Akashi, H. 1994  Synonymous codon usage in Drosophila melanogaster:  Natural selection and translational accuracy.  Genetics 136: 927-935

Akashi, H. 1995  Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA.  Genetics 139: 1067-1076

Kreitman M., and H. Akashi. 1995  Molecular evidence for natural selection. Annual Review of Ecology and Systematics 26: 403-22

Dorit, R. L., H. Akashi, and W. Gilbert. 1995  Absence of polymorphism at the ZFY locus on the human Y chromosome.  Science 268: 1183-1185

Akashi, H. 1996  Molecular evolution between Drosophila melanogaster and D. simulans: Reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster.  Genetics 144: 1297-1307

Akashi, H., and S. Schaeffer. 1997  Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila.  Genetics 146: 295-307

Akashi, H., R. Kliman, and A. Eyre-Walker. 1998  Mutation pressure, natural selection and the evolution of base composition in Drosophila.  Genetica 102/103: 49-60

Akashi, H., A. Eyre-Walker. 1998  Translational Selection and Molecular Evolution.  Current Opinions in Genetics and Development 8: 688-693.

Akashi, H. 1999  Inferring the fitness effects of DNA mutations from patterns of polymorphism and divergence:  Statistical power to detect directional selection under stationarity and free recombination.  Genetics 151: 221-238.

Akashi, H., 1999  Within and between species DNA sequence variation and the "footprint" of natural selection. Gene 238: 39-51.

Iida, K., and H. Akashi,  2000   A test of translational selection in the human genome: Base composition comparisons in alternatively spliced genes. Gene 261: 93-105.

Akashi, H., 2001 Gene expression and molecular evolution. Curr. Op. Genet. Dev. 11: 660-666.

Akashi, H, and T. Gojobori, 2002 Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl. Acad. Sci., USA. 99: 3695-3700.

Nielsen, R., and H. Akashi, 2003 Purifying Selection: Action on Silent Sites. In: Cooper DN (ed.) Nature Encyclopedia of the Human Genome, vol. 4, pp. 945-948. London: Nature Publishing Group.

Akashi, H. 2003 Translational selection and yeast proteome evolution. Genetics 164: 1291-1303.

Ko, W-Y., R. David, and H. Akashi, 2003 Molecular phylogeny of the Drosophila melanogaster species subgroup. J. Mol. Evol. 57: 562-573.