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Items: 1 to 20 of 52


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 Mar 24. pii: genetics.116.190660. doi: 10.1534/genetics.116.190660. [Epub ahead of print]


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 Feb 9.


Population genomics of Paramecium species.

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

Mol Biol Evol. 2017 Feb 13. doi: 10.1093/molbev/msx074. [Epub ahead of print] No abstract available.


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 Jun 3.


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 Sep 1.


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):1187-98. 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.

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