Katz Lab

Parfrey, L.W., D. Lahr and L.A. Katz. 2008. The dynamic nature of eukaryotic genomes Mol. Biol. Evol. 25(4):787-794 (PDF)

Cole J., Anderson O.R., Tekle Y. I., J. Grant, Katz L. A., Nerad T.  Submitted. A Description of a New 'Amoebozoa' isolated from the American Lobster, Homarus americanus

Yoon, H-S, J.R. Grant, Y.I. Tekle, M. Wu, B.C. Chao, J.C. Cole, J.M. Logsdon, D.J. Patterson, D. Bhattacharya, and L.A. Katz. A broadly sampled multigene tree of eukaryotes. BMC Evolutionary Biology 2008, 8:14 (PDF)

Tekle, Y.I., J.R. Grant, L. O.R. Anderson, J.C. Cole, T. Nerad, and L.A. Katz.  In Press.  Multigene phylogenetic analyses of diverse amoebae and assessment of stability of clades within ‘Amoebozoa’ based on rate corrected SSU-rDNA analysis. Mol. Phylogenet. Evol. (PDF)

*Robinson, T. and L.A. Katz.  In Press. Non-Mendelian inheritance of two cytoskeletal genes in the ciliate Chilodonella uncinata.  Mol. Biol. Evol. 24(11):2495–2503. 2007 (PDF)

Tekle, Y.I., J.R. Grant, O.R. Anderson, J.C. Cole, T. Nerad, D.J. Patterson and L.A. Katz.  2007.  A multigene analysis of Corallomyxa tenera sp. nov. suggests its membership in a clade that include Gromia, Haplosporidia and Foraminifera.  Protist.

McGrath, C., R. A. Zufall and L.A. Katz.  2007. Variation in macronuclear genome content of three ciliates with extensive chromosomal fragmentation: a preliminary analysis. J. Eukaryot. Microbiol. 54(3): 242-246. (PDF)

Zufall, R.A. and L.A. Katz. 2007. Micronuclear and macronuclear forms of β-tubulin genes in the ciliate Chilodonella uncinata reveal insights into genome processing and protein evolution.  J. Eukaryot. Microbiol. 54(3): 275-282. (PDF)

Parfrey, L.W., E. *Barbero, E. *Lasser, M.S. Dunthorn, D. Bhattacharya, D.J. Patterson and L.A. Katz.  2006.  Evaluating support for the current classification of eukaryotic diversity.  PLOS Genetics 2: 2062-2073. (PDF)

Katz, L.A. 2006.  Epigenomics and the Future of Genome Science. Current Biology . 16: R996-R997 (PDF)

Zufall, R.A., *C. McGrath, S. Muse and L.A. Katz.  2006.   Genome architecture drives protein evolution in ciliates.  Mol. Biol. Evol.23: 1681-1687. (PDF)

Katz, L.A., O.L.O. Snoeyenbos-West and F. P. Doerder. 2006.  Unusual patterns of molecular evolution at the SerH surface antigen locus in Tetrahymena thermophila: implication for estimates of effective population.  Mol. Biol. Evol. 23: 608-614.(PDF)

Zufall, R.A., *T. Robinson and L.A. Katz.  2005.  Evolution of developmentally regulated genome rearrangements in eukaryotes.  J. Exp. Zool. Part B. (Mol. Dev. Evol.) 304B: 448-455. (PDF)

Bhattacharya Lab

Nosenko, T., and D. Bhattacharya. 2008. Endosymbiotic and horizontal gene transfer in chromalveolates. J. Phycol. 44:7-10. (journal cover)

Moustafa, A., and D. Bhattacharya. 2008. PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas. BMC Evol. Biol. 8:6.

Phillips, N., S. Calhoun, A. Moustafa, D. Bhattacharya, and E.L. Braun. 2008. Genomic insights into evolutionary relationships among heterokont lineages emphasizing the Phaeophyceae. J. Phycol. 44:15-18.

Zhang, H., D. Bhattacharya, L. Maranda, and S. Lin. 2007. Mitochondrial cob and cox1 and their mRNA editing in Dinophysis acuminata from Narragansett Bay, with special reference to the phylogenetic position of Dinophysis. Appl. Environ. Microbiol. 75:1546-1554.

Bhattacharya, D., J.M. Archibald, A.P.M. Weber, and A. Reyes-Prieto. 2007. How do endosymbionts become organelles? Understanding early events in plastid evolution. Biosssays 29:1239-1246.

Reyes-Prieto, A., and D. Bhattacharya. 2007. Phylogeny of nuclear encoded plastid targeted proteins suggests an early divergence of glaucophytes within Plantae. Mol. Biol. Evol. 24:2358-2361.

Reyes-Prieto, A., H.S. Yoon, and D. Bhattacharya. 2008. Marine protist (algal) genomics and evolution.  Encyclopedia of Life Sciences. [in press]

Tyra, H.M., Linka, M., Weber, A.P.M., and D. Bhattacharya. 2007. Host origin of plastid solute transporters in the first photosynthetic eukaryotes. Genome Biol. 8:R212.

Nosenko, T., and D. Bhattacharya. 2007. Horizontal gene transfer in chromalveolates. BMC Evol. Biol. 7:173.

Reyes-Prieto, A., A. Weber, and D. Bhattacharya. 2007. The origin and establishment of the plastid in algae and plants. Annu. Rev. Genet. 41:147-168.

Hackett, J.D., H.S. Yoon, S. Li, A. Reyes-Prieto, S.E. Ruemmele, and D. Bhattacharya. 2007. Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of 'Rhizaria' with chromalveolates. Mol. Biol. Evol. 24:1702-1713.

Hackett, J.D., H.S. Yoon, N.J. Butterfield, M.J. Sanderson, and D. Bhattacharya. 2007. Plastid endosymbiosis: origins and timing of events. In: Evolution of Aquatic Photoautotrophs, Eds. Falkowski, P., and A. Knoll, Elsevier.

Nosenko, T., B. Boese, and D. Bhattacharya. 2007. Pulsed field gel electrophoresis analysis of genome size and structure in Pavlova gyrans and Diacronema sp. (Haptophyta). J. Phycol. :763-767.

Reyes Prieto, A., and D. Bhattacharya. 2007. Phylogeny of Calvin cycle enzymes supports Plantae monophyly. Mol. Phylogenet. Evol. 45:384-391.

Zhang, H., S. Lin, and D. Bhattacharya. 2007. A three-gene dinoflagellate phylogeny suggests a basal position for Amphidinium, Katodinium, and Heterocapsa. J. Mol. Evol. 65:463-474.

Reyes-Prieto, A., J.D. Hackett, M.F. Bonaldo, M.B. Soares, and D. Bhattacharya. 2006. Cyanobacterial contribution to algal nuclear genomes is primarily limited to plastid functions. Curr. Biol. 16:2320-2325. (with accompanying commentary)

Bhattacharya, D., and J.M. Archibald. 2006. Response to Theissen and Martin, “The difference between organelles and endosymbionts”. Curr. Biol. 16:R1017-1018.

Yoon, H.S.,  C. Ciniglia, M. Wu, J. Comeron, G. Pinto, A. Pollio, and D. Bhattacharya. 2006. Establishment of endolithic populations of extremophilic Cyanidiales (Rhodophyta). BMC Evol. Biol. 6:78.

Yoon, H.S., A. Reyes-Prieto, M. Melkonian, and D. Bhattacharya. 2006. Minimal plastid genome evolution in the Paulinella endosymbiont. Curr. Biol. 16:R670-R672. (with accompanying commentary)

Nosenko, T., K.L. Lidie, F.M. Van Dolah, E. Lindquist, J.-F. Cheng, US Department of Energy–Joint Genome Institute, and D. Bhattacharya. 2006. Chimeric plastid proteome in the Florida “Red Tide” dinoflagellate Karenia brevis. Mol. Biol. Evol. 23:2026-2038.

Lin, S., H. Zhang, Y. Hou, and D. Bhattacharya. 2006. Development of a dinoflagellate-oriented PCR primer set leads to the detection of picoplanktonic dinoflagellates from Long Island Sound. Appl. Environ. Microbiol. 72:5626-5630.

Reyes-Prieto, A., H.S. Yoon and D. Bhattacharya. 2006. Phylogenomics and its growing impact on algal phylogeny and evolution. Algae21:1-10.

Yoon, H.S., K.M. Müller, R.G. Sheath, F.D. Ott, and D. Bhattacharya. 2006. Defining the major lineages of red algae (Rhodophyta). J. Phycol. 42:482-492.

Weber, A., M. Linka, and D. Bhattacharya. 2006. Single, ancient origin of a plastid metabolite translocator family in Plantae from an endomembrane-derived ancestor.  Eukaryot. Cell. 5:609-612.

Li, S., T. Nosenko, J.D. Hackett, and D. Bhattacharya. 2006. Phylogenomic analysis provides evidence for the endosymbiotic transfer of red algal genes in chromalveolates. Mol. Biol. Evol. 23:663-674.

Hackett, J.D., T.E. Scheetz, H.S. Yoon, M.B. Soares, M.F. Bonaldo, T.L. Casavant, and D. Bhattacharya. 2005. Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics 6:80.

Yoon, H.S., J.D. Hackett, F.M. Van Dolah, T. Nosenko, K.L. Lidie, and D. Bhattacharya. 2005. Tertiary endosymbiosis driven genome evolution in dinoflagellate algae. Mol. Biol. Evol. 22:1299-1308.

Zhang, H., D. Bhattacharya, and S. Lin. 2005. Phylogeny of dinoflagellates based on mitochondrial cytochrome b and nuclear small subunit rDNA sequence comparisons. J. Phycol. 41:411-420.

Bhattacharya, D., H.S. Yoon, and J.D. Hackett. 2004. Chromalveolates unite: endosymbiosis connects the dots. Bioessays 26:50-60.

Ciniglia, C., H.S. Yoon, A. Pollio, G. Pinto, and D. Bhattacharya. 2004. Hidden biodiversity of the extremophilic Cyanidiales red algae. Mol. Ecol. 13:1827-1838.