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Mitochondrial DNA Variation and Selfish Propagation Following Experimental Bottlenecking in Two Distantly Related Caenorhabditis briggsae Isolates.

Wagner JT, Howe DK, Estes S, Denver DR.

Genes (Basel). 2020 Jan 10;11(1). pii: E77. doi: 10.3390/genes11010077.


Complex Transmission Patterns and Age-Related Dynamics of a Selfish mtDNA Deletion.

Sullins JA, Coleman-Hulbert AL, Gallegos A, Howe DK, Denver DR, Estes S.

Integr Comp Biol. 2019 Oct 1;59(4):983-993. doi: 10.1093/icb/icz128.


Variable Abundance and Distribution of Wolbachia and Cardinium Endosymbionts in Plant-Parasitic Nematode Field Populations.

Wasala SK, Brown AMV, Kang J, Howe DK, Peetz AB, Zasada IA, Denver DR.

Front Microbiol. 2019 May 7;10:964. doi: 10.3389/fmicb.2019.00964. eCollection 2019.


Sex and Mitonuclear Adaptation in Experimental Caenorhabditis elegans Populations.

Wernick RI, Christy SF, Howe DK, Sullins JA, Ramirez JF, Sare M, Penley MJ, Morran LT, Denver DR, Estes S.

Genetics. 2019 Mar;211(3):1045-1058. doi: 10.1534/genetics.119.301935. Epub 2019 Jan 22.


Comparative Genomics of Wolbachia-Cardinium Dual Endosymbiosis in a Plant-Parasitic Nematode.

Brown AMV, Wasala SK, Howe DK, Peetz AB, Zasada IA, Denver DR.

Front Microbiol. 2018 Oct 16;9:2482. doi: 10.3389/fmicb.2018.02482. eCollection 2018.


First Report of the Gastropod-Killing Nematode, Phasmarhabditis hermaphrodita, in Oregon, U.S.A.

Mc Donnell RJ, Lutz MS, Howe DK, Denver DR.

J Nematol. 2018 May 31;50(1):77-78. doi: 10.21307/jofnem-2018-014. No abstract available.


Comparative Genomic Analysis of 130 Bacteriophages Infecting Bacteria in the Genus Pseudomonas.

Ha AD, Denver DR.

Front Microbiol. 2018 Jul 4;9:1456. doi: 10.3389/fmicb.2018.01456. eCollection 2018.


Molecular signatures of host specificity linked to habitat specialization in Exaiptasia sea anemones.

Bellis ES, Edlund RB, Berrios HK, Lessios HA, Denver DR.

Ecol Evol. 2018 Apr 30;8(11):5413-5426. doi: 10.1002/ece3.4058. eCollection 2018 Jun.


Natural Variation in Responses to Acute Heat and Cold Stress in a Sea Anemone Model System for Coral Bleaching.

Bellis ES, Denver DR.

Biol Bull. 2017 Oct;233(2):168-181. doi: 10.1086/694890. Epub 2017 Dec 8.


Adaptive Evolution under Extreme Genetic Drift in Oxidatively Stressed Caenorhabditis elegans.

Christy SF, Wernick RI, Lue MJ, Velasco G, Howe DK, Denver DR, Estes S.

Genome Biol Evol. 2017 Nov 1;9(11):3008-3022. doi: 10.1093/gbe/evx222.


Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles.

Cronn R, Dolan PC, Jogdeo S, Wegrzyn JL, Neale DB, St Clair JB, Denver DR.

BMC Genomics. 2017 Jul 24;18(1):558. doi: 10.1186/s12864-017-3916-y.


The Draft Genome of Globodera ellingtonae.

Phillips WS, Howe DK, Brown AMV, Eves-van den Akker S, Dettwyler L, Peetz AB, Denver DR, Zasada IA.

J Nematol. 2017 Jun;49(2):127-128.


Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts.

Brown AM, Wasala SK, Howe DK, Peetz AB, Zasada IA, Denver DR.

Sci Rep. 2016 Oct 13;6:34955. doi: 10.1038/srep34955.


Paternal Mitochondrial Transmission in Intra-Species Caenorhabditis briggsae Hybrids.

Ross JA, Howe DK, Coleman-Hulbert A, Denver DR, Estes S.

Mol Biol Evol. 2016 Dec;33(12):3158-3160. Epub 2016 Sep 9.


The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers.

Phillips WS, Brown AM, Howe DK, Peetz AB, Blok VC, Denver DR, Zasada IA.

BMC Genomics. 2016 Sep 5;17:706. doi: 10.1186/s12864-016-3047-x.


Genome Skimming: A Rapid Approach to Gaining Diverse Biological Insights into Multicellular Pathogens.

Denver DR, Brown AM, Howe DK, Peetz AB, Zasada IA.

PLoS Pathog. 2016 Aug 4;12(8):e1005713. doi: 10.1371/journal.ppat.1005713. eCollection 2016 Aug. No abstract available.


Paths of Heritable Mitochondrial DNA Mutation and Heteroplasmy in Reference and gas-1 Strains of Caenorhabditis elegans.

Wernick RI, Estes S, Howe DK, Denver DR.

Front Genet. 2016 Apr 13;7:51. doi: 10.3389/fgene.2016.00051. eCollection 2016.


Genome-wide polymorphism and signatures of selection in the symbiotic sea anemone Aiptasia.

Bellis ES, Howe DK, Denver DR.

BMC Genomics. 2016 Feb 29;17:160. doi: 10.1186/s12864-016-2488-6.


The genomic basis of parasitism in the Strongyloides clade of nematodes.

Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, Tracey A, Cotton JA, Stanley EJ, Beasley H, Bennett HM, Brooks K, Harsha B, Kajitani R, Kulkarni A, Harbecke D, Nagayasu E, Nichol S, Ogura Y, Quail MA, Randle N, Xia D, Brattig NW, Soblik H, Ribeiro DM, Sanchez-Flores A, Hayashi T, Itoh T, Denver DR, Grant W, Stoltzfus JD, Lok JB, Murayama H, Wastling J, Streit A, Kikuchi T, Viney M, Berriman M.

Nat Genet. 2016 Mar;48(3):299-307. doi: 10.1038/ng.3495. Epub 2016 Feb 1.


Comparative Genomics of a Plant-Parasitic Nematode Endosymbiont Suggest a Role in Nutritional Symbiosis.

Brown AM, Howe DK, Wasala SK, Peetz AB, Zasada IA, Denver DR.

Genome Biol Evol. 2015 Sep 10;7(9):2727-46. doi: 10.1093/gbe/evv176.


Selfish Mitochondrial DNA Proliferates and Diversifies in Small, but not Large, Experimental Populations of Caenorhabditis briggsae.

Phillips WS, Coleman-Hulbert AL, Weiss ES, Howe DK, Ping S, Wernick RI, Estes S, Denver DR.

Genome Biol Evol. 2015 Jun 24;7(7):2023-37. doi: 10.1093/gbe/evv116.


Endogenous ROS levels in C. elegans under exogenous stress support revision of oxidative stress theory of life-history tradeoffs.

Smith SW, Latta LC 4th, Denver DR, Estes S.

BMC Evol Biol. 2014 Jul 24;14:161. doi: 10.1186/s12862-014-0161-8.


Sea anemones possess dynamic mitogenome structures.

Emblem Å, Okkenhaug S, Weiss ES, Denver DR, Karlsen BO, Moum T, Johansen SD.

Mol Phylogenet Evol. 2014 Jun;75:184-93. doi: 10.1016/j.ympev.2014.02.016. Epub 2014 Mar 6.


Using mitogenomic and nuclear ribosomal sequence data to investigate the phylogeny of the Xiphinema americanum species complex.

Zasada IA, Peetz A, Howe DK, Wilhelm LJ, Cheam D, Denver DR, Smythe AB.

PLoS One. 2014 Feb 27;9(2):e90035. doi: 10.1371/journal.pone.0090035. eCollection 2014.


A broadly implementable research course in phage discovery and genomics for first-year undergraduate students.

Jordan TC, Burnett SH, Carson S, Caruso SM, Clase K, DeJong RJ, Dennehy JJ, Denver DR, Dunbar D, Elgin SC, Findley AM, Gissendanner CR, Golebiewska UP, Guild N, Hartzog GA, Grillo WH, Hollowell GP, Hughes LE, Johnson A, King RA, Lewis LO, Li W, Rosenzweig F, Rubin MR, Saha MS, Sandoz J, Shaffer CD, Taylor B, Temple L, Vazquez E, Ware VC, Barker LP, Bradley KW, Jacobs-Sera D, Pope WH, Russell DA, Cresawn SG, Lopatto D, Bailey CP, Hatfull GF.

mBio. 2014 Feb 4;5(1):e01051-13. doi: 10.1128/mBio.01051-13.


Evolution of a higher intracellular oxidizing environment in Caenorhabditis elegans under relaxed selection.

Joyner-Matos J, Hicks KA, Cousins D, Keller M, Denver DR, Baer CF, Estes S.

PLoS One. 2013 Jun 11;8(6):e65604. doi: 10.1371/journal.pone.0065604. Print 2013.


Natural variation in Caenorhabditis briggsae mitochondrial form and function suggests a novel model of organelle dynamics.

Hicks KA, Denver DR, Estes S.

Mitochondrion. 2013 Jan;13(1):44-51. doi: 10.1016/j.mito.2012.12.006. Epub 2012 Dec 23.


In vivo quantification reveals extensive natural variation in mitochondrial form and function in Caenorhabditis briggsae.

Hicks KA, Howe DK, Leung A, Denver DR, Estes S.

PLoS One. 2012;7(8):e43837. doi: 10.1371/journal.pone.0043837. Epub 2012 Aug 28.


Selfish little circles: transmission bias and evolution of large deletion-bearing mitochondrial DNA in Caenorhabditis briggsae nematodes.

Clark KA, Howe DK, Gafner K, Kusuma D, Ping S, Estes S, Denver DR.

PLoS One. 2012;7(7):e41433. doi: 10.1371/journal.pone.0041433. Epub 2012 Jul 31.


The worm in the world and the world in the worm.

Blaxter M, Denver DR.

BMC Biol. 2012 Jun 25;10:57. doi: 10.1186/1741-7007-10-57.


Variation in base-substitution mutation in experimental and natural lineages of Caenorhabditis nematodes.

Denver DR, Wilhelm LJ, Howe DK, Gafner K, Dolan PC, Baer CF.

Genome Biol Evol. 2012;4(4):513-22. doi: 10.1093/gbe/evs028. Epub 2012 Mar 20.


Fitness recovery and compensatory evolution in natural mutant lines of C. elegans.

Estes S, Phillips PC, Denver DR.

Evolution. 2011 Aug;65(8):2335-44. doi: 10.1111/j.1558-5646.2011.01276.x. Epub 2011 Apr 11.


Reproductive mode evolution in nematodes: insights from molecular phylogenies and recently discovered species.

Denver DR, Clark KA, Raboin MJ.

Mol Phylogenet Evol. 2011 Nov;61(2):584-92. doi: 10.1016/j.ympev.2011.07.007. Epub 2011 Jul 20. Review.


Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Pope WH, Jacobs-Sera D, Russell DA, Peebles CL, Al-Atrache Z, Alcoser TA, Alexander LM, Alfano MB, Alford ST, Amy NE, Anderson MD, Anderson AG, Ang AA, Ares M Jr, Barber AJ, Barker LP, Barrett JM, Barshop WD, Bauerle CM, Bayles IM, Belfield KL, Best AA, Borjon A Jr, Bowman CA, Boyer CA, Bradley KW, Bradley VA, Broadway LN, Budwal K, Busby KN, Campbell IW, Campbell AM, Carey A, Caruso SM, Chew RD, Cockburn CL, Cohen LB, Corajod JM, Cresawn SG, Davis KR, Deng L, Denver DR, Dixon BR, Ekram S, Elgin SC, Engelsen AE, English BE, Erb ML, Estrada C, Filliger LZ, Findley AM, Forbes L, Forsyth MH, Fox TM, Fritz MJ, Garcia R, George ZD, Georges AE, Gissendanner CR, Goff S, Goldstein R, Gordon KC, Green RD, Guerra SL, Guiney-Olsen KR, Guiza BG, Haghighat L, Hagopian GV, Harmon CJ, Harmson JS, Hartzog GA, Harvey SE, He S, He KJ, Healy KE, Higinbotham ER, Hildebrandt EN, Ho JH, Hogan GM, Hohenstein VG, Holz NA, Huang VJ, Hufford EL, Hynes PM, Jackson AS, Jansen EC, Jarvik J, Jasinto PG, Jordan TC, Kasza T, Katelyn MA, Kelsey JS, Kerrigan LA, Khaw D, Kim J, Knutter JZ, Ko CC, Larkin GV, Laroche JR, Latif A, Leuba KD, Leuba SI, Lewis LO, Loesser-Casey KE, Long CA, Lopez AJ, Lowery N, Lu TQ, Mac V, Masters IR, McCloud JJ, McDonough MJ, Medenbach AJ, Menon A, Miller R, Morgan BK, Ng PC, Nguyen E, Nguyen KT, Nguyen ET, Nicholson KM, Parnell LA, Peirce CE, Perz AM, Peterson LJ, Pferdehirt RE, Philip SV, Pogliano K, Pogliano J, Polley T, Puopolo EJ, Rabinowitz HS, Resiss MJ, Rhyan CN, Robinson YM, Rodriguez LL, Rose AC, Rubin JD, Ruby JA, Saha MS, Sandoz JW, Savitskaya J, Schipper DJ, Schnitzler CE, Schott AR, Segal JB, Shaffer CD, Sheldon KE, Shepard EM, Shepardson JW, Shroff MK, Simmons JM, Simms EF, Simpson BM, Sinclair KM, Sjoholm RL, Slette IJ, Spaulding BC, Straub CL, Stukey J, Sughrue T, Tang TY, Tatyana LM, Taylor SB, Taylor BJ, Temple LM, Thompson JV, Tokarz MP, Trapani SE, Troum AP, Tsay J, Tubbs AT, Walton JM, Wang DH, Wang H, Warner JR, Weisser EG, Wendler SC, Weston-Hafer KA, Whelan HM, Williamson KE, Willis AN, Wirtshafter HS, Wong TW, Wu P, Yang Yj, Yee BC, Zaidins DA, Zhang B, Zúniga MY, Hendrix RW, Hatfull GF.

PLoS One. 2011 Jan 27;6(1):e16329. doi: 10.1371/journal.pone.0016329.


Natural variation in life history and aging phenotypes is associated with mitochondrial DNA deletion frequency in Caenorhabditis briggsae.

Estes S, Coleman-Hulbert AL, Hicks KA, de Haan G, Martha SR, Knapp JB, Smith SW, Stein KC, Denver DR.

BMC Evol Biol. 2011 Jan 12;11:11. doi: 10.1186/1471-2148-11-11.


Selective sweeps and parallel mutation in the adaptive recovery from deleterious mutation in Caenorhabditis elegans.

Denver DR, Howe DK, Wilhelm LJ, Palmer CA, Anderson JL, Stein KC, Phillips PC, Estes S.

Genome Res. 2010 Dec;20(12):1663-71. doi: 10.1101/gr.108191.110. Epub 2010 Oct 29.


High rate of large deletions in Caenorhabditis briggsae mitochondrial genome mutation processes.

Howe DK, Baer CF, Denver DR.

Genome Biol Evol. 2009 Dec 23;2:29-38. doi: 10.1093/gbe/evp055.


Spontaneous mutations decrease sensitivity of gene expression to random environmental variation in Caenorhabditis elegans.

Baer CF, Denver DR.

PLoS One. 2010 Jan 18;5(1):e8750. doi: 10.1371/journal.pone.0008750.


Evolution of Caenorhabditis mitochondrial genome pseudogenes and Caenorhabditis briggsae natural isolates.

Raboin MJ, Timko AF, Howe DK, Félix MA, Denver DR.

Mol Biol Evol. 2010 May;27(5):1087-96. doi: 10.1093/molbev/msp318. Epub 2009 Dec 21.


High mitogenomic evolutionary rates and time dependency.

Subramanian S, Denver DR, Millar CD, Heupink T, Aschrafi A, Emslie SD, Baroni C, Lambert DM.

Trends Genet. 2009 Nov;25(11):482-6. doi: 10.1016/j.tig.2009.09.005. Epub 2009 Oct 14.


A genome-wide view of Caenorhabditis elegans base-substitution mutation processes.

Denver DR, Dolan PC, Wilhelm LJ, Sung W, Lucas-Lledó JI, Howe DK, Lewis SC, Okamoto K, Thomas WK, Lynch M, Baer CF.

Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16310-4. doi: 10.1073/pnas.0904895106. Epub 2009 Sep 10.


Molecular evolution in Panagrolaimus nematodes: origins of parthenogenesis, hermaphroditism and the Antarctic species P. davidi.

Lewis SC, Dyal LA, Hilburn CF, Weitz S, Liau WS, Lamunyon CW, Denver DR.

BMC Evol Biol. 2009 Jan 16;9:15. doi: 10.1186/1471-2148-9-15.


Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans.

Jordan IK, Katz LS, Denver DR, Streelman JT.

BMC Syst Biol. 2008 Nov 13;2:96. doi: 10.1186/1752-0509-2-96.


TileQC: a system for tile-based quality control of Solexa data.

Dolan PC, Denver DR.

BMC Bioinformatics. 2008 May 28;9:250. doi: 10.1186/1471-2105-9-250.


Muller's Ratchet and compensatory mutation in Caenorhabditis briggsae mitochondrial genome evolution.

Howe DK, Denver DR.

BMC Evol Biol. 2008 Feb 26;8:62. doi: 10.1186/1471-2148-8-62.


High intraspecific recombination rate in a native population of Candidatus pelagibacter ubique (SAR11).

Vergin KL, Tripp HJ, Wilhelm LJ, Denver DR, Rappé MS, Giovannoni SJ.

Environ Microbiol. 2007 Oct;9(10):2430-40.


Mutation rate variation in multicellular eukaryotes: causes and consequences.

Baer CF, Miyamoto MM, Denver DR.

Nat Rev Genet. 2007 Aug;8(8):619-31. Review.


The relative roles of three DNA repair pathways in preventing Caenorhabditis elegans mutation accumulation.

Denver DR, Feinberg S, Steding C, Durbin MD, Lynch M.

Genetics. 2006 Sep;174(1):57-65. Epub 2006 Jun 18.


The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans.

Denver DR, Morris K, Streelman JT, Kim SK, Lynch M, Thomas WK.

Nat Genet. 2005 May;37(5):544-8. Epub 2005 Apr 24.


Mutation rates, spectra and hotspots in mismatch repair-deficient Caenorhabditis elegans.

Denver DR, Feinberg S, Estes S, Thomas WK, Lynch M.

Genetics. 2005 May;170(1):107-13. Epub 2005 Feb 16.

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