Publications

August 2012

Selected prior publications:

Scaling metagenome sequence assembly with probabilistic De Bruijn graphs. Jason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje, and C. Titus Brown. Proc Natl Acad Sci USA. 2012. (Open Access) [ journal | materials ] dry, tools, metagenomics, k-mers, assembly
Standing Genetic Variation in Contingency Loci Drives the Rapid Adaptation of Campylobacter jejuni to a Novel Host. Jerome JP, Bell JA, Plovanich-Jones AE, Barrick JE, Brown CT, Manfield LS. PLoS One 6 (1), e16399, Jan 24 2011. [Link] wet, experimental evolution, genomics
Exploring the future of bioinformatics data sharing and mining with Pygr and Worldbase Christopher Lee (UCLA), Alexander Alekseyenko (NYU), C. Titus Brown (MSU), in Proceedings of the 8th Python in Science conference (SciPy 2009), G Varoquaux, S van der Walt, J Millman (Eds.), pp. 62-67 [ link ] dry, tools
Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. Pernthaler A, Dekas AE, Brown CT, Goffredi SK, Embaye T, Orphan VJ. Proc Natl Acad Sci USA. 2008 May 13;105(19):7052-7. [Link] microbial, metagenomics, dry
Computational approaches to finding and analyzing cis-regulatory elements. Brown CT. Methods Cell Biol. 2008;87:337-65. [Link] dry, regulatory genomics
High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution. Howard-Ashby M, Materna SC, Brown CT, Tu Q, Oliveri P, Cameron RA, Davidson EH. Dev Biol. 2006 Dec 1;300(1):27-34. [Link] dry, regulatory genomics
The Genome of the Sea Urchin Strongylocentrotuts purpuratus. Sea Urchin Genome Sequencing Consortium. Science. 2006 Nov 10;314(5801):941-52. [Link] genomics
Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus. M. Howard-Ashby, S.C. Materna, C.T. Brown, L. Chen, R.A. Cameron, and E.H. Davidson. Dev Biol. 2006 Aug 22 (epub). [Link] dry, genomics, large-scale
Anaerobic regulation by an atypical Arc system in Shewanella oneidensis. J.A. Gralnick, C.T. Brown, and D.K. Newman. Mol Microbiol. 2005 Jun;56(5):1347-57. [Link] microbial, regulatory genomics
Paircomp, FamilyRelationsII and Cartwheel: Tools for Interspecific Sequence Comparison. C. T. Brown (corresponding author), Y. Xie, E.H. Davidson, R.A. Cameron. BMC Bioinformatics. 2005 Mar 24;6(1):70. [Link] dry, regulatory genomics, animal
Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli. Brown CT, Callan CG Jr. Proc Natl Acad Sci USA. 2004 Feb 24;101(8):2404-9. [Link] dry, microbial, regulatory genomics
A genomic regulatory network for development. Davidson, E.H., Rast, J.P, Oliveri, P., Ransick, A., Calestani, C., Yuh, C.-H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., Otim, O., Brown, C.T., Livi, C.B., Lee, P.Y, Revilla, R., Schilstra, M.J., Clarke, P.J.C., Rust, A.G., Pan, Z.J., Arnone, M.I., Rowen, L., Cameron, R.A., McClay, D.R., Hood, L., and Bolouri, H. Science 295, 1669-1678, 2002. [Link] gene regulatory networks

For all prior publications by Dr. Brown, search for 'brown ct' in PubMed (ignore the urology publications, that's a different 'brown ct').