Llopart A, Comeron JM. (2008) Recurrent events of positive selection in independent Drosophila lineages at the spermatogenesis gene Roughex. Genetics 179: 1009-1020

Hadany L, Comeron JM. (2008) Why are sex and recombination so common? Annals NY Acad. Sci. 1133: 26-43 [Abstract]

Lanier W, Moustafa A, Bhattacharya D, Comeron JM. (2008) EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes. PLoS ONE 3(5): e2171

Llopart A, Mabillé A, Peters-Hall JR, Comeron JM, Kliman RM. (2008) A new test for selection applied to codon usage in Drosophila simulans and D. mauritiana. J. Mol. Evol. 66: 224-231

Comeron JM, Williford A, Kliman RM. (2008) The Hill-Robertson effect: evolutionary consequences of weak selection and linkage in finite populations. Heredity 100: 19-31

Drosophila 12 genomes consortium (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218

Comeron JM. (2007) Evolution of noncoding DNA in eukaryotes. Genetics and Genomics. Edited R.A. Meyers Vol.1: Ch. 10.: 325-336.

Comeron JM. (2006) Weak selection and recent mutational changes influence polymorphic synonymous mutations in humans. Proc. Natl. Acad. Sci. USA, 103 (18): 6940-6945 [with Supporting Information]

Yoon HS, Ciniglia C, Wu M, Comeron JM, Pinto G, Pollio A and Bhattacharya D. (2006) Establishment of endolithic populations of extremophilic Cyanidiales (Rhodophyta). BMC Evol. Biol. 6:78

Kalari KR, Casavant M, Bair TB, Keen HL, Comeron JM, Casavant TL, Scheetz TE. (2006) First exons and introns - a survey of GC content and gene structure in the human genome. In Silico Biology 6, 0022

Comeron JM, Guthrie T. (2005) Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila. Mol. Biol. Evol. 22: 2519-2530.

Comeron JM. (2005) Repetitive sequence and noncoding DNA evolution eukaryotes. Encyclopedia Mol. Cell. Biol. and Mol. Med. Edited R.A. Meyers (2nd Ed.) Vol.12: 127-137.

Comeron JM. (2004) Selective and mutational patterns associated with gene expression in humans: Influences on exon-intron structure and synonymous composition. Genetics 167: 1293-1304.

Qin H, Wu WB, Comeron JM, Kreitman M, Li W-L. (2004) Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes. Genetics 168: 2245-2260.

Haring SJ, Lautner LJ, Comeron JM, Malone RE. (2004) A test of the CoHR motif associated with meiotic double-strand breaks in Saccharomyces cerevisiae. EMBO Rep. 5:41-46.

Comeron JM, Kreitman M, de la Vega FM. (2003) On the power to detect SNP/Phenotype association in candidate quantitative trait loci genomic regions: A simulation study. Pac. Symp. Biocomput. 2003:478-489.

Duan J, Wainwright MS, Comeron JM, Saitou N, Sanders AR, Gelernter J, Gejman PV. (2003) Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum. Mol. Genet. 12(3):205-216

Comeron JM, Kreitman M. (2002) Population, evolutionary and genomic consequences of interference selection. Genetics 161(1):389-410.

Llopart A, Comeron JM, Brunet FG, Lachaise D, Long M. (2002) Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection. Proc. Natl. Acad. Sci. U S A. 99(12):8121-8126.

Comeron JM. (2001) What controls the length of noncoding DNA? Curr. Opin. Genet. Dev. 11(6):652-659.

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. (2001) Genetic diversity of the human serotonin receptor 1B (HTR1B) gene. Genomics 72:1-14.

Comeron JM, Kreitman M. (2000) The correlation between intron length and recombination in drosophila. Dynamic equilibrium between mutational and selective forces. Genetics 156(3):1175-1190.

Comeron JM, Kreitman M, Aguadé M. (1999) Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila. Genetics 151(1):239-249.

Kreitman M, Comeron JM. (1999) Coding sequence evolution. Curr. Opin. Genet. Dev. 9(6):637-641.

Comeron JM. (1999) K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals. Bioinformatics 15(9):763-764.

Comeron JM, Kreitman M. (1998) The correlation between synonymous and nonsynonymous substitutions in Drosophila: mutation, selection or relaxed constraints? Genetics 150(2):767-775.

Comeron JM, Aguadé M. (1998) An evaluation of measures of synonymous codon usage bias. J. Mol. Evol. 47(3):268-274.

Zeng LW, Comeron JM, Chen B, Kreitman M. (1998) The molecular clock revisited: the rate of synonymous vs. replacement change in Drosophila. Genetica 102-103(1-6):369-382.