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    Indiana University

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  • Biography

    Kehry, M.R., T.G. Doak & F.W. Dahlquist. 1984. Stimulus-induced changes in methylesterase activity during chemotaxis in Escherichia coli. J. Biol. Chem. 259:11828-11836.

    Kehry, M.R., T.G. Doak & F.W. Dahlquist. 1985. Aberrant regulation of methylesterase activity in cheD chemotaxis. J. Bact. 163:105-112.

    Kehry, M.R., T.G. Doak & F.W. Dahlquist. 1985. Sensory adaptation in bacterial chemotaxis:regulation of demethylation. J. Bact. 163:983-990.

    Roth, J.R., C. Grabau & T.G. Doak. 1990. Genetic approaches to the synthesis and physiological significance of B12 in Salmonella typhimurium. Chemical Aspects of Enzyme Biotechnology. Ed. T.O. Baldwin et al., Plenum Press, New York.

    Williams, K., T.G. Doak & G. Herrick. 1993. Precise excision of Oxytricha trifallax Telomere-Bearing Elements and formation of circles closed by a copy of the flanking target duplication. EMBO J. 12:4593-4601.

    Doak, T. G., F. P. Doerder, C. Jahn, and G. Herrick. 1994. A family of transposase genes in transposons found in prokaryotes, multicellular eukaryotes and ciliated protozoans. Proc. Natl. Acad. Sci. USA 91: 942-946.

    Seegmiller, A., K.R. Williams, R.L. Hammersmith, T.G. Doak, T. Messick, D.J. Witherspoon, L.L. Storjohann & G. Herrick. 1996. Internal eliminated sequences of Oxytricha: allelic fixation, divergence, conservation and conversions. Mol. Biol. Evol. 13:1351-1362.

    Witherspoon, D.J., T.G. Doak, K. Williams, J. Seger & G. Herrick. 1997. Selection on the protein-coding genes of the TBE1 family of transposable elements in the ciliates Oxytricha fallax and O. trifallax. Mol Biol Evol. 14:696-706.

    Doak, T. G., D. J. Witherspoon, F. Doerder, K. Williams, and G. Herrick. 1997. Conserved features of ciliate TBE1 transposons. Genetica 101: 75-86.

    Doak, T.G. 2001. Ph.D. Dissertation. Transposons in ciliated protozoa. University of Utah, Salt Lake City.

    Williams, K. R, T. G. Doak, and G. Herrick. 2002. Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax: alternatively processed regions have multiple telomere addition sites. BMC Genetics 3: 16.

    Doak T. G., D. J. Witherspoon, C. Jahn, and G. Herrick. 2003. Selection on the genes of Euplotes crassus Tec1 and Tec2 transposons: evolutionary appearance of a programmed frameshift in a Tec2 gene encoding a tyrosine-family, site-specific recombinase. Eukaryotic Cell 2: 95-102.

    Doak T.G., A.R.O. Cavalcanti, N.A. Stover, D.M. Dunn, R. Weiss, G. Herrick & L.F. Landweber. 2003. Sequencing the Oxytricha trifallax macronuclear genome: a pilot project. Trends Genet. 19:603-607.

    Cavalcanti ARO, Stover NA, Orecchia L, Doak T.G, Landweber L.F. 2004. Coding properties of Oxytricha trifallax ( Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project. Chromosoma. 113:69-76.

    Cavalcanti ARO, DM Dunn, R Weiss, G Herrick, LF. Landweber and TG. Doak. 2004. Sequence features of Oxytricha trifallax (Class Spirotrichea) macronuclear telomeric and subtelomeric sequences. Protist 155:311–322, September

    Chang W-J, T.G. Doak. 2006. Mechanisms and evolution of genome reorganization in ciliated protozoa. Endocytobiosis Cell Res. 17:119-124.

    Nowacki, M., V. Vijayan, Y. Zhou, K. Schotanus, T. G. Doak, and L. F. Landweber. 2008. RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature 451: 153-158.

    Möllenbeck M., Y. Zhou, A.R. Cavalcanti, F. Jönsson, B.P. Higgins, W.J. Chang, Juranek S, T.G. Doak, G. Rozenberg, H.J. Lipps and L.F. Landweber. 2008. The pathway for detangling a scrambled gene. PLoS ONE 3:e2330.

    Holland R.A., J.L. Kirschvink, T.G. Doak and M. Wikelski. 2008. Bats use magnetite to detect the earth’s magnetic field. PLoS ONE. 3:e1676.

    Nowacki M, B.P. Higgins, G.M.Maquilan, E.C. Swart, T.G. Doak and L.F. Landweber. 2009. A functional role for transposases in a large eukaryotic genome. Science 324:935-938.

    Ye Y, Doak TG. 2009. A Parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol 5(8): e1000465.

    Neethu Shah, Haixu Tang, Thomas G. Doak and Yuzhen Ye. 2011. Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Pac Symp Biocomput. 2011:165-176.

    Mina Rho, Yu-Wei Wu, Haixu Tang, Thomas G. Doak, Yuzhen Ye. 2011. Diverse CRISPRs evolving in human microbiomes. PLOS Genetics. PLoS Genet 8(6): e1002441. doi:10.1371/journal.pgen.1002441.

    Stephen D. Zoller, Robert L. Hammersmith, Brian P. Higgins, Estienne Swart, Thomas G. Doak, Glenn Herrick, and Laura F. Landweber. 2011. Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple conserved gene sequences: limitations and problems in identifying ciliate genera by only morphology. Protist. 163:643–657.

    Sung, W., A.E. Tucker, T.G. Doak, E. Choi, W.K. Thomas, M. Lynch. 2011. Extraordinary genome stability in the ciliate Paramecium tetraurelia. Science. Proc Natl Acad Sci U S A. 109: 19339–19344.

    Estienne C. Swart, Mariusz Nowacki, Justine Shum, Heather Stiles, Brian P. Higgins, Thomas G. Doak, Klaas Schotanus, Vincent J. Magrini, Patrick Minx, Elaine R. Mardis and Laura F. Landweber1. 2011. The Oxytricha trifallax mitochondrial genome. Genome Biology and Evolution, 4: 136-154.

    Quan Zhang, Thomas G. Doak, YuZhan Ye. 2012. Artificial functional differences between microbial communities caused by length differences of sequencing reads. Pac Symp Biocomput. 2012:259-70.

    Yu-Wei Wu, Mina Rho, Thomas G. Doak, Yuzhen Ye. 2012. Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes. Appl Environ Microbiol. 78:5288.

    Yu-Wei Wu, Mina Rho, Thomas G. Doak, and Yuzhen Ye. 2012. Stitching Gene Fragments with a Network Matching Algorithm Improves Gene Assembly for Metagenomics. ECCB.

    Ke Xu, Thomas G. Doak, Hans J. Lipps, Jingmei Wang, Estienne C. Swart, Wei-Jen Chang. 2012. Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax. Gene. 505:75-80.

    Sung, W., M. S. Ackerman, S.F. Miller, T.G Doak, M.Lynch. 2012. Drift-barrier hypothesis and mutation-rate evolution. Proc Natl Acad Sci U S A. 109: 18488-92.

    Swart, E.C., J.R. Bracht, V. Magrini, P. Minx, X. Chen, L.F. … Landweber. 2013. The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes. PLoS Biol 11: e1001473.

    Raymann, K., L-M. Bobay, T. G. Doak, M. Lynch, and S. Gribaldo. 2013. A genomic survey of Reb homologues suggests widespread occurrence of R-bodies in Proteobacteria. G3 3:505-516.

    Yu-Wei Wu, Thomas G. Doak, and Yuzhen Ye. 2013. The Gain and Loss of Chromosomal Integron Systems in the Treponema Species. BMC Evolutionary Biology 2013, 13:16.

    Zhang, Q., M. Rho, H. Tang, T. G. Doak, Y. Ye. 2013. CRISPRs target a diverse collection of invasive mobile genetic elements in human microbiomes. Genome Biology, 14: R40.

    Christie AE, Roncalli V, Wu LS, Ganote CL, Doak TG, Lenz PH. 2013. Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): In silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome. Gen Comp Endocrinol. 187C:117-135.

    Francesco Catania, Casey L. McGrath, Thomas G. Doak and Michael Lynch. 2013. Spliced DNA sequences in the Paramecium germline: their properties and evolutionary potential. Genome Biol Evol. 2013 Jun 4.

    LeDuc, R., Wu, L.-S., Ganote, C., Doak, T.G., Blood, P., Vaughn, M., and Williams, B. (2013) National Center for Genome Analysis Support Leverages XSEDE to Support Life Science Research. Proceedings of XSEDE 13, San Diego CA. 7/22/2013. (

    Boscaro V, Felletti M, Vannini C, Ackerman MS, Chain PS, Malfatti S, Vergez LM, Shin M, Doak TG, Lynch M, Petroni G. 2013 Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria. Proc Natl Acad Sci U S A. Oct 28.

    Sung W, Ackerman MS, Miller SF, Doak TG, Lynch M. 2013 Reply to Massey: Drift does influence mutation-rate evolution. Proc Natl Acad Sci U S A. Mar 5;110(10):E860.

    Quan Zhang, Thomas G. Doak, Mina Rho, Yuzhen Ye. 2013. Expanding the Catalog of cas Genes with Metagenomes. Nucleic Acids Res. 2013 Dec 6. [Epub ahead of print].

    Wang MJ, TG Doak, YZ Ye. 2014. Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes. In preparation.

    Xiao Chen, John R. Bracht, Aaron D. Goldman, Egor Dolzhenko, Derek M. Clay, Estienne C. Swart, David H. Perlman, Thomas G. Doak, Andrew Stuart, Chris T. Amemiya, Robert P. Sebra, Laura F. Landweber. 2014. The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Cell, in press.

    McGrath, C. L., Gout, J. F., Doak, T. G., Yanagi, A., Lynch, M. 2014. The Paramecium caudatum genome sequence provides insights into three whole-genome duplications. Genetics, in press.

    C. L. McGrath, J. F. Gout, P. Johri, T. G. Doak, and M. Lynch. 2014. Differential retention and divergent resolution of duplicate genes following whole-genome duplication. Genome Research, in press.

    Hongan Long, Way Sung, Samuel F. Miller, Matthew S. Ackerman, Thomas G. Doak, Michael Lynch. 2014. Mutation rate, spectrum, topology and context-dependency in the DNA mismatch repair (MMR) deficient Pseudomonas fluorescens Migula ATCC948. In preparation.

    Hongan Long, Sibel Kucukyildirim, Way Sung, Emily Williams, Matthew Ackerman, Thomas G. Doak, Michael Lynch. 2014. Mutations are biased to GC in Deinococcus radiodurans. In preparation