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Thomas G. Doak, Ph.D. - Publications

Affiliations: 
2001 University of Utah, Salt Lake City, UT 
Area:
Genetics, Molecular Biology
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56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Gout JF, Hao Y, Johri P, Arnaiz O, Doak TG, Bhullar S, Couloux A, Guérin F, Malinsky S, Potekhin A, Sawka N, Sperling L, Labadie K, Meyer E, Duharcourt S, et al. Dynamics of gene loss following ancient whole-genome duplication in the cryptic Paramecium complex. Molecular Biology and Evolution. PMID 37154524 DOI: 10.1093/molbev/msad107  0.337
2022 Johri P, Gout JF, Doak TG, Lynch M. A population-genetic lens into the process of gene loss following whole-genome duplication. Molecular Biology and Evolution. PMID 35639978 DOI: 10.1093/molbev/msac118  0.321
2021 Li C, Chen X, Zheng W, Doak TG, Fan G, Song W, Yan Y. Chromosome organization and gene expansion in the highly fragmented genome of the ciliate Strombidium stylifer. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 34452852 DOI: 10.1016/j.jgg.2021.05.014  0.425
2020 Kucukyildirim S, Behringer M, Sung W, Brock DA, Doak TG, Mergen H, Queller DC, Strassmann JC, Lynch M. Low Base-Substitution Mutation Rate but High Rate of Slippage Mutations in the Sequence Repeat-Rich Genome of . G3 (Bethesda, Md.). PMID 32732307 DOI: 10.1534/G3.120.401578  0.425
2020 Kucukyildirim S, Behringer M, Williams EM, Doak TG, Lynch M. Estimation of the Genome-Wide Mutation Rate and Spectrum in the Archaeal Species . Genetics. PMID 32513815 DOI: 10.1534/Genetics.120.303299  0.393
2020 Zheng W, Chen J, Doak TG, Song W, Yan Y. ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data. Bioinformatics (Oxford, England). PMID 32246828 DOI: 10.1093/Bioinformatics/Btaa226  0.367
2019 Johri P, Marinov GK, Doak TG, Lynch M. Population genetics of Paramecium mitochondrial genomes: recombination, mutation spectrum, and efficacy of selection. Genome Biology and Evolution. PMID 30980669 DOI: 10.1093/Gbe/Evz081  0.382
2018 Long H, Doak TG, Lynch M. Limited Mutation-Rate Variation Within the Species Complex. G3 (Bethesda, Md.). PMID 29794165 DOI: 10.1534/G3.118.200420  0.319
2018 Behringer MG, Choi BI, Miller SF, Doak TG, Karty JA, Guo W, Lynch M. cultures maintain stable subpopulation structure during long-term evolution. Proceedings of the National Academy of Sciences of the United States of America. PMID 29712844 DOI: 10.1073/Pnas.1708371115  0.372
2018 Zheng W, Wang C, Yan Y, Gao F, Doak TG, Song W. Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina. Genome Biology and Evolution. 10: 883-894. PMID 29608728 DOI: 10.1093/Gbe/Evy055  0.5
2017 Zaila KE, Doak TG, Ellerbrock H, Tung CH, Martins ML, Kolbin D, Yao MC, Cassidy-Hanley DM, Clark TG, Chang WJ. Diversity and Universality of Endosymbiotic Rickettsia in the Fish Parasite Ichthyophthirius multifiliis. Frontiers in Microbiology. 8: 189. PMID 28232825 DOI: 10.3389/Fmicb.2017.00189  0.305
2017 Johri P, Krenek S, Marinov K, Doak TG, Berendonk TU, Lynch M. Population genomics of Paramecium species. Molecular Biology and Evolution. PMID 28204679 DOI: 10.1093/Molbev/Msx074  0.46
2016 Szokoli F, Castelli M, Sabaneyeva E, Schrallhammer M, Krenek S, Doak TG, Berendonk TU, Petroni G. 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. Applied and Environmental Microbiology. PMID 27742680 DOI: 10.1128/Aem.02284-16  0.377
2016 Lee H, Doak TG, Popodi E, Foster PL, Tang H. Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli. Nucleic Acids Research. PMID 27431326 DOI: 10.1093/Nar/Gkw647  0.505
2016 Nimkulrat S, Lee H, Doak TG, Ye Y. Genomic and Metagenomic Analysis of Diversity-Generating Retroelements Associated with Treponema denticola. Frontiers in Microbiology. 7: 852. PMID 27375574 DOI: 10.3389/Fmicb.2016.00852  0.432
2016 Kucukyildirim S, Long H, Sung W, Miller SF, Doak TG, Lynch M. The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis, a Bacterium Naturally Devoid of the Post-replicative Mismatch Repair Pathway. G3 (Bethesda, Md.). PMID 27194804 DOI: 10.1534/G3.116.030130  0.328
2015 Suzuki H, Dapper AL, Jackson CE, Lee H, Pejaver V, Doak TG, Lynch M, Preer JR. Draft Genome Sequence of Caedibacter varicaedens, a Kappa Killer Endosymbiont Bacterium of the Ciliate Paramecium biaurelia. Genome Announcements. 3. PMID 26543129 DOI: 10.1128/Genomea.01310-15  0.448
2015 Wang M, Doak TG, Ye Y. Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes. Genome Biology. 16: 243. PMID 26527161 DOI: 10.1186/S13059-015-0804-0  0.31
2015 Bao G, Wang M, Doak TG, Ye Y. Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota. Frontiers in Microbiology. 6: 896. PMID 26388849 DOI: 10.3389/Fmicb.2015.00896  0.379
2015 Farlow A, Long H, Arnoux S, Sung W, Doak TG, Nordborg M, Lynch M. The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe. Genetics. 201: 737-44. PMID 26265703 DOI: 10.1534/Genetics.115.177329  0.356
2015 Long H, Kucukyildirim S, Sung W, Williams E, Lee H, Ackerman M, Doak TG, Tang H, Lynch M. Background Mutational Features of the Radiation-Resistant Bacterium Deinococcus radiodurans. Molecular Biology and Evolution. PMID 25976352 DOI: 10.1093/Molbev/Msv119  0.312
2015 Long H, Sung W, Miller SF, Ackerman MS, Doak TG, Lynch M. Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948. Genome Biology and Evolution. 7: 262-71. PMID 25539726 DOI: 10.1093/Gbe/Evu284  0.348
2014 Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, Perlman DH, Doak TG, Stuart A, Amemiya CT, Sebra RP, Landweber LF. The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Cell. 158: 1187-98. PMID 25171416 DOI: 10.1016/J.Cell.2014.07.034  0.47
2014 McGrath CL, Gout JF, Johri P, Doak TG, Lynch M. Differential retention and divergent resolution of duplicate genes following whole-genome duplication. Genome Research. 24: 1665-75. PMID 25085612 DOI: 10.1101/Gr.173740.114  0.41
2014 McGrath CL, Gout JF, Doak TG, Yanagi A, Lynch M. Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence. Genetics. 197: 1417-28. PMID 24840360 DOI: 10.1534/Genetics.114.163287  0.453
2014 Zhang Q, Doak TG, Ye Y. Expanding the catalog of cas genes with metagenomes. Nucleic Acids Research. 42: 2448-59. PMID 24319142 DOI: 10.1093/Nar/Gkt1262  0.413
2013 Boscaro V, Felletti M, Vannini C, Ackerman MS, Chain PS, Malfatti S, Vergez LM, Shin M, Doak TG, Lynch M, Petroni G. Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria. Proceedings of the National Academy of Sciences of the United States of America. 110: 18590-5. PMID 24167248 DOI: 10.1073/Pnas.1316687110  0.407
2013 Catania F, McGrath CL, Doak TG, Lynch M. Spliced DNA sequences in the Paramecium germline: their properties and evolutionary potential. Genome Biology and Evolution. 5: 1200-11. PMID 23737328 DOI: 10.1093/Gbe/Evt087  0.446
2013 Zhang Q, Rho M, Tang H, Doak TG, Ye Y. CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes. Genome Biology. 14: R40. PMID 23628424 DOI: 10.1186/Gb-2013-14-4-R40  0.396
2013 Raymann K, Bobay LM, Doak TG, Lynch M, Gribaldo S. A genomic survey of Reb homologs suggests widespread occurrence of R-bodies in proteobacteria. G3 (Bethesda, Md.). 3: 505-16. PMID 23450193 DOI: 10.1534/G3.112.005231  0.343
2013 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, ... ... Doak TG, et al. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. Plos Biology. 11: e1001473. PMID 23382650 DOI: 10.1371/Journal.Pbio.1001473  0.705
2013 Wu YW, Doak TG, Ye Y. The gain and loss of chromosomal integron systems in the Treponema species. Bmc Evolutionary Biology. 13: 16. PMID 23339550 DOI: 10.1186/1471-2148-13-16  0.356
2013 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, ... ... Doak TG, et al. Comparison of key ciliate macronuclear genomes. Plos Biology. DOI: 10.1371/Journal.Pbio.1001473.G002  0.381
2012 Sung W, Tucker AE, Doak TG, Choi E, Thomas WK, Lynch M. Extraordinary genome stability in the ciliate Paramecium tetraurelia. Proceedings of the National Academy of Sciences of the United States of America. 109: 19339-44. PMID 23129619 DOI: 10.1073/Pnas.1210663109  0.394
2012 Sung W, Ackerman MS, Miller SF, Doak TG, Lynch M. Drift-barrier hypothesis and mutation-rate evolution. Proceedings of the National Academy of Sciences of the United States of America. 109: 18488-92. PMID 23077252 DOI: 10.1073/Pnas.1216223109  0.345
2012 Wu YW, Rho M, Doak TG, Ye Y. Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. Bioinformatics (Oxford, England). 28: i363-i369. PMID 22962453 DOI: 10.1093/Bioinformatics/Bts388  0.397
2012 Rho M, Wu YW, Tang H, Doak TG, Ye Y. Diverse CRISPRs evolving in human microbiomes. Plos Genetics. 8: e1002441. PMID 22719260 DOI: 10.1371/Journal.Pgen.1002441  0.451
2012 Xu K, Doak TG, Lipps HJ, Wang J, Swart EC, Chang WJ. Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax. Gene. 505: 75-80. PMID 22669045 DOI: 10.1016/J.Gene.2012.05.045  0.402
2012 Wu YW, Rho M, Doak TG, Ye Y. Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes. Applied and Environmental Microbiology. 78: 5288-96. PMID 22635997 DOI: 10.1128/Aem.00564-12  0.449
2012 Zoller SD, Hammersmith RL, Swart EC, Higgins BP, Doak TG, Herrick G, Landweber LF. Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology. Protist. 163: 643-57. PMID 22325790 DOI: 10.1016/J.Protis.2011.12.006  0.69
2012 Swart EC, Nowacki M, Shum J, Stiles H, Higgins BP, Doak TG, Schotanus K, Magrini VJ, Minx P, Mardis ER, Landweber LF. The Oxytricha trifallax mitochondrial genome. Genome Biology and Evolution. 4: 136-54. PMID 22179582 DOI: 10.1093/Gbe/Evr136  0.38
2009 Ye Y, Doak TG. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. Plos Computational Biology. 5: e1000465. PMID 19680427 DOI: 10.1371/Journal.Pcbi.1000465  0.384
2009 Nowacki M, Higgins BP, Maquilan GM, Swart EC, Doak TG, Landweber LF. A functional role for transposases in a large eukaryotic genome. Science (New York, N.Y.). 324: 935-8. PMID 19372392 DOI: 10.1126/Science.1170023  0.435
2008 Möllenbeck M, Zhou Y, Cavalcanti AR, Jönsson F, Higgins BP, Chang WJ, Juranek S, Doak TG, Rozenberg G, Lipps HJ, Landweber LF. The pathway to detangle a scrambled gene. Plos One. 3: e2330. PMID 18523559 DOI: 10.1371/Journal.Pone.0002330  0.44
2008 Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG, Landweber LF. RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature. 451: 153-8. PMID 18046331 DOI: 10.1038/Nature06452  0.383
2004 Cavalcanti AR, Dunn DM, Weiss R, Herrick G, Landweber LF, Doak TG. Sequence features of Oxytricha trifallax (class Spirotrichea) macronuclear telomeric and subtelomeric sequences. Protist. 155: 311-22. PMID 15552058 DOI: 10.1078/1434461041844196  0.715
2004 Cavalcanti AR, Stover NA, Orecchia L, Doak TG, Landweber LF. Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project. Chromosoma. 113: 69-76. PMID 15258807 DOI: 10.1007/S00412-004-0295-3  0.476
2003 Doak TG, Cavalcanti AR, Stover NA, Dunn DM, Weiss R, Herrick G, Landweber LF. Sequencing the Oxytricha trifallax macronuclear genome: a pilot project. Trends in Genetics : Tig. 19: 603-7. PMID 14585610 DOI: 10.1016/J.Tig.2003.09.013  0.702
2003 Doak TG, Witherspoon DJ, Jahn CL, Herrick G. 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 Eukaryotic Cell. 2: 95-102. PMID 12582126 DOI: 10.1128/Ec.2.1.95-102.2003  0.744
2002 Williams KR, Doak TG, Herrick G. Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax: alternatively processed regions have multiple telomere addition sites. Bmc Genetics. 3: 16. PMID 12199911 DOI: 10.1186/1471-2156-3-16  0.657
2002 Williams KR, Doak TG, Herrick G. Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax: Alternatively processed regions have multiple telomere addition sites Bmc Genetics. 3. DOI: 10.1186/1471-2156-3-16  0.627
1997 Doak TG, Witherspoon DJ, Paul Doerder F, Williams K, Herrick G. Conserved features of TBE1 transposons in ciliated protozoa Genetica. 101: 75-86. PMID 9465400 DOI: 10.1023/A:1018331118647  0.757
1997 Witherspoon DJ, Doak TG, Williams KR, Seegmiller A, Seger J, Herrick G. Selection on the protein-coding genes of the TBE1 family of transposable elements in the ciliates Oxytricha fallax and O. trifallax Molecular Biology and Evolution. 14: 696-706. PMID 9214742 DOI: 10.1093/Oxfordjournals.Molbev.A025809  0.781
1996 Seegmiller A, Williams KR, Hammersmith RL, Doak TG, Witherspoon D, Messick T, Storjohann LL, Herrick G. Internal eliminated sequences interrupting the Oxytricha 81 locus: Allelic divergence, conservation, conversions, and possible transposon origins Molecular Biology and Evolution. 13: 1351-1362. PMID 8952079 DOI: 10.1093/Oxfordjournals.Molbev.A025581  0.774
1994 Doak TG, Doerder FP, Jahn CL, Herrick G. A proposed superfamily of transposase genes: Transposon-like elements in ciliated protozoa and a common "D35E" motif Proceedings of the National Academy of Sciences of the United States of America. 91: 942-946. PMID 8302872 DOI: 10.1073/Pnas.91.3.942  0.657
1993 Williams K, Doak TG, Herrick G. Developmental precise excision of Oxytricha trifallax telomere-bearing elements and formation of circles closed by a copy of the flanking target duplication Embo Journal. 12: 4593-4601. PMID 8223469 DOI: 10.1002/J.1460-2075.1993.Tb06148.X  0.656
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