75 Publications (Page 2 of 3)
2014
Expanding the catalog of cas genes with metagenomes.
Zhang, Quan⋅Doak, Thomas and Ye, Yuzhen
Nucleic acids research, vol. 42, (no. 4), pp. 2448-59, 2014/Feb. | Journal Article
 
Insights into Three Whole-Genome Duplications Gleaned from the Paramecium caudatum Genome Sequence
McGrath, Casey L⋅McGrath, Casey L⋅Gout, Jean-Francois⋅Gout, Jean-Francois⋅Doak, Thomas G⋅Doak, Thomas⋅Yanagi, Akira⋅Yanagi, Akira⋅Lynch, Michael and Lynch, Michael
Genetics, vol. 197, (no. 4), pp. 1417-8SI, Aug 2014. | Journal Article
 
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development.
Chen, Xiao⋅Bracht, John R⋅Goldman, Aaron David⋅Dolzhenko, Egor⋅Clay, Derek M⋅Swart, Estienne C⋅Perlman, David H⋅Doak, Thomas G⋅Stuart, Andrew⋅Amemiya, Chris T⋅Sebra, Robert P and Landweber, Laura F
Cell, vol. 158, (no. 5), pp. 1187-1198, August 28, 2014. | Journal Article
2013
A genomic survey of Reb homologs suggests widespread occurrence of R-bodies in proteobacteria.
Raymann, Kasie⋅Raymann, Kasie⋅Bobay, Louis-Marie⋅Bobay, Louis-Marie⋅Doak, Thomas G⋅Doak, Thomas⋅Lynch, Michael⋅Lynch, Michael⋅Gribaldo, Simonetta and Gribaldo, Simonetta
G3 (Bethesda, Md.), vol. 3, (no. 3), pp. 505-16, 2013/Mar. | Journal Article
 
CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes
Zhang, Quan⋅Rho, Mina⋅Tang, Haixu⋅Doak, Thomas and Ye, Yuzhen
Genome Biology, vol. 14, (no. 4), pp. R40, 2013. | Journal Article
 
Making campus bridging work for researchers: A case study with mlRho
Thota, A.⋅Michael, S.⋅Xu, S.⋅Haubold, B.⋅Doak, T. and Henschel, R.
ACM International Conference Proceeding Series. | Conference Proceeding
 
National Center for Genome Analysis support leverages XSEDE to support life science research
LeDuc, Richard D⋅Doak, Thomas⋅Wu, Le-Shin⋅Blood, Philip D⋅Ganote, Carrie L and Vaughn, Matthew. | Conference Proceeding
 
Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): in silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome.
Christie, Andrew E⋅Roncalli, Vittoria⋅Wu, Le-Shin⋅Ganote, Carrie L⋅Doak, Thomas and Lenz, Petra H
General and comparative endocrinology, vol. 187, pp. 117-35, 2013/Jun/15. | Journal Article
 
Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria.
Boscaro, Vittorio⋅Felletti, Michele⋅Vannini, Claudia⋅Ackerman, Matthew S⋅Chain, Patrick S⋅Malfatti, Stephanie⋅Vergez, Lisa M⋅Shin, Maria⋅Doak, Thomas⋅Lynch, Michael and Petroni, Giulio
Proceedings of the National Academy of Sciences of the United States of America, vol. 110, (no. 46), pp. 18590-5, 2013/Nov/12. | Journal Article
 
Reply to Massey: Drift does influence mutation-rate evolution.
Sung, Way⋅Ackerman, Matthew S⋅Miller, Samuel F⋅Doak, Thomas and Lynch, Michael
Proceedings of the National Academy of Sciences of the United States of America, vol. 110, (no. 10), pp. E860, 2013/Mar/5. | Journal Article
 
Reply to Massey: Drift does influence mutation-rate evolution.
Sung, Way⋅Ackerman, Matthew S⋅Miller, Samuel F⋅Doak, Thomas G and Lynch, Michael
(pp. E860). March 5, 2013
 
Spliced DNA sequences in the Paramecium germline: their properties and evolutionary potential.
Catania, Francesco⋅McGrath, Casey L⋅Doak, Thomas and Lynch, Michael
Genome biology and evolution, vol. 5, (no. 6), pp. 1200-11, 2013. | Journal Article
 
The gain and loss of chromosomal integron systems in the Treponema species.
Wu, Yu-Wei⋅Doak, Thomas and Ye, Yuzhen
BMC evolutionary biology, vol. 13, pp. 16, 2013. | Journal Article
 
The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.
Swart, Estienne C⋅Bracht, John R⋅Magrini, Vincent⋅Minx, Patrick⋅Chen, Xiao⋅Zhou, Yi⋅Khurana, Jaspreet S⋅Goldman, Aaron D⋅Nowacki, Mariusz⋅Schotanus, Klaas⋅Jung, Seolkyoung⋅Fulton, Robert⋅Ly, Amy⋅McGrath, Sean⋅Haub, Kevin⋅Wiggins, Jessica L⋅Storton, Donna⋅Matese, John C⋅Parsons, Lance⋅Chang, Wei-Jen⋅Bowen, Michael S⋅Stover, Nicholas A⋅Jones, Thomas A⋅Eddy, Sean R⋅Herrick, Glenn A⋅Doak, Thomas⋅Wilson, Richard K⋅Mardis, Elaine R and Landweber, Laura F
PLoS biology, vol. 11, (no. 1), pp. e1001473, 2013. | Journal Article
2012
Artificial functional difference between microbial communities caused by length difference of sequencing reads
Zhang, Q.⋅Doak, T.G. and Ye, Y.
17th Pacific Symposium on Biocomputing, PSB 2012, pp. 259-270. | Conference Proceeding
 
Artificial functional difference between microbial communities caused by length difference of sequencing reads.
Zhang, Quan⋅Doak, Thomas and Ye, Yuzhen
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp. 259-70, 2012. | Journal Article
 
Characterization and Taxonomic Validity of the Ciliate Oxytricha trifallax (Class Spirotrichea) Based on Multiple Gene Sequences: Limitations in Identifying Genera Solely by Morphology
Zoller, Stephen D⋅Hammersmith, Robert L⋅Swart, Estienne C⋅Higgins, Brian P⋅Doak, Thomas⋅Herrick, Glenn A and Landweber, Laura F
Protist, vol. 163, (no. 4), pp. 643-657, 2012. | Journal Article
 
Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax.
Xu, Ke⋅Doak, Thomas⋅Lipps, Hans J⋅Wang, Jingmei⋅Swart, Estienne C and Chang, Wei-Jen
Gene, vol. 505, (no. 1), pp. 75-80, 2012/Aug/15. | Journal Article
 
Diverse CRISPRs evolving in human microbiomes.
Rho, Mina⋅Guttman, David S⋅Rho, Mina⋅Wu, Yu-Wei⋅Wu, Yu-Wei⋅Tang, Haixu⋅Tang, Haixu⋅Doak, Thomas⋅Doak, Thomas G⋅Ye, Yuzhen and Ye, Yuzhen
PLoS genetics, vol. 8, (no. 6), pp. e1002441, 2012. | Journal Article
 
Drift-barrier hypothesis and mutation-rate evolution
Sung, Way⋅Ackerman, Matthew S⋅Miller, Samuel F⋅Doak, Thomas and Lynch, Michael
Proceedings of the National Academy of Sciences of the United States of America, vol. 109, (no. 45), Nov 6, 2012. | Journal Article
 
Extraordinary genome stability in the ciliate Paramecium tetraurelia
Sung, Way⋅Tucker, Abraham E⋅Doak, Thomas⋅Choi, Eunjin⋅Thomas, William K and Lynch, Michael
Proceedings of the National Academy of Sciences of the United States of America, vol. 109, (no. 47), Nov 20, 2012. | Journal Article
 
Oral Spirochetes Implicated in Dental Diseases Are Widespread in Normal Human Subjects and Carry Extremely Diverse Integron Gene Cassettes
Wu, Yu-Wei⋅Rho, Mina⋅Doak, Thomas and Ye, Yuzhen
Applied and Environmental Microbiology, vol. 78, (no. 15), Aug 2012. | Journal Article
 
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics
Wu, Yu-Wei⋅Rho, Mina⋅Doak, Thomas and Ye, Yuzhen
Bioinformatics, vol. 28, (no. 18), pp. i363-i369, 2012. | Journal Article
 
The Oxytricha trifallax mitochondrial genome.
Swart, Estienne C⋅Nowacki, Mariusz⋅Shum, Justine⋅Stiles, Heather⋅Higgins, Brian P⋅Doak, Thomas⋅Schotanus, Klaas⋅Magrini, Vincent⋅Minx, Patrick⋅Mardis, Elaine R and Landweber, Laura F
Genome biology and evolution, vol. 4, (no. 2), pp. 136-54, 2012. | Journal Article
2011
A Parsimony Approach to Biological Pathway Reconstruction/Inference for Metagenomes
Ye, Y. and Doak, T.G.
2011