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Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection.

Johri P, Marinov GK, Doak TG, Lynch M.

Genome Biol Evol. 2019 May 1;11(5):1398-1416. doi: 10.1093/gbe/evz081.


Limited Mutation-Rate Variation Within the Paramecium aurelia Species Complex.

Long H, Doak TG, Lynch M.

G3 (Bethesda). 2018 Jul 2;8(7):2523-2526. doi: 10.1534/g3.118.200420.


Escherichia coli cultures maintain stable subpopulation structure during long-term evolution.

Behringer MG, Choi BI, Miller SF, Doak TG, Karty JA, Guo W, Lynch M.

Proc Natl Acad Sci U S A. 2018 May 15;115(20):E4642-E4650. doi: 10.1073/pnas.1708371115. Epub 2018 Apr 30.


Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina.

Zheng W, Wang C, Yan Y, Gao F, Doak TG, Song W.

Genome Biol Evol. 2018 Mar 1;10(3):883-894. doi: 10.1093/gbe/evy055.


Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data.

Ackerman MS, Johri P, Spitze K, Xu S, Doak TG, Young K, Lynch M.

Genetics. 2017 May;206(1):105-118. doi: 10.1534/genetics.116.190660. Epub 2017 Mar 24.


Diversity and Universality of Endosymbiotic Rickettsia in the Fish Parasite Ichthyophthirius multifiliis.

Zaila KE, Doak TG, Ellerbrock H, Tung CH, Martins ML, Kolbin D, Yao MC, Cassidy-Hanley DM, Clark TG, Chang WJ.

Front Microbiol. 2017 Feb 9;8:189. doi: 10.3389/fmicb.2017.00189. eCollection 2017.


Population Genomics of Paramecium Species.

Johri P, Krenek S, Marinov GK, Doak TG, Berendonk TU, Lynch M.

Mol Biol Evol. 2017 May 1;34(5):1194-1216. doi: 10.1093/molbev/msx074.


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 F, Castelli M, Sabaneyeva E, Schrallhammer M, Krenek S, Doak TG, Berendonk TU, Petroni G.

Appl Environ Microbiol. 2016 Nov 21;82(24):7236-7247. Print 2016 Dec 15.


Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli.

Lee H, Doak TG, Popodi E, Foster PL, Tang H.

Nucleic Acids Res. 2016 Sep 6;44(15):7109-19. doi: 10.1093/nar/gkw647. Epub 2016 Jul 18.


Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola.

Nimkulrat S, Lee H, Doak TG, Ye Y.

Front Microbiol. 2016 Jun 3;7:852. doi: 10.3389/fmicb.2016.00852. eCollection 2016.


The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis, a Bacterium Naturally Devoid of the Postreplicative Mismatch Repair Pathway.

Kucukyildirim S, Long H, Sung W, Miller SF, Doak TG, Lynch M.

G3 (Bethesda). 2016 Jul 7;6(7):2157-63. doi: 10.1534/g3.116.030130.


Draft Genome Sequence of Caedibacter varicaedens, a Kappa Killer Endosymbiont Bacterium of the Ciliate Paramecium biaurelia.

Suzuki H, Dapper AL, Jackson CE, Lee H, Pejaver V, Doak TG, Lynch M, Preer JR Jr.

Genome Announc. 2015 Nov 5;3(6). pii: e01310-15. doi: 10.1128/genomeA.01310-15.


Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes.

Wang M, Doak TG, Ye Y.

Genome Biol. 2015 Nov 2;16:243. doi: 10.1186/s13059-015-0804-0.


Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota.

Bao G, Wang M, Doak TG, Ye Y.

Front Microbiol. 2015 Sep 1;6:896. doi: 10.3389/fmicb.2015.00896. eCollection 2015.


The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe.

Farlow A, Long H, Arnoux S, Sung W, Doak TG, Nordborg M, Lynch M.

Genetics. 2015 Oct;201(2):737-44. doi: 10.1534/genetics.115.177329. Epub 2015 Aug 10.


Background Mutational Features of the Radiation-Resistant Bacterium Deinococcus radiodurans.

Long H, Kucukyildirim S, Sung W, Williams E, Lee H, Ackerman M, Doak TG, Tang H, Lynch M.

Mol Biol Evol. 2015 Sep;32(9):2383-92. doi: 10.1093/molbev/msv119. Epub 2015 May 14.


Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948.

Long H, Sung W, Miller SF, Ackerman MS, Doak TG, Lynch M.

Genome Biol Evol. 2014 Dec 23;7(1):262-71. doi: 10.1093/gbe/evu284.


The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development.

Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, Perlman DH, Doak TG, Stuart A, Amemiya CT, Sebra RP, Landweber LF.

Cell. 2014 Aug 28;158(5):1187-1198. doi: 10.1016/j.cell.2014.07.034.


Differential retention and divergent resolution of duplicate genes following whole-genome duplication.

McGrath CL, Gout JF, Johri P, Doak TG, Lynch M.

Genome Res. 2014 Oct;24(10):1665-75. doi: 10.1101/gr.173740.114. Epub 2014 Aug 1.


Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence.

McGrath CL, Gout JF, Doak TG, Yanagi A, Lynch M.

Genetics. 2014 Aug;197(4):1417-28. doi: 10.1534/genetics.114.163287. Epub 2014 May 19.


Expanding the catalog of cas genes with metagenomes.

Zhang Q, Doak TG, Ye Y.

Nucleic Acids Res. 2014 Feb;42(4):2448-59. doi: 10.1093/nar/gkt1262. Epub 2013 Dec 6.


Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria.

Boscaro V, Felletti M, Vannini C, Ackerman MS, Chain PS, Malfatti S, Vergez LM, Shin M, Doak TG, Lynch M, Petroni G.

Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):18590-5. doi: 10.1073/pnas.1316687110. Epub 2013 Oct 28.


Spliced DNA sequences in the Paramecium germline: their properties and evolutionary potential.

Catania F, McGrath CL, Doak TG, Lynch M.

Genome Biol Evol. 2013;5(6):1200-11. doi: 10.1093/gbe/evt087.


CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes.

Zhang Q, Rho M, Tang H, Doak TG, Ye Y.

Genome Biol. 2013 Apr 29;14(4):R40. doi: 10.1186/gb-2013-14-4-r40.


Reply to Massey: Drift does influence mutation-rate evolution.

Sung W, Ackerman MS, Miller SF, Doak TG, Lynch M.

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):E860. No abstract available.


A genomic survey of Reb homologs suggests widespread occurrence of R-bodies in proteobacteria.

Raymann K, Bobay LM, Doak TG, Lynch M, Gribaldo S.

G3 (Bethesda). 2013 Mar;3(3):505-16. doi: 10.1534/g3.112.005231. Epub 2013 Mar 1.


The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.

Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, Khurana JS, Goldman AD, Nowacki M, Schotanus K, Jung S, Fulton RS, Ly A, McGrath S, Haub K, Wiggins JL, Storton D, Matese JC, Parsons L, Chang WJ, Bowen MS, Stover NA, Jones TA, Eddy SR, Herrick GA, Doak TG, Wilson RK, Mardis ER, Landweber LF.

PLoS Biol. 2013;11(1):e1001473. doi: 10.1371/journal.pbio.1001473. Epub 2013 Jan 29.


The gain and loss of chromosomal integron systems in the Treponema species.

Wu YW, Doak TG, Ye Y.

BMC Evol Biol. 2013 Jan 22;13:16. doi: 10.1186/1471-2148-13-16.


Extraordinary genome stability in the ciliate Paramecium tetraurelia.

Sung W, Tucker AE, Doak TG, Choi E, Thomas WK, Lynch M.

Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19339-44. doi: 10.1073/pnas.1210663109. Epub 2012 Nov 5.


Drift-barrier hypothesis and mutation-rate evolution.

Sung W, Ackerman MS, Miller SF, Doak TG, Lynch M.

Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18488-92. doi: 10.1073/pnas.1216223109. Epub 2012 Oct 17.


Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics.

Wu YW, Rho M, Doak TG, Ye Y.

Bioinformatics. 2012 Sep 15;28(18):i363-i369. doi: 10.1093/bioinformatics/bts388.


Diverse CRISPRs evolving in human microbiomes.

Rho M, Wu YW, Tang H, Doak TG, Ye Y.

PLoS Genet. 2012;8(6):e1002441. doi: 10.1371/journal.pgen.1002441. Epub 2012 Jun 13.


Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax.

Xu K, Doak TG, Lipps HJ, Wang J, Swart EC, Chang WJ.

Gene. 2012 Aug 15;505(1):75-80. doi: 10.1016/j.gene.2012.05.045. Epub 2012 Jun 2.


Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes.

Wu YW, Rho M, Doak TG, Ye Y.

Appl Environ Microbiol. 2012 Aug;78(15):5288-96. doi: 10.1128/AEM.00564-12. Epub 2012 May 25.


Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology.

Zoller SD, Hammersmith RL, Swart EC, Higgins BP, Doak TG, Herrick G, Landweber LF.

Protist. 2012 Jul;163(4):643-57. doi: 10.1016/j.protis.2011.12.006. Epub 2012 Feb 9.


The Oxytricha trifallax mitochondrial genome.

Swart EC, Nowacki M, Shum J, Stiles H, Higgins BP, Doak TG, Schotanus K, Magrini VJ, Minx P, Mardis ER, Landweber LF.

Genome Biol Evol. 2012;4(2):136-54. doi: 10.1093/gbe/evr136. Epub 2011 Dec 16.


A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.

Ye Y, Doak TG.

PLoS Comput Biol. 2009 Aug;5(8):e1000465. doi: 10.1371/journal.pcbi.1000465. Epub 2009 Aug 14.


A functional role for transposases in a large eukaryotic genome.

Nowacki M, Higgins BP, Maquilan GM, Swart EC, Doak TG, Landweber LF.

Science. 2009 May 15;324(5929):935-8. doi: 10.1126/science.1170023. Epub 2009 Apr 16.


The pathway to detangle a scrambled gene.

M├Âllenbeck M, Zhou Y, Cavalcanti AR, J├Ânsson F, Higgins BP, Chang WJ, Juranek S, Doak TG, Rozenberg G, Lipps HJ, Landweber LF.

PLoS One. 2008 Jun 4;3(6):e2330. doi: 10.1371/journal.pone.0002330.


Bats use magnetite to detect the earth's magnetic field.

Holland RA, Kirschvink JL, Doak TG, Wikelski M.

PLoS One. 2008 Feb 27;3(2):e1676. doi: 10.1371/journal.pone.0001676.


RNA-mediated epigenetic programming of a genome-rearrangement pathway.

Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG, Landweber LF.

Nature. 2008 Jan 10;451(7175):153-8. Epub 2007 Nov 28.


Sequence features of Oxytricha trifallax (class Spirotrichea) macronuclear telomeric and subtelomeric sequences.

Cavalcanti AR, Dunn DM, Weiss R, Herrick G, Landweber LF, Doak TG.

Protist. 2004 Sep;155(3):311-22.


Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project.

Cavalcanti AR, Stover NA, Orecchia L, Doak TG, Landweber LF.

Chromosoma. 2004 Sep;113(2):69-76. Epub 2004 Jul 16.


Sequencing the Oxytricha trifallax macronuclear genome: a pilot project.

Doak TG, Cavalcanti AR, Stover NA, Dunn DM, Weiss R, Herrick G, Landweber LF.

Trends Genet. 2003 Nov;19(11):603-7. No abstract available.


Selection on the protein-coding genes of the TBE1 family of transposable elements in the ciliates Oxytricha fallax and O. trifallax.

Witherspoon DJ, Doak TG, Williams KR, Seegmiller A, Seger J, Herrick G.

Mol Biol Evol. 1997 Jul;14(7):696-706.


Conserved features of TBE1 transposons in ciliated protozoa.

Doak TG, Witherspoon DJ, Doerder FP, Williams K, Herrick G.

Genetica. 1997;101(2):75-86.


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