9.
- Peters LL, Robledo RF, Bult CJ, Churchill GA, Paigen BJ, Svenson KL. 2007. The mouse as a model for human biology: a resource guide for complex trait analysis. Nat Rev Genet 8(1):58-69.
- Bouma GJ, Affourtit JP, Bult CJ, Eicher EM. 2007. Transcriptional profile of mouse pre-granulosa and Sertoli cells isolated from early-differentiated fetal gonads. Gene Expr Patterns. 7(1-2):113-23.
- Kim, S, Huang LW, Snow KJ, Ablamunits V, Hasham MG, Young TH, Paulk AC, Richardson JE, Affourtit JP, Barak TS, Bult CJ, Barak Y. 2007. A mouse model of conditional lipodystrophy. PNAS 104:16627-16632.
- Collins F, Rossant J, Wurst W and the International Mouse Knockout Consortium. 2007. A mouse for all reasons. Cell 128:9-13.
- Frith MC, Bailey TL, Kasukawa T, Mignone F, Kummerfeld SK, Madera M, Sunkara S, Furuno M, Bult CJ, Quackenbush J, Kai C, Kawai J, Carninci P, Hayashizaki Y, Pesole G, Mattick JS. 2006. Discrimination of non-protein-coding transcripts from protein-coding mRNA. RNA Biol. 3(1):40-8.
- Furuno M, Pang KC, Ninomiya N, Fukuda S, Firth MC, Bult CJ, Mattick JS and Suzuki H. 2006. Clustering of internally-primed transcripts reveals novel long non-coding RNAs. PLOS Genetics 2(4):e37.
- Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, EngstrÃ¶m PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, et al. 2006. Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet. 2(4):e62.