Research interests

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.

Publications

• 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, Engström 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.

Grants

• 2004 to 2009 — — Electronic Access to Mouse Tumor Data from NIH
• 2006 to 2011 — — Genome Informatics - Genome Features and Maps from NIH
• 2007 to 2009 — — MouseCyc: A Biochemical Pathway Database for the Mouse from NIH
• 2007 to 2009 — — Cancer Geographic Information System from Department of Defense
• 2007 to 2012 — — Data Coordination Center for the Knockout Mouse Project (KOMP) from NIH
• 2008 to 2010 — — Developmental Cancer Genomics from Maine Cancer Foundation