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T. Doak · SciRah

Researcher profile · Semantic Scholar

T. Doak

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T. Doak — researcher profile on SciRah

h-index: 33
Works: 105
Citations: 5,111

Most-cited papers

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes
Yuzhen Ye, T. Doak
2009PLoS Comput. Biol.602 citations Open access
Semantic Scholar
Drift-barrier hypothesis and mutation-rate evolution
Way Sung, Matthew S. Ackerman, Samuel F. Miller, T. Doak +1 more
2012Proceedings of the National Academy of Sciences of the United States of America399 citations Open access
Semantic Scholar
RNA-mediated epigenetic programming of a genome-rearrangement pathway
M. Nowacki, Vikram Vijayan, Yi Zhou, Klaas Schotanus +2 more
2008Nature308 citations Open access
Semantic Scholar
STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq
B. Haas, A. Dobin, N. Stransky, Bo Li +10 more
2017bioRxiv279 citations Open access
Semantic Scholar
The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes
E. Swart, J. Bracht, V. Magrini, P. Minx +25 more
2013PLoS Biology229 citations Open access
Semantic Scholar
Comparing Bacterial Communities Inferred from 16s Rrna Gene Sequencing and Shotgun Metagenomics
Neethu Shah, Hai-Xu Tang, T. Doak, Yuzhen Ye
2011Pacific Symposium on Biocomputing212 citations Open access
Semantic Scholar
The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development
Xiao Chen, J. Bracht, A. Goldman, E. Dolzhenko +8 more
2014Cell179 citations Open access
Semantic Scholar
A Functional Role for Transposases in a Large Eukaryotic Genome
M. Nowacki, B. Higgins, Genevieve M. Maquilan, E. Swart +2 more
2009Science145 citations Open access
Semantic Scholar
Bats Use Magnetite to Detect the Earth's Magnetic Field
R. Holland, J. Kirschvink, T. Doak, M. Wikelski
2008PLoS ONE142 citations Open access
Semantic Scholar
Diverse CRISPRs Evolving in Human Microbiomes
Mina Rho, Yu-Wei Wu, Hai-Xu Tang, T. Doak +1 more
2012PLoS Genetics139 citations Open access
Semantic Scholar
The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe
A. Farlow, Hongan Long, S. Arnoux, Way Sung +3 more
2015Genetics136 citations Open access
Semantic Scholar
Differential retention and divergent resolution of duplicate genes following whole-genome duplication
Casey McGrath, Jean-François Goût, Parul Johri, T. Doak +1 more
2014Genome Research129 citations Open access
Semantic Scholar
Extraordinary genome stability in the ciliate Paramecium tetraurelia
Way Sung, Abraham E. Tucker, T. Doak, E. Choi +2 more
2012Proceedings of the National Academy of Sciences of the United States of America118 citations Open access
Semantic Scholar
Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli
Heewook Lee, T. Doak, E. Popodi, P. Foster +1 more
2016Nucleic Acids Research89 citations Open access
Semantic Scholar
Insights into Three Whole-Genome Duplications Gleaned from the Paramecium caudatum Genome Sequence
Casey McGrath, Jean-François Goût, T. Doak, A. Yanagi +1 more
2014Genetics87 citations Open access
Semantic Scholar
Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria
V. Boscaro, M. Felletti, C. Vannini, Matthew S. Ackerman +7 more
2013Proceedings of the National Academy of Sciences of the United States of America79 citations Open access
Semantic Scholar
Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): in silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome.
A. Christie, V. Roncalli, Le-Shin Wu, C. Ganote +2 more
2013General and Comparative Endocrinology72 citations
Semantic Scholar
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
Franziska Szokoli, M. Castelli, E. Sabaneyeva, M. Schrallhammer +4 more
2016Applied and Environmental Microbiology71 citations Open access
Semantic Scholar
Mutation Rate, Spectrum, Topology, and Context-Dependency in the DNA Mismatch Repair-Deficient Pseudomonas fluorescens ATCC948
Hongan Long, Way Sung, Samuel F. Miller, Matthew S. Ackerman +2 more
2014Genome Biology and Evolution68 citations Open access
Semantic Scholar
Background Mutational Features of the Radiation-Resistant Bacterium Deinococcus radiodurans.
Hongan Long, Sibel Kucukyildirim, Way Sung, Emily Williams +5 more
2015Molecular biology and evolution64 citations Open access
Semantic Scholar
CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes
Quan Zhang, Mina Rho, Hai-Xu Tang, T. Doak +1 more
2013Genome Biology59 citations Open access
Semantic Scholar
The Oxytricha trifallax Mitochondrial Genome
E. Swart, M. Nowacki, Justine Shum, H. Stiles +7 more
2011Genome Biology and Evolution57 citations Open access
Semantic Scholar
The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis, a Bacterium Naturally Devoid of the Postreplicative Mismatch Repair Pathway
Sibel Kucukyildirim, Hongan Long, Way Sung, Samuel F. Miller +2 more
2016G3: Genes, Genomes, Genetics56 citations Open access
Semantic Scholar
Escherichia coli cultures maintain stable subpopulation structure during long-term evolution
Megan G. Behringer, Brian I. Choi, Samuel F. Miller, T. Doak +3 more
2018Proceedings of the National Academy of Sciences of the United States of America55 citations Open access
Semantic Scholar
Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data
Matthew S. Ackerman, Parul Johri, K. Spitze, Sen Xu +3 more
2016Genetics48 citations Open access
Semantic Scholar
The Pathway to Detangle a Scrambled Gene
M. Möllenbeck, Yi Zhou, Andre R. O. Cavalcanti, F. Jönsson +7 more
2008PLoS ONE47 citations Open access
Semantic Scholar
Sequencing the Oxytricha trifallax macronuclear genome: a pilot project.
T. Doak, Andre R. O. Cavalcanti, N. Stover, D. Dunn +3 more
2003Trends in Genetics42 citations Open access
Semantic Scholar
Selection on the protein-coding genes of the TBE1 family of transposable elements in the ciliates Oxytricha fallax and O. trifallax.
D. Witherspoon, T. Doak, Kevin Williams, Adam C. Seegmiller +2 more
1997Molecular biology and evolution42 citations Open access
Semantic Scholar
Dynamics of Gene Loss following Ancient Whole-Genome Duplication in the Cryptic Paramecium Complex
Jean-François Goût, Yue Hao, Parul Johri, O. Arnaiz +12 more
2023Molecular biology and evolution39 citations Open access
Semantic Scholar
Harnessing the NEON data revolution to advance open environmental science with a diverse and data‐capable community
R. C. Nagy, J. Balch, E. Bissell, M. Cattau +116 more
2021Ecosphere35 citations Open access
Semantic Scholar
Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax.
Ke Xu, T. Doak, H. Lipps, Jingmei Wang +2 more
2012Gene33 citations
Semantic Scholar
Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina
Wei-Bo Zheng, Chundi Wang, Ying Yan, Feng Gao +2 more
2018Genome Biology and Evolution32 citations Open access
Semantic Scholar
Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project
Andre R. O. Cavalcanti, N. Stover, L. Orecchia, T. Doak +1 more
2004Chromosoma31 citations
Semantic Scholar
Population Genomics of Paramecium Species
Parul Johri, S. Krenek, G. Marinov, T. Doak +2 more
2017Molecular biology and evolution30 citations Open access
Semantic Scholar
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
T. Doak, D. Witherspoon, C. L. Jahn, Glenn Herrick
2003Eukaryotic Cell30 citations Open access
Semantic Scholar
Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota
Guan-Hui Bao, Ming-Jie Wang, T. Doak, Yuzhen Ye
2015Frontiers in Microbiology29 citations Open access
Semantic Scholar
A Genomic Survey of Reb Homologs Suggests Widespread Occurrence of R-Bodies in Proteobacteria
K. Raymann, L. Bobay, T. Doak, M. Lynch +1 more
2013G3: Genes, Genomes, Genetics29 citations Open access
Semantic Scholar
Sequence features of Oxytricha trifallax (class Spirotrichea) macronuclear telomeric and subtelomeric sequences.
Andre R. O. Cavalcanti, D. Dunn, R. Weiss, Glenn Herrick +2 more
2004Protist29 citations
Semantic Scholar
Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection
Parul Johri, G. Marinov, T. Doak, M. Lynch
2018bioRxiv28 citations Open access
Semantic Scholar
Expanding the catalog of cas genes with metagenomes
Quan Zhang, T. Doak, Yuzhen Ye
2013Nucleic Acids Research28 citations Open access
Semantic Scholar
A Population-Genetic Lens into the Process of Gene Loss Following Whole-Genome Duplication
Parul Johri, Jean-François Goût, T. Doak, Michael Lynch
2022Molecular biology and evolution25 citations Open access
Semantic Scholar
Diversity and Universality of Endosymbiotic Rickettsia in the Fish Parasite Ichthyophthirius multifiliis
K. E. Zaila, T. Doak, Hannah Ellerbrock, Che-huang Tung +6 more
2017Frontiers in Microbiology25 citations Open access
Semantic Scholar
Limited Mutation-Rate Variation Within the Paramecium aurelia Species Complex
Hongan Long, T. Doak, M. Lynch
2018G3: Genes, Genomes, Genetics23 citations Open access
Semantic Scholar
Oral Spirochetes Implicated in Dental Diseases Are Widespread in Normal Human Subjects and Carry Extremely Diverse Integron Gene Cassettes
Yu-Wei Wu, Mina Rho, T. Doak, Yuzhen Ye
2012Applied and Environmental Microbiology23 citations Open access
Semantic Scholar
The gain and loss of chromosomal integron systems in the Treponema species
Yu-Wei Wu, T. Doak, Yuzhen Ye
2013BMC Evolutionary Biology21 citations Open access
Semantic Scholar
Characterization and Taxonomic Validity of the Ciliate Oxytricha trifallax (Class Spirotrichea) Based on Multiple Gene Sequences: Limitations in Identifying Genera Solely by Morphology
Stephen D Zoller, R. L. Hammersmith, E. Swart, B. Higgins +3 more
2012Protist21 citations Open access
Semantic Scholar
Chromosome organization and gene expansion in the highly fragmented genome of the ciliate Strombidium stylifer.
Chao Li, Xiao Chen, Wei-Bo Zheng, T. Doak +3 more
2021Journal of genetics and genomics = Yi chuan xue bao20 citations
Semantic Scholar
Conserved features of TBE1 transposons in ciliated protozoa
T. Doak, D. Witherspoon, F. Doerder, K. Williams +1 more
2004Genetica18 citations
Semantic Scholar
Spliced DNA Sequences in the Paramecium Germline: Their Properties and Evolutionary Potential
Francesco Catania, Casey McGrath, T. Doak, M. Lynch
2013Genome Biology and Evolution16 citations Open access
Semantic Scholar
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics
Yu-Wei Wu, Mina Rho, T. Doak, Yuzhen Ye
2012Bioinform.16 citations Open access
Semantic Scholar

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