List of works by Thomas G Doak

A functional role for transposases in a large eukaryotic genome

scientific article published on 16 April 2009

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

scientific article

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

scientific article

ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data

scientific article published on 04 April 2020

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

scientific article

Background Mutational Features of the Radiation-Resistant Bacterium Deinococcus radiodurans

scientific article published on 14 May 2015

Bats use magnetite to detect the earth's magnetic field

scientific article

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

scientific article

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

scientific article

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

scientific article published on 16 July 2004

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

scientific article published in January 2011

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

scientific article published on 02 June 2012

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

scientific article

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

scientific article (publication date: 15 December 2016)

Diverse CRISPRs evolving in human microbiomes.

scientific article

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

scientific article published on 09 February 2017

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

scientific article

Drift-barrier hypothesis and mutation-rate evolution.

scientific article

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

scientific article

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

scientific article

Estimating seven coefficients of pairwise relatedness using population genomic data

article

Estimation of the Genome-Wide Mutation Rate and Spectrum in the Archaeal Species Haloferax volcanii

scientific article published on 08 June 2020

Expanding the catalog of cas genes with metagenomes

scientific article

Extraordinary genome stability in the ciliate Paramecium tetraurelia

scientific article

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

scientific article published on 03 June 2016

Harnessing the NEON data revolution to advance open environmental science with a diverse and data‐capable community

scientific article published in December 2021

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

scientific article published on 18 July 2016

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

scientific article

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

scientific article

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

scientific article published on 2 July 2018

Low Base-Substitution Mutation Rate but High Rate of Slippage Mutations in the Sequence Repeat-Rich Genome of Dictyostelium discoideum

scientific article published on 30 July 2020

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

scientific article

National Center for Genome Analysis support leverages XSEDE to support life science research

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

scientific article

Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): in silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome.

scientific article published on 8 April 2013

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

scientific article

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

article

Population Genomics of Paramecium Species.

scientific article published on 13 February 2017

RNA-mediated epigenetic programming of a genome-rearrangement pathway

scientific article

Reply to Massey: Drift does influence mutation-rate evolution

scientific article published in March 2013

Selection on the genes of Euplotes crassus Tec1 and Tec2 transposons: evolutionary appearance of a programmed frameshift in a Tec2 gene encoding a tyrosine family site-specific recombinase

scientific article

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

scientific article published on July 1, 1997

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

scientific article published on September 2004

Sequencing the Oxytricha trifallax macronuclear genome: a pilot project

scientific article published on 01 November 2003

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

scientific article

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

scientific article published on September 2012

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

scientific article published on September 2015

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

scientific article published on 2 November 2015

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

scientific article

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

scientific article

The Oxytricha trifallax mitochondrial genome

scientific article

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

scientific article published on 18 May 2016

The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe

scientific article

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

scientific article

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

scientific article

The pathway to detangle a scrambled gene

scientific article

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