75 Publications (Page 1 of 3)
2020
ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data
Zheng, Weibo⋅Chen, Jing⋅Doak, Thomas G⋅Song, Weibo and Yan, Ying
Bioinformatics (Oxford, England), 2020-Apr-04. | Journal Article
 
Estimation of the Genome-Wide Mutation Rate and Spectrum in the Archaeal Species Haloferax volcanii
Kucukyildirim, Sibel⋅Kucukyildirim, Sibel⋅Behringer, Megan⋅Behringer, Megan⋅Williams, Emily M.⋅Williams, Emily M⋅Doak, Thomas G⋅Doak, Thomas G.⋅Lynch, Michael and Lynch, Michael
Genetics, vol. 215, pp. 1107–1116. | Journal Article
 
Low Base-Substitution Mutation Rate but High Rate of Slippage Mutations in the Sequence Repeat-Rich Genome of Dictyostelium discoideum
Kucukyildirim, Sibel⋅Behringer, Megan⋅Sung, Way⋅Brock, Debra A⋅Doak, Thomas G⋅Mergen, Hatice⋅Queller, David C⋅Strassmann, Joan E and Lynch, Michael
G3: Genes|Genomes|Genetics. | Journal Article
2019
Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection
Johri, Parul⋅Marinov, Georgi K⋅Doak, Thomas G and Lynch, Michael
Genome biology and evolution, vol. 11, (no. 5), pp. 1416, 2019-May-01. | Journal Article
2018
Escherichia coli cultures maintain stable subpopulation structure during long-term evolution
Behringer, Megan G⋅Choi, Brian I⋅Miller, Samuel F⋅Doak, Thomas G⋅Karty, Jonathan A⋅Guo, Wanfeng and Lynch, Michael
Proceedings of the National Academy of Sciences of the United States of America, vol. 115, (no. 20), pp. E4650, 2018-May-15. | Journal Article
 
Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina
Zheng, Weibo⋅Wang, Chundi⋅Yan, Ying⋅Gao, Feng⋅Doak, Thomas G and Song, Weibo
Genome biology and evolution, vol. 10, (no. 3), pp. 894, 2018-03-01. | Journal Article
 
Limited Mutation-Rate Variation Within the Paramecium aurelia Species Complex.
Long, Hongan⋅Doak, Thomas G and Lynch, Michael
G3 (Bethesda, Md.), May 24, 2018. | Journal Article
2017
A voice for bioinformatics
Ganote, C.L.⋅Sanders, S.A.⋅Papudeshi, B.N.⋅Blood, P.D. and Doak, T.G.
ACM International Conference Proceeding Series, vol. Part F128771. | Conference Proceeding
 
Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data
Ackerman, Matthew S⋅Ackerman, Matthew S⋅Ackerman, Matthew S⋅Johri, Parul⋅Johri, Parul⋅Johri, Parul⋅Spitze, Ken⋅Spitze, Ken⋅Spitze, Ken⋅Xu, Sen⋅Xu, Sen⋅Xu, Sen⋅Doak, Thomas G⋅Doak, Thomas G⋅Doak, Thomas G⋅Young, Kimberly⋅Young, Kimberly⋅Young, Kimberly⋅Lynch, Michael⋅Lynch, Michael and Lynch, Michael
Genetics, vol. 206, (no. 1), pp. 118, 2017-05-00. | Journal Article
 
Population genomics of Paramecium species.
Johri, Parul⋅Krenek, Sascha⋅Marinov, K⋅Doak, Thomas G⋅Berendonk, Thomas U and Lynch, Michael
Molecular biology and evolution, February 13, 2017. | Journal Article
2016
Disentangling the Taxonomy of Rickettsiales and Description of Two Novel Symbionts (“Candidatus Bealeia paramacronuclearis” and “Candidatus Fokinia cryptica”) Sharing the Cytoplasm of the Ciliate Protist Paramecium biaurelia
Szokoli, Franziska⋅Castelli, Michele⋅Sabaneyeva, Elena⋅Schrallhammer, Martina⋅Krenek, Sascha⋅Doak, Thomas G⋅Berendonk, Thomas U and Petroni, Giulio
Applied and environmental microbiology, vol. 82, (no. 24), pp. 7247, 2016-12-15. | Journal Article
 
Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola
Nimkulrat, Sutichot⋅Nimkulrat, Sutichot⋅Lee, Heewook⋅Lee, Heewook⋅Doak, Thomas G⋅Doak, Thomas G⋅Ye, Yuzhen and Ye, Yuzhen
Frontiers in microbiology, vol. 7, pp. 852, 2016-00-00. | Journal Article
 
Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli.
Lee, Heewook⋅Lee, Heewook⋅Doak, Thomas G⋅Doak, Thomas G⋅Popodi, Ellen⋅Popodi, Ellen⋅Foster, Patricia L⋅Foster, Patricia L⋅Tang, Haixu and Tang, Haixu
Nucleic acids research, vol. 44, (no. 15), pp. 7109-7119, September 6, 2016. | Journal Article
 
Mutation rate: mutation accumulation in a laboratory population
Sung, W⋅Tucker, AE⋅Doak, Tg⋅Choi, E⋅Thomas, WK and Lynch, M
An Introduction to Molecular Evolution and Phylogenetics, pp. 91. | Journal Article
 
The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis, a Bacterium Naturally Devoid of the Postreplicative Mismatch Repair Pathway
Kucukyildirim, Sibel⋅Long, Hongan⋅Sung, Way⋅Miller, Samuel F⋅Doak, Thomas G and Lynch, Michael
G3 (Bethesda, Md.), vol. 6, (no. 7), pp. 2163, 2016-07-07. | Journal Article
2015
Background Mutational Features of the Radiation-Resistant Bacterium Deinococcus radiodurans.
Long, Hongan⋅Long, Hongan⋅Kucukyildirim, Sibel⋅Kucukyildirim, Sibel⋅Sung, Way⋅Sung, Way⋅Williams, Emily⋅Williams, Emily⋅Lee, Heewook⋅Lee, Heewook⋅Ackerman, Matthew⋅Ackerman, Matthew⋅Doak, Thomas G⋅Doak, Thomas G⋅Tang, Haixu⋅Tang, Haixu⋅Lynch, Michael and Lynch, Michael
Molecular biology and evolution, vol. 32, (no. 9), pp. 2383-2392, September 2015. | Journal Article
 
Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome
Wu, L.-S.⋅Barnett, W.⋅Ganote, C.L.⋅Mockaitis, K.⋅Doak, T.G. and Stewart, C.A.
ACM International Conference Proceeding Series, vol. 2015-July. | Conference Proceeding
 
Draft Genome Sequence of Caedibacter varicaedens, a Kappa Killer Endosymbiont Bacterium of the Ciliate Paramecium biaurelia.
Suzuki, Haruo⋅Dapper, Amy L⋅Jackson, Craig E⋅Lee, Heewook⋅Pejaver, Vikas⋅Doak, Thomas G⋅Lynch, Michael and Preer, John R
Genome announcements, vol. 3, (no. 6), 2015. | Journal Article
 
Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948.
Long, Hongan⋅Sung, Way⋅Miller, Samuel F⋅Ackerman, Matthew S⋅Doak, Thomas G and Lynch, Michael
Genome biology and evolution, vol. 7, (no. 1), pp. 262-271, January 2015. | Journal Article
 
Providing National Cyberinfrastructure to Biologists, esp. genomicists
Barnett, William K and Doak, Thomas G
. | Journal Article
 
RNA-Seq Demo on Galaxy
Ganote, Carrie⋅Wu, Le-Shin and Doak, Thomas
. | Journal Article
 
Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota
Bao, Guanhui⋅Bao, Guanhui⋅Wang, Mingjie⋅Wang, Mingjie⋅Doak, Thomas G⋅Doak, Thomas G⋅Ye, Yuzhen and Ye, Yuzhen
Frontiers in microbiology, vol. 6, pp. 896, 2015-00-00. | Journal Article
 
Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes.
Wang, Mingjie⋅Doak, Thomas G and Ye, Yuzhen
Genome biology, vol. 16, pp. 243, 2015. | Journal Article
 
The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe
Farlow, Ashley⋅Farlow, Ashley⋅Long, Hongan⋅Long, Hongan⋅Arnoux, Stéphanie⋅Arnoux, Stéphanie⋅Sung, Way⋅Sung, Way⋅Doak, Thomas⋅Doak, Thomas G⋅Nordborg, Magnus⋅Nordborg, Magnus⋅Lynch, Michael and Lynch, Michael
Genetics, vol. 201, (no. 2), pp. 737-5SI, Oct 2015. | Journal Article
2014
Differential retention and divergent resolution of duplicate genes following whole-genome duplication.
McGrath, Casey L⋅Gout, Jean-Francois⋅Johri, Parul⋅Doak, Thomas G and Lynch, Michael
Genome research, vol. 24, (no. 10), pp. 1665-1675, October 2014. | Journal Article