• Distinguishing Among Evolutionary Forces Acting on Genome-Wide Base Composition: Computer Simulation Analysis of Approximate Methods for Inferring Site Frequency Spectra of Derived Mutations
• Matsumoto T, Akashi H
• G3 8:1755-1769. 2018.

• Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations
• Matsumoto T, John A, Baeza-Centurion P, Li B, Akashi H
• Mol Biol Evol 33:1580–1589. 2016.

• Disease Outbreaks: Critical Biological Factors and Control Strategies
• Kawashima K, Matsumoto T, Akashi H
• In: Urban Resilience. Vol. 22. 4 ed. Advanced Sciences and Technologies for Security Applications. Cham: Springer International Publishing. pp. 173–204. 2016.

• The intricate relationship between sexually antagonistic selection and the evolution of sex chromosome fusions
• Matsumoto T, Kitano J
• J Theor Biol 404:97–108. 2016.

• Assembly constraints drive co-evolution among ribosomal constituents
• Mallik S, Akashi H, Kundu S
• Nucleic Acids Res 43:5352–5363. 2015.

• Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution
• Matsumoto T, Akashi H, Yang Z
• Genetics 200:873–890. 2015.

• Complex patterns of cis-regulatory polymorphisms in ebony underlie standing pigmentation variation in Drosophila melanogaster
• Miyagi R, Akiyama N, Osada N, Takahashi A
• Mol Ecol 24:5829–5841. 2015.

• An Individual-Based Diploid Model Predicts Limited Conditions Under Which Stochastic Gene Expression Becomes Advantageous
• Matsumoto T, Mineta K, Osada N, Araki H
• Front Genet 6:336. 2015.

• Population genetics of non-genetic traits: evolutionary roles of stochasticity in gene expression
• Mineta K, Matsumoto T, Osada N, Araki H
• Gene 562:16–21. 2015.

• The genome landscape of the african green monkey kidney-derived vero cell line
• Osada N, Kohara A, Yamaji T, Hirayama N, Kasai F, Sekizuka T, Kuroda M, Hanada K
• DNA Research 21:673–683. 2014.

• Extracting population genetics information from a diploid genome sequence
• Osada N
• Front. Ecol. Evol. 2. 2014.

• Weak selection and protein evolution
• Akashi H, Osada N, Ohta T
• Genetics 192:15–31. 2012.

• Mitochondrial-Nuclear Interactions and Accelerated Compensatory Evolution: Evidence from the Primate Cytochrome c Oxidase Complex
• Osada N, Akashi H
• Mol Biol Evol 29:337–346. 2012.

• CpG site degeneration triggered by the loss of functional constraint created a highly polymorphic macaque drug-metabolizing gene, CYP1A2
• Uno Y, Osada N
• BMC Evol Biol 11:283. 2011.

• Phylogenetic Inconsistency Caused by Ancient Sex-Biased Gene Migration
• Osada N
• PLoS ONE 6:e25549. 2011.

• Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome‐wide admixture
• Wang WK, Ho CW, Hung KH, Wang KH, Huang CC, Araki H, Hwang CC, Hsu TW, Osada N, Chiang TY
• New Phytol 188:488–500. 2010.

• Do amino acid biosynthetic costs constrain protein evolution in Saccharomyces cerevisiae?
• Raiford DW, Heizer EM, Miller RV, Akashi H, Raymer ML, Krane DE
• J Mol Evol 67:621–630. 2008.

• Ancestral inference and the study of codon bias evolution: implications for molecular evolutionary analyses of the Drosophila melanogaster subgroup
• Akashi H, Goel P, John A
• PLoS ONE 2:e1065. 2007.

• 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, et al
• Nature 450:203–218. 2007.

• Strong regional heterogeneity in base composition evolution on the Drosophila X chromosome
• Ko W-Y, Piao S, Akashi H
• Genetics 174:349–362. 2006.

• Molecular evolution in the Drosophila melanogaster species subgroup: frequent parameter fluctuations on the timescale of molecular divergence
• Akashi H, Ko W-Y, Piao S, John A, Goel P, Lin C-F, Vitins AP
• Genetics 172:1711–1726. 2006.

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

• Translational selection and yeast proteome evolution
• Akashi H
• Genetics 164:1291–1303. 2003.

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

• Gene expression and molecular evolution
• Akashi H
• Curr Opin Genet Dev 11:660–666. 2001.

• Purifying Selection: Action on Silent Sites
• Nielsen R, Akashi H
• Chichester, UK: John Wiley & Sons, Ltd. 2001.

• A test of translational selection at “silent” sites in the human genome: base composition comparisons in alternatively spliced genes
• Iida K, Akashi H
• Gene 261:93–105. 2000.

• Within- and between-species DNA sequence variation and the “footprint” of natural selection
• Akashi H
• Gene 238:39–51. 1999.

• Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination
• Akashi H
• Genetics 151:221–238. 1999

• Translational selection and molecular evolution
• Akashi H, Eyre-Walker A
• Curr Opin Genet Dev 8:688–693. 1998.

• Mutation pressure, natural selection, and the evolution of base composition in Drosophila
• Akashi H, Kliman RM, Eyre-Walker A
• Genetics 146:295–307. 1998.

• Codon bias evolution in Drosophila. Population genetics of mutation-selection drift
• Akashi H
• Gene 205:269–278. 1997.

• Natural selection and the frequency distributions of “silent” DNA polymorphism in Drosophila
• Akashi H, Schaeffer SW
• Genetics 146:295–307. 1997.

• Distinguishing the effects of mutational biases and natural selection on DNA sequence variation
• Akashi H
• Genetics 147:1989–1991. 1997.

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

• Inferring weak selection from patterns of polymorphism and divergence at “silent” sites in Drosophila DNA
• Akashi H
• Genetics 139:1067–1076. 1995.

• Molecular Evidence for Natural Selection
• M Kreitman A, Akashi H
• Annual Review of Ecology and Systematics 26:403–422. 1995.

• Absence of polymorphism at the ZFY locus on the human Y chromosome
• Dorit RL, Akashi H, Gilbert W
• Science 268:1183–1185. 1995.

• Synonymous Codon Usage in Drosophila Melanogaster: Natural Selection and Translational Accuracy
• Akashi H
• CGenetics 136:927–935. 1994.