Biography:

Dr. Pontius received her PhD from the Free University of Brussels in 1998, where she developed computational techniques for the validation of proposed protein crystallographic structures. Postdoctoral study included the analysis of three-dimensional structures of DNA and RNA at the Nucleic Acid Database (NDB) at Rutgers University. Prior to joining LGD, she was working on the UniGene and HomoloGene project at the National Center for Biotechnology Information (NCBI).

Research:

1. The availability of several mammalian genomes from Whole Genome Shotgun sequencing experiments will present a challenge in annotation, especially in the absence of largescale cDNA libraries representing the genome. Our annotation of the cat genome was done by detecting regions of cat that are orthologous to thoroughly annotated genomes, and then using those annotations to assign putative genes to the cat. This method allows cross-referencing of putative genes and loci in cat to their corresponding genes and loci in other mammals.

Publications:

Pontius JU, Mullikin JC, Smith DR; Agencourt Sequencing Team, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schaffer AA, Agarwala R, Narfstrom K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson WE, Bourque G, Tesler G, NISC Comparative Sequencing Program, O'Brien SJ:  Initial sequence and comparative analysis of the cat genome. Genome Res. 2007 Nov; 17(11):1675-89.   [PDF]

Pontius JU, O'Brien SJ:  Genome Annotation Resource Fields GARFIELD: A Genome Browser for Felis catus. J Hered Sept-Oct; 98(5): 386-9.  Epub 2007. July 23.   [PDF]

Antunes A, Pontius J, Ramos MJ, O'Brien SJ, Johnson WE: Mitochondrial introgressions into the nuclear genome of the domestic cat. J Hered  2007 Sept-Oct; 98(5): 414-20. Epub 2007 Jul 28.   [PDF]

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Church DM, DiCuccio M, Edgar R, Federhen S, Helmberg W, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pontius JU, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D39-45.  [PDF]

Klein SL, Strausberg RL, Wagner L, Pontius J, Clifton SW, Richardson P. Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative. Dev Dyn. 2002 Dec;225(4):384-91.

FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002 Dec 5;420(6915):563-73

Hudson TJ, Church DM, Greenaway S, Nguyen H, Cook A, Steen RG, Van Etten WJ, Castle AB, Strivens MA, Trickett P, Heuston C, Davison C, Southwell A, Hardisty R, Varela-Carver A, Haynes AR, Rodriguez-Tome P, Doi H, Ko MS, Pontius J, Schriml L, Wagner L, Maglott D, Brown SD, Lander ES, Schuler G, Denny P. A radiation hybrid map of mouse genes. Nat Genet. 2001 Oct;29(2):201-5.