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Items: 40

1.

Support for the Dominance Theory in Drosophila Transcriptomes.

Llopart A, Brud E, Pettie N, Comeron JM.

Genetics. 2018 Oct;210(2):703-718. doi: 10.1534/genetics.118.301229. Epub 2018 Aug 21.

2.

Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies.

Comeron JM.

Philos Trans R Soc Lond B Biol Sci. 2017 Dec 19;372(1736). pii: 20160471. doi: 10.1098/rstb.2016.0471.

3.

A Mismatch EndoNuclease Array-Based Methodology (MENA) for Identifying Known SNPs or Novel Point Mutations.

Comeron JM, Reed J, Christie M, Jacobs JS, Dierdorff J, Eberl DF, Manak JR.

Microarrays (Basel). 2016 Apr 5;5(2). pii: E7. doi: 10.3390/microarrays5020007.

4.

Predictive Models of Recombination Rate Variation across the Drosophila melanogaster Genome.

Adrian AB, Corchado JC, Comeron JM.

Genome Biol Evol. 2016 Sep 2;8(8):2597-612. doi: 10.1093/gbe/evw181.

5.

Background selection as baseline for nucleotide variation across the Drosophila genome.

Comeron JM.

PLoS Genet. 2014 Jun 26;10(6):e1004434. doi: 10.1371/journal.pgen.1004434. eCollection 2014 Jun.

6.
7.

The many landscapes of recombination in Drosophila melanogaster.

Comeron JM, Ratnappan R, Bailin S.

PLoS Genet. 2012;8(10):e1002905. doi: 10.1371/journal.pgen.1002905. Epub 2012 Oct 11.

8.

Microarray-based capture of novel expressed cell type-specific transfrags (CoNECT) to annotate tissue-specific transcription in Drosophila melanogaster.

Hong X, Doddapaneni H, Comeron JM, Rodesch MJ, Halvensleben HA, Nien CY, Bolei F, Metpally R, Richmond TA, Albert TJ, Manak JR.

G3 (Bethesda). 2012 Aug;2(8):873-82. doi: 10.1534/g3.112.003194. Epub 2012 Aug 1.

9.

Evolutionary toxicogenomics: diversification of the Cyp12d1 and Cyp12d3 genes in Drosophila species.

McDonnell CM, King D, Comeron JM, Li H, Sun W, Berenbaum MR, Schuler MA, Pittendrigh BR.

J Mol Evol. 2012 Jun;74(5-6):281-96. doi: 10.1007/s00239-012-9506-3. Epub 2012 Jul 19.

PMID:
22811321
10.

Local effects of limited recombination: historical perspective and consequences for population estimates of adaptive evolution.

Williford A, Comeron JM.

J Hered. 2010 Mar-Apr;101 Suppl 1:S127-34. doi: 10.1093/jhered/esq012. Review.

PMID:
20421321
11.

Unexpected dynamic gene family evolution in algal actins.

Wu M, Comeron JM, Yoon HS, Bhattacharya D.

Mol Biol Evol. 2009 Feb;26(2):249-53. doi: 10.1093/molbev/msn263. Epub 2008 Nov 13.

PMID:
19008527
12.

Why are sex and recombination so common?

Hadany L, Comeron JM.

Ann N Y Acad Sci. 2008;1133:26-43. doi: 10.1196/annals.1438.011. Review.

PMID:
18559814
13.

Recurrent events of positive selection in independent Drosophila lineages at the spermatogenesis gene roughex.

Llopart A, Comeron JM.

Genetics. 2008 Jun;179(2):1009-20. doi: 10.1534/genetics.107.086231. Epub 2008 May 27.

14.

EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes.

Lanier W, Moustafa A, Bhattacharya D, Comeron JM.

PLoS One. 2008 May 14;3(5):e2171. doi: 10.1371/journal.pone.0002171.

15.

A new test for selection applied to codon usage in Drosophila simulans and D. mauritiana.

Llopart A, Mabillé A, Peters-Hall JR, Comeron JM, Kliman RM.

J Mol Evol. 2008 Mar;66(3):224-31. doi: 10.1007/s00239-008-9072-x. Epub 2008 Feb 21.

PMID:
18288436
16.

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
17.

The Hill-Robertson effect: evolutionary consequences of weak selection and linkage in finite populations.

Comeron JM, Williford A, Kliman RM.

Heredity (Edinb). 2008 Jan;100(1):19-31. Epub 2007 Sep 19. Review.

18.

Establishment of endolithic populations of extremophilic Cyanidiales (Rhodophyta).

Yoon HS, Ciniglia C, Wu M, Comeron JM, Pinto G, Pollio A, Bhattacharya D.

BMC Evol Biol. 2006 Oct 5;6:78.

19.

First exons and introns--a survey of GC content and gene structure in the human genome.

Kalari KR, Casavant M, Bair TB, Keen HL, Comeron JM, Casavant TL, Scheetz TE.

In Silico Biol. 2006;6(3):237-42.

PMID:
16922687
20.

Weak selection and recent mutational changes influence polymorphic synonymous mutations in humans.

Comeron JM.

Proc Natl Acad Sci U S A. 2006 May 2;103(18):6940-5. Epub 2006 Apr 21.

21.

Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila.

Comeron JM, Guthrie TB.

Mol Biol Evol. 2005 Dec;22(12):2519-30. Epub 2005 Aug 24.

PMID:
16120803
22.

Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes.

Qin H, Wu WB, Comeron JM, Kreitman M, Li WH.

Genetics. 2004 Dec;168(4):2245-60.

24.

A test of the CoHR motif associated with meiotic double-strand breaks in Saccharomyces cerevisiae.

Haring SJ, Lautner LJ, Comeron JM, Malone RE.

EMBO Rep. 2004 Jan;5(1):41-6.

25.
26.

Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor.

Duan J, Wainwright MS, Comeron JM, Saitou N, Sanders AR, Gelernter J, Gejman PV.

Hum Mol Genet. 2003 Feb 1;12(3):205-16.

PMID:
12554675
27.

Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection.

Llopart A, Comeron JM, Brunet FG, Lachaise D, Long M.

Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8121-6.

28.

Population, evolutionary and genomic consequences of interference selection.

Comeron JM, Kreitman M.

Genetics. 2002 May;161(1):389-410.

29.

What controls the length of noncoding DNA?

Comeron JM.

Curr Opin Genet Dev. 2001 Dec;11(6):652-9. Review.

PMID:
11682309
30.

Genetic diversity of the human serotonin receptor 1B (HTR1B) gene.

Sanders AR, Cao Q, Taylor J, Levin TE, Badner JA, Cravchik A, Comeron JM, Naruya S, Del Rosario A, Salvi DA, Walczyk KA, Mowry BJ, Levinson DF, Crowe RR, Silverman JM, Gejman PV.

Genomics. 2001 Feb 15;72(1):1-14.

PMID:
11247661
32.

Coding sequence evolution.

Kreitman M, Comeron JM.

Curr Opin Genet Dev. 1999 Dec;9(6):637-41. Review.

PMID:
10607619
33.
34.
36.

An evaluation of measures of synonymous codon usage bias.

Comeron JM, Aguadé M.

J Mol Evol. 1998 Sep;47(3):268-74.

PMID:
9732453
37.

The molecular clock revisited: the rate of synonymous vs. replacement change in Drosophila.

Zeng LW, Comeron JM, Chen B, Kreitman M.

Genetica. 1998;102-103(1-6):369-82.

PMID:
9720289
38.
39.
40.

Intraspecific and interspecific variation at the y-ac-sc region of Drosophila simulans and Drosophila melanogaster.

Martín-Campos JM, Comerón JM, Miyashita N, Aguadé M.

Genetics. 1992 Apr;130(4):805-16.

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