Thomas G Doak

Thomas G Doak

UNVERIFIED PROFILE

Are you Thomas G Doak?   Register this Author

Register author
Thomas G Doak

Thomas G Doak

Publications by authors named "Thomas G Doak"

Are you Thomas G Doak?   Register this Author

48Publications

723Reads

6Profile Views

Limited Mutation-Rate Variation Within the Species Complex.

G3 (Bethesda) 2018 07 2;8(7):2523-2526. Epub 2018 Jul 2.

Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287.

View Article

Download full-text PDF

Source
http://g3journal.org/lookup/doi/10.1534/g3.118.200420
Publisher Site
http://dx.doi.org/10.1534/g3.118.200420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027866PMC
July 2018

cultures maintain stable subpopulation structure during long-term evolution.

Proc Natl Acad Sci U S A 2018 05 30;115(20):E4642-E4650. Epub 2018 Apr 30.

Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1708371115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5960275PMC
May 2018

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

Genome Biol Evol 2018 03;10(3):883-894

Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.

View Article

Download full-text PDF

Source
https://academic.oup.com/gbe/article/10/3/883/4935244
Publisher Site
http://dx.doi.org/10.1093/gbe/evy055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5863220PMC
March 2018

Population Genomics of Paramecium Species.

Mol Biol Evol 2017 05;34(5):1194-1216

Department of Biology, Indiana University, Bloomington, IN.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msx074DOI Listing
May 2017

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

Genetics 2017 05 24;206(1):105-118. Epub 2017 Mar 24.

Department of Biology, Indiana University, Bloomington, Indiana 47405.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1534/genetics.116.190660DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5419463PMC
May 2017

Diversity and Universality of Endosymbiotic in the Fish Parasite .

Front Microbiol 2017 9;8:189. Epub 2017 Feb 9.

Department of Biology, Hamilton College, ClintonNY, USA; Institute of Molecular Biology, Academia SinicaTaipei, Taiwan.

View Article

Download full-text PDF

Source
http://journal.frontiersin.org/article/10.3389/fmicb.2017.00
Publisher Site
http://dx.doi.org/10.3389/fmicb.2017.00189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299013PMC
February 2017

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

Nucleic Acids Res 2016 09 18;44(15):7109-19. Epub 2016 Jul 18.

School of Informatics and Computing, Indiana University, Bloomington, IN 47401, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkw647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009759PMC
September 2016

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

Front Microbiol 2016 3;7:852. Epub 2016 Jun 3.

School of Informatics and Computing, Indiana University, Bloomington IN, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2016.00852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4891356PMC
July 2016

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

Genome Biol 2015 Nov 2;16:243. Epub 2015 Nov 2.

School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA.

View Article

Download full-text PDF

Source
http://genomebiology.com/2015/16/1/243
Publisher Site
http://dx.doi.org/10.1186/s13059-015-0804-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4630832PMC
November 2015

The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe.

Genetics 2015 Oct 10;201(2):737-44. Epub 2015 Aug 10.

Department of Biology, Indiana University, Bloomington, Indiana 47405

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1534/genetics.115.177329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596680PMC
October 2015

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

Genome Res 2014 Oct 1;24(10):1665-75. Epub 2014 Aug 1.

Department of Biology, Indiana University, Bloomington, Indiana 47408, USA;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.173740.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199370PMC
October 2014

Expanding the catalog of cas genes with metagenomes.

Nucleic Acids Res 2014 Feb 6;42(4):2448-59. Epub 2013 Dec 6.

School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA, Department of Biology, Indiana University, Bloomington, IN 47405, USA and National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47408, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkt1262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3936711PMC
February 2014

Artificial functional difference between microbial communities caused by length difference of sequencing reads.

Pac Symp Biocomput 2012 :259-70

School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.

View Article

Download full-text PDF

Source
December 2013

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

Genome Biol Evol 2013 ;5(6):1200-11

Institute for Evolution and Biodiversity, University of Münster, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/gbe/evt087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3698930PMC
December 2013

Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics.

Pac Symp Biocomput 2011 :165-76

School Of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1142/9789814335058_0018DOI Listing
November 2013

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

G3 (Bethesda) 2013 Mar 1;3(3):505-16. Epub 2013 Mar 1.

Institut Pasteur, Unité Biologie Moleculare du Gene chez les Extremophiles, Departement de Microbiologie, Paris, 75724 Cedex 15, France.

View Article

Download full-text PDF

Source
http://g3journal.org/lookup/doi/10.1534/g3.112.005231
Publisher Site
http://dx.doi.org/10.1534/g3.112.005231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583457PMC
March 2013

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

BMC Evol Biol 2013 Jan 22;13:16. Epub 2013 Jan 22.

School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2148-13-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3607928PMC
January 2013

Drift-barrier hypothesis and mutation-rate evolution.

Proc Natl Acad Sci U S A 2012 Nov 17;109(45):18488-92. Epub 2012 Oct 17.

Department of Biology, Indiana University, Bloomington, IN 47401, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1216223109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494944PMC
November 2012

Extraordinary genome stability in the ciliate Paramecium tetraurelia.

Proc Natl Acad Sci U S A 2012 Nov 5;109(47):19339-44. Epub 2012 Nov 5.

Department of Biology, Indiana University, Bloomington, IN 47405, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1210663109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511141PMC
November 2012

Diverse CRISPRs evolving in human microbiomes.

PLoS Genet 2012 13;8(6):e1002441. Epub 2012 Jun 13.

School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1002441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374615PMC
September 2012

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

Bioinformatics 2012 Sep;28(18):i363-i369

School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bts388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436815PMC
September 2012

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

Appl Environ Microbiol 2012 Aug 25;78(15):5288-96. Epub 2012 May 25.

School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.00564-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416431PMC
August 2012

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

Gene 2012 Aug 2;505(1):75-80. Epub 2012 Jun 2.

Department of Biology, Hamilton College, Clinton, NY 13323, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gene.2012.05.045DOI Listing
August 2012

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

PLoS Comput Biol 2009 Aug 14;5(8):e1000465. Epub 2009 Aug 14.

School of Informatics, Indiana University, Bloomington, IN, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1000465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714467PMC
August 2009

A functional role for transposases in a large eukaryotic genome.

Science 2009 May 16;324(5929):935-8. Epub 2009 Apr 16.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1170023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491810PMC
May 2009

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

PLoS One 2008 Feb 27;3(2):e1676. Epub 2008 Feb 27.

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001676PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246016PMC
February 2008

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

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

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/nature06452
Publisher Site
http://dx.doi.org/10.1038/nature06452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647009PMC
January 2008

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

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

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00412-004-0295-3DOI Listing
September 2004

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

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

Department of Ecology and Evolutionary Biology, Princeton University, NJ 08544, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1078/1434461041844196DOI Listing
September 2004

Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax: alternatively processed regions have multiple telomere addition sites.

BMC Genet 2002 Aug 28;3:16. Epub 2002 Aug 28.

Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132-2501, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC128808PMC
http://dx.doi.org/10.1186/1471-2156-3-16DOI Listing
August 2002