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Items: 1 to 50 of 143

1.

Baker's Yeast Clinical Isolates Provide a Model for How Pathogenic Yeasts Adapt to Stress.

Raghavan V, Aquadro CF, Alani E.

Trends Genet. 2019 Sep 13. pii: S0168-9525(19)30164-7. doi: 10.1016/j.tig.2019.08.002. [Epub ahead of print] Review.

PMID:
31526615
2.

The importance of the Neutral Theory in 1968 and 50 years on: A response to Kern and Hahn 2018.

Jensen JD, Payseur BA, Stephan W, Aquadro CF, Lynch M, Charlesworth D, Charlesworth B.

Evolution. 2019 Jan;73(1):111-114. doi: 10.1111/evo.13650. Epub 2018 Nov 27.

3.

Incompatibilities in Mismatch Repair Genes MLH1-PMS1 Contribute to a Wide Range of Mutation Rates in Human Isolates of Baker's Yeast.

Raghavan V, Bui DT, Al-Sweel N, Friedrich A, Schacherer J, Aquadro CF, Alani E.

Genetics. 2018 Dec;210(4):1253-1266. doi: 10.1534/genetics.118.301550. Epub 2018 Oct 22.

PMID:
30348651
4.

Mismatch Repair Incompatibilities in Diverse Yeast Populations.

Bui DT, Friedrich A, Al-Sweel N, Liti G, Schacherer J, Aquadro CF, Alani E.

Genetics. 2017 Apr;205(4):1459-1471. doi: 10.1534/genetics.116.199513. Epub 2017 Feb 13.

5.

Recent and Long-Term Selection Across Synonymous Sites in Drosophila ananassae.

Choi JY, Aquadro CF.

J Mol Evol. 2016 Aug;83(1-2):50-60. doi: 10.1007/s00239-016-9753-9. Epub 2016 Aug 1.

6.

Inversions and adaptation to the plant toxin ouabain shape DNA sequence variation within and between chromosomal inversions of Drosophila subobscura.

Pegueroles C, Ferrés-Coy A, Martí-Solano M, Aquadro CF, Pascual M, Mestres F.

Sci Rep. 2016 Mar 31;6:23754. doi: 10.1038/srep23754.

7.

Molecular Evolution of Drosophila Germline Stem Cell and Neural Stem Cell Regulating Genes.

Choi JY, Aquadro CF.

Genome Biol Evol. 2015 Oct 27;7(11):3097-114. doi: 10.1093/gbe/evv207.

8.

The Drosophila bag of marbles Gene Interacts Genetically with Wolbachia and Shows Female-Specific Effects of Divergence.

Flores HA, Bubnell JE, Aquadro CF, Barbash DA.

PLoS Genet. 2015 Aug 20;11(8):e1005453. doi: 10.1371/journal.pgen.1005453. eCollection 2015 Aug.

9.

Population Genomics of Infectious and Integrated Wolbachia pipientis Genomes in Drosophila ananassae.

Choi JY, Bubnell JE, Aquadro CF.

Genome Biol Evol. 2015 Aug 8;7(8):2362-82. doi: 10.1093/gbe/evv158.

10.

A Genetic Incompatibility Accelerates Adaptation in Yeast.

Bui DT, Dine E, Anderson JB, Aquadro CF, Alani EE.

PLoS Genet. 2015 Jul 31;11(7):e1005407. doi: 10.1371/journal.pgen.1005407. eCollection 2015 Jul.

11.

Correction: A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus.

Zaborske JM, Bauer DuMont VL, Wallace EW, Pan T, Aquadro CF, Drummond DA.

PLoS Biol. 2015 Apr 29;13(4):e1002150. doi: 10.1371/journal.pbio.1002150. eCollection 2015 Apr.

12.

Adaptive evolution of genes involved in the regulation of germline stem cells in Drosophila melanogaster and D. simulans.

Flores HA, DuMont VL, Fatoo A, Hubbard D, Hijji M, Barbash DA, Aquadro CF.

G3 (Bethesda). 2015 Feb 9;5(4):583-92. doi: 10.1534/g3.114.015875.

13.

A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus.

Zaborske JM, DuMont VL, Wallace EW, Pan T, Aquadro CF, Drummond DA.

PLoS Biol. 2014 Dec 9;12(12):e1002015. doi: 10.1371/journal.pbio.1002015. eCollection 2014 Dec. Erratum in: PLoS Biol. 2015 Apr;13(4):e1002150.

14.
15.

Evolutionary rate covariation identifies new members of a protein network required for Drosophila melanogaster female post-mating responses.

Findlay GD, Sitnik JL, Wang W, Aquadro CF, Clark NL, Wolfner MF.

PLoS Genet. 2014 Jan;10(1):e1004108. doi: 10.1371/journal.pgen.1004108. Epub 2014 Jan 16.

16.

Fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome.

Singh ND, Stone EA, Aquadro CF, Clark AG.

Genetics. 2013 Jun;194(2):375-87. doi: 10.1534/genetics.112.146746. Epub 2013 Feb 14.

17.

Gene flow and gene flux shape evolutionary patterns of variation in Drosophila subobscura.

Pegueroles C, Aquadro CF, Mestres F, Pascual M.

Heredity (Edinb). 2013 Jun;110(6):520-9. doi: 10.1038/hdy.2012.118. Epub 2013 Jan 16.

18.

Evolutionary rate covariation in meiotic proteins results from fluctuating evolutionary pressure in yeasts and mammals.

Clark NL, Alani E, Aquadro CF.

Genetics. 2013 Feb;193(2):529-38. doi: 10.1534/genetics.112.145979. Epub 2012 Nov 26.

19.

Inferences of demography and selection in an African population of Drosophila melanogaster.

Singh ND, Jensen JD, Clark AG, Aquadro CF.

Genetics. 2013 Jan;193(1):215-28. doi: 10.1534/genetics.112.145318. Epub 2012 Oct 26.

20.

Evolutionary rate covariation reveals shared functionality and coexpression of genes.

Clark NL, Alani E, Aquadro CF.

Genome Res. 2012 Apr;22(4):714-20. doi: 10.1101/gr.132647.111. Epub 2012 Jan 27.

21.

Temporally variable selection on proteolysis-related reproductive tract proteins in Drosophila.

Wong A, Turchin M, Wolfner MF, Aquadro CF.

Mol Biol Evol. 2012 Jan;29(1):229-38. doi: 10.1093/molbev/msr197. Epub 2011 Sep 22.

22.

A novel method to detect proteins evolving at correlated rates: identifying new functional relationships between coevolving proteins.

Clark NL, Aquadro CF.

Mol Biol Evol. 2010 May;27(5):1152-61. doi: 10.1093/molbev/msp324. Epub 2009 Dec 31.

23.

Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population.

Rebeiz M, Pool JE, Kassner VA, Aquadro CF, Carroll SB.

Science. 2009 Dec 18;326(5960):1663-7. doi: 10.1126/science.1178357.

24.

Coevolution of interacting fertilization proteins.

Clark NL, Gasper J, Sekino M, Springer SA, Aquadro CF, Swanson WJ.

PLoS Genet. 2009 Jul;5(7):e1000570. doi: 10.1371/journal.pgen.1000570. Epub 2009 Jul 24.

25.

Positively selected disease response orthologous gene sets in the cereals identified using Sorghum bicolor L. Moench expression profiles and comparative genomics.

Zamora A, Sun Q, Hamblin MT, Aquadro CF, Kresovich S.

Mol Biol Evol. 2009 Sep;26(9):2015-30. doi: 10.1093/molbev/msp114. Epub 2009 Jun 8.

26.

Estimation of fine-scale recombination intensity variation in the white-echinus interval of D. melanogaster.

Singh ND, Aquadro CF, Clark AG.

J Mol Evol. 2009 Jul;69(1):42-53. doi: 10.1007/s00239-009-9250-5. Epub 2009 Jun 6.

27.

Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila.

Singh ND, Arndt PF, Clark AG, Aquadro CF.

Mol Biol Evol. 2009 Jul;26(7):1591-605. doi: 10.1093/molbev/msp071. Epub 2009 Apr 7.

28.
29.

Inferring selection in partially sequenced regions.

Jensen JD, Thornton KR, Aquadro CF.

Mol Biol Evol. 2008 Feb;25(2):438-46. doi: 10.1093/molbev/msm273. Epub 2007 Dec 28.

PMID:
18165259
30.

Evidence for positive selection on Drosophila melanogaster seminal fluid protease homologs.

Wong A, Turchin MC, Wolfner MF, Aquadro CF.

Mol Biol Evol. 2008 Mar;25(3):497-506. Epub 2007 Dec 4.

PMID:
18056920
31.

Patterns of mutation and selection at synonymous sites in Drosophila.

Singh ND, Bauer DuMont VL, Hubisz MJ, Nielsen R, Aquadro CF.

Mol Biol Evol. 2007 Dec;24(12):2687-97. Epub 2007 Nov 13.

PMID:
18000010
32.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087
33.

Approaches for identifying targets of positive selection.

Jensen JD, Wong A, Aquadro CF.

Trends Genet. 2007 Nov;23(11):568-77. Epub 2007 Oct 23. Review.

PMID:
17959267
34.

Mitch a rapidly evolving component of the Ndc80 kinetochore complex required for correct chromosome segregation in Drosophila.

Williams B, Leung G, Maiato H, Wong A, Li Z, Williams EV, Kirkpatrick C, Aquadro CF, Rieder CL, Goldberg ML.

J Cell Sci. 2007 Oct 15;120(Pt 20):3522-33. Epub 2007 Sep 25.

35.

Patterns of sequence variability and divergence at the diminutive gene region of Drosophila melanogaster: complex patterns suggest an ancestral selective sweep.

Jensen JD, Bauer DuMont VL, Ashmore AB, Gutierrez A, Aquadro CF.

Genetics. 2007 Oct;177(2):1071-85. Epub 2007 Aug 24.

36.
37.

On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations.

Jensen JD, Thornton KR, Bustamante CD, Aquadro CF.

Genetics. 2007 Aug;176(4):2371-9. Epub 2007 Jun 11.

38.

Evidence of amino acid diversity-enhancing selection within humans and among primates at the candidate sperm-receptor gene PKDREJ.

Hamm D, Mautz BS, Wolfner MF, Aquadro CF, Swanson WJ.

Am J Hum Genet. 2007 Jul;81(1):44-52. Epub 2007 May 8.

39.

Phylogenetic incongruence in the Drosophila melanogaster species group.

Wong A, Jensen JD, Pool JE, Aquadro CF.

Mol Phylogenet Evol. 2007 Jun;43(3):1138-50. Epub 2006 Sep 9.

40.
41.

Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila.

Nielsen R, Bauer DuMont VL, Hubisz MJ, Aquadro CF.

Mol Biol Evol. 2007 Jan;24(1):228-35. Epub 2006 Oct 13.

PMID:
17041152
42.

History and structure of sub-Saharan populations of Drosophila melanogaster.

Pool JE, Aquadro CF.

Genetics. 2006 Oct;174(2):915-29. Epub 2006 Sep 1.

43.

Mutation, selection and the future of human evolution.

Reed FA, Aquadro CF.

Trends Genet. 2006 Sep;22(9):479-84. Epub 2006 Jul 20. Review.

PMID:
16857288
44.
45.

Challenges of detecting directional selection after a bottleneck: lessons from Sorghum bicolor.

Hamblin MT, Casa AM, Sun H, Murray SC, Paterson AH, Aquadro CF, Kresovich S.

Genetics. 2006 Jun;173(2):953-64. Epub 2006 Mar 17.

46.

Negative epistasis between natural variants of the Saccharomyces cerevisiae MLH1 and PMS1 genes results in a defect in mismatch repair.

Heck JA, Argueso JL, Gemici Z, Reeves RG, Bernard A, Aquadro CF, Alani E.

Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3256-61. Epub 2006 Feb 21.

47.
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