Thomas G. Doak, Ph.D. - Publications

Affiliations: 
2001 University of Utah, Salt Lake City, UT 
Area:
Genetics, Molecular Biology

34 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
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  0.44
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  0.44
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  0.44
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  0.44
2015 Wu LS, Barnett W, Ganote CL, Mockaitis K, Doak TG, Stewart CA. Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome Acm International Conference Proceeding Series. 2015. DOI: 10.1145/2792745.2792748  0.44
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  0.44
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  0.44
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  0.44
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  0.44
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  0.44
2013 Sung W, Ackerman MS, Miller SF, Doak TG, Lynch M. Reply to Massey: Drift does influence mutation-rate evolution. Proceedings of the National Academy of Sciences of the United States of America. 110: E860. PMID 23593647 DOI: 10.1073/Pnas.1220650110  0.44
2013 Christie AE, Roncalli V, Wu LS, Ganote CL, Doak T, Lenz PH. Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): in silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome. General and Comparative Endocrinology. 187: 117-35. PMID 23578900 DOI: 10.1016/j.ygcen.2013.03.018  0.44
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  0.44
2013 Thota A, Michael S, Xu S, Haubold B, Doak T, Henschel R. Making campus bridging work for researchers: A case study with mlRho Acm International Conference Proceeding Series. DOI: 10.1145/2484762.2484803  0.44
2013 Leduc RD, Wu LS, Ganote CL, Doak T, Blood PD, Vaughn M. National center for genome analysis support leverages XSEDE to support life science research Acm International Conference Proceeding Series. DOI: 10.1145/2484762.2484790  0.44
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  0.44
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  0.44
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  0.44
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  0.44
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  0.44
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 Holland RA, Kirschvink JL, Doak TG, Wikelski M. Bats use magnetite to detect the earth's magnetic field. Plos One. 3: e1676. PMID 18301753 DOI: 10.1371/Journal.Pone.0001676  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  0.44
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  0.44
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  0.44
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  0.44
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  0.44
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  0.44
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  0.44
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  0.44
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  0.44
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  0.44
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  0.44
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  0.44
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