Yokoyama Lab                 

Simplicity is the ultimate sophistication   - Leonardo Da Vinci

Genetics & adaptation of vertebrate vision

• Yokoyama, S. (2012)
  Synthesis of experimental molecular biology and evolutionary biology. BioScience (invited review).
• Yokoyama , S., Altun, A. and DeNardo, D. F. (2011)
  Molecular convergence of infrared vision in snakes. Mol. Biol. Evol. 28 (1): 45-48.
• Yokoyama, S. and Tada, T. (2010)
  Evolutionary dynamics of rhodopsin type 2 (RH2) opsins in vertebrates. Mol. Biol. Evol. 27 (1): 133-141.
• Tada, T., Altun, A. and Yokoyama, S. (2009)
  Evolutionary replacement of UV vision by violet vision in fish. Proc. Natl. Acad. Sci. USA 106: 17457-17462.
• Yokoyama, S., Tada, T., Zhang, H. and Britt, L. (2008)
  Elucidation of phenotypic adaptations: molecular analyses of dim-light vision proteins in vertebrates. Proc. Natl. Acad. Sci. USA 105: 13480-13485.
• Yokoyama, S., Yang, H. and Starmer, W. T. (2008)
  Molecular basis of spectral tuning in the red- and green-sensitive (M/LWS) pigments in vertebrates. Genetics 179: 2037-2043.
• Yokoyama, S. (2008)
  Evolution of dim-light and color vision pigments. Annu. Rev. Genomics Hum. Genet. 9: 259-282.
• Yokoyama, S., Tada, T. and Yamato, T. (2007)
  Modulation of the absorption maximum of rhodopsin by amino acids in the C-terminus. Photochem. Photobiol. 83: 236-241.
• Yokoyama, S., Takenaka, N and Blow, N. S. (2007)
  A novel spectral tuning in the short wavelength-sensitive (SWS1 and SWS2) pigments of bluefin killifish (Lucania goodei). Gene 396: 196-202.
• Takenaka, N. and Yokoyama, S. (2007)
  Mechanisms of spectral tuning in the RH2 pigments of Tokay gecko and American chameleon. Gene 399: 26-32.
• Yokoyama, S. and Tada, T. (2007)
  The evolution of ultraviolet vision in vertebrates. In: Evolution of Nervous Systems. (T. H. Bulloch, ed.). Elsevier, Amsterdam. Pp. 349-353.
• Yokoyama, S., Starmer, W. T., Takahashi, Y. & Tada, T. (2006)
  Tertiary structure and spectral tuning of UV and violet pigments in vertebrates. Gene 365: 95-103.
• Yokoyama, S. (September 2006)
  Visual pigment genes: Evolution. In: ENCYCLOPEDIA OF LIFE SCIENCES. John Wiley & Sons, Ltd: Chichester http://www.net/[doi: 10.1002/npg.els.0006148].
• Yokoyama, S. and Takenaka, N. (2005)
  Statistical and molecular analyses of evolutionary significance of red-green color vision and color blindness in vertebrates. Mol. Biol. Evol. 22: 968-975.
• Yokoyama, S., Takenaka, N., Agnew, D. W. and Shoshani, J. (2005)
  Elephants and human color-blind deuteranopes have identical sets of visual pigments. Genetics 170: 335-344.
• Takahashi, Y. and Yokoyama, S. (2005)
  Genetic basis of spectral tuning in the violet-sensitive visual pigments of African clawed frog, Xenopus laevis. Genetics 171: 1153-1160.
• Yokoyama, S. and Takenaka, N. (2004)
  The molecular basis of adaptive evolution of squirrelfish rhodopsins. Mol. Biol. Evol. 21: 2071-2078.
• Hiramatsu, C., Radlwimmer, F. B., Yokoyama, S. and Kawamura, S. (2004)
  Mutagenesis and reconstitution of middle-to-long wavelength-sensitive visual pigments of New World monkeys for testing the tuning effect of residues at sites 229 and 233. Vision Res. 44: 2225-2231.
• Yokoyama, S. and Tada, T. (2003)
  The spectral tuning in the short wavelength-sensitive type 2 pigments. Gene 306: 91-98.
• Deeb, S. S., Wakefield, M. J., Tada, T., Marotte, L., Yokoyama, S. and Graves, J. A. M. (2003)
  The cone visual pigments of an Australian marsupial, the tammar wallaby (Macropus eugenii): sequence, spectral tuning and evolution. Mol. Biol. Evol. 20:1642-1649.
• Shi, Y. and Yokoyama, S. (2003)
  Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates. Proc. Natl. Acad. Sci. USA 100: 8308-8313.
• Yokoyama, S. (2002)
  Molecular evolution of color vision in vertebrates. Gene 300: 69-78.
• Yokoyama, S. (2002)
  Evaluating adaptive evolution (News & Views). Nature Genet. 30: 350-351.
• Yokoyama, S and Blow, N. S. (2001)
  Molecular evolution of the cone visual pigments in the pure rod-retina of the nocturnal gecko, Gekko gekko. Gene 276: 117-125.
• Yokoyama, S. and Radlwimmer, F. B. (2001)
  The molecular genetics and evolution of red and green color vision in vertebrates. Genetics 158: 1697-1710.
• Kawamura, S., Hirai, M., Takenaka, O., Radlwimmer, F. B. and Yokoyama, S. (2001)
  Genomic and spectral analyses of long to middle wavelength-sensitive visual pigments of common marmoset (Calithrix jacchus). Gene 269: 45-51.
• Shi, Y., Radlwimmer, F. B. and Yokoyama, S. (2001)
  Molecular genetics and the evolution of ultraviolet vision in vertebrates. Proc. Natl. Acad. Sci. USA 98: 11731- 11736.
• Yokoyama, S. (2000)
  Color vision of the coelacanth (Latimeria chalumnae) and adaptive evolution of rhodopsin (RH1) and rhodopsin-like (RH2) pigments. J. Heredity 91: 215-220.
• Yokoyama, S, Radlwimmer, F. B. and Blow, N. S. (2000)
  Ultraviolet pigments in birds evolved from violet pigments by a single amino acid change. Proc. Natl. Acad. Sci. USA 97: 7366-7371.
• Yokoyama, S. and Shi, Y. (2000)
  Genetics and evolution of ultraviolet vision in vertebrates. FEBS Lett. 486: 167-172.
• Yokoyama, S., Blow, N. S. and Radlwimmer, F. B. (2000)
  Molecular evolution of color vision in zebra finch. Gene 259: 17-24.
• Yokoyama, S. and Tada, T. (2000)
  Adaptive evolution of the African and Indonesian coelacanths to deep-sea environments. Gene 261: 35-42.
• Yokoyama, S. (2000)
  Phylogenetic analysis and experimental approaches to study color vision in vertebrates. In:Vertebrate Phototransduction and the Visual Cycle. Methods in Enzymology 315: 312-325.
• Yokoyama, S. (2000)
  Molecular evolution of vertebrate visual pigments. Prog. Ret. Eye Res. 19: 385-419.
• Yokoyama, S. and Yokoyama, R. (2000)
  Comparative molecular biology of visual pigments. in Handbook of Biological Physics, D. G. Stavenga, W. J. de Grip & E. N. Pugh, Jr. (eds.), pp. 257-296. Elesevier, Amsterdam.
• Yokoyama, S. (1999)
  Molecular bases of color vision in vertebrates. Genes Genet. Syst. 74: 189-199.
• Yokoyama, S., Zhang, H., Radlwimmer, F. B. and Blow, N. S. (1999)
  Adaptive evolution of color vision of the Comoran coelacanth (Latimeria chalumnae). Proc. Natl. Acad. Sci. USA 96: 6279-6284.
• Yokoyama, S. and Radlwimmer, F. B. (1999)
  The molecular genetics of red and green color vision in mammals. Genetics 153: 919-932.
• Kawamura, S., Blow, N. S. and Yokoyama, S. (1999)
  Genetic analyses of visual pigments of the pigeon (Columba livia). Genetics 153: 1839-1850.
• Kawamura, S. and Yokoyama, S. (1998)
  Functional characterization of visual and nonvisual pigments of American chameleon (Anolis carolinensis). Vision Res. 38: 37-44.
• Yokoyama, S. and Radlwimmer, F. B. (1998)
  The "five-sites" rule and the evolution of red and green color vision in mammals. Mol. Biol. Evol. 15: 560-567.
• Yokoyama, S., Radlwimmer, F. B. and Kawamura, S. (1998)
  Regeneration of ultraviolet pigments of vertebrates. FEBS Lett. 423: 155-158.
• Radlwimmer, F. B. and Yokoyama, S. (1998)
  Genetic analyses of the green visual pigments of rabbit (Oryctolagus cuniculus) and rat (Rattus norvegicus). Gene 218: 103-109.
• Kawamura, S. and Yokoyama, S. (1997)
  Expression of visual and nonvisual opsins in American chameleon. Vision Res. 37: 1867-1871.
• Zhang, H. and Yokoyama, S. (1997)
  Molecular evolution of the rhodopsin gene of marine lamprey, Petromyzon marinus. Gene 191: 1-6.
• Nei, M., Zhang, J. and Yokoyama, S. (1997)
  Color vision of ancestral organisms of higher primates. Mol. Biol. Evol. 14: 611-618.
• Radlwimmer, F. B. and Yokoyama, S. (1997)
  Cloning and expression of the red visual pigment gene of goat (Capra hircus). Gene 198: 211-215.
• Yokoyama, S. and Zhang, H. (1997)
  Cloning and characterization of the pineal gland-specific opsin gene of marine lamprey (Petromyzon marinus). Gene 202: 89-93.
• Yokoyama, S. (1997)
  Molecular genetic basis of adaptive selection: Examples from color vision in vertebrates. Annu. Rev. Genet. 31: 315-336.
• Yokoyama, S. (1996)
  Molecular evolution of retinal and nonretinal opsins. Genes To Cells 1: 787-794.
• Kawamura, S. and Yokoyama, S. (1996)
  Phylogenetic relationships among short wavelength-sensitive opsin genes of American chameleon (Anolis carolinensis) and other vertebrates. Vision Res. 36: 2797-2804.
• Kawamura, S. and Yokoyama, S. (1996)
  Molecular characterization of the pigeon P-opsin gene. Gene 182: 213-214.
• Yokoyama, S. and Starmer, W. T. (1996)
  Evolution of G-protein-coupled receptor superfamily. in Human Genome Evolution. M. S. Jackson, T. Strachan, and G. Dover (eds), Pp. 93-119, BIOS Scientific, Oxford.
• Yokoyama, S. and Yokoyama, R. (1996)
  Adaptive evolution of photoreceptors and visual pigments in vertebrates. Annu. Rev. Ecol. Syst. 27: 543-567.
• Kawamura, S. and Yokoyama, S. (1995)
  Paralogous origin of the rhodopsin-like opsin genes in lizards. J. Mol. Evol. 40:594-600.
• Yokoyama, R., Knox, B. E. and Yokoyama, S. (1995)
  Rhodopsin from the fish, Astyanax: Role of tyrosine 261 in the red shift. Invest. Ophthalmol. Vis. Sci. 36: 939-945.
• Yokoyama, S., Meany, A., Wilkens, H. and Yokoyama, R. (1995)
  Initial mutational steps towards loss of opsin gene function in cavefish. Mol. Biol. Evol. 12: 527-532.
• Yokoyama, S. (1995)
  Amino acid replacements and wavelength absorption of visual pigments in vertebrates. Mol. Biol. Evol. 12: 53-61.
• Yokoyama, S. (1994)
  Gene duplications and evolution of the short wavelength- sensitive visual pigment genes in vertebrates. Mol. Biol. Evol. 11: 32-39.
• Register, E. A., Yokoyama, R. and Yokoyama, S. (1994)
  Multiple origins of the green- sensitive opsin genes in fish. J. Mol. Evol. 39: 268-273.
• Kawamura, S. and Yokoyama, S. (1994)
  Cloning of the rhodopsin-encoding gene from the rod-less lizard Anolis carolinensis. Gene 149: 267-270.
• Wilkie, T. M. and Yokoyama, S. (1994)
  Evolution of the G protein alpha subunit gene family. in Molecular Evolution of Physiological Processes. D. M. Fambrough (ed), Pp. 249-270, The Rockefeller Univ. Press, New York.
• Yokoyama, R. and Yokoyama, S. (1993)
  Molecular characterization of the blue visual pigment gene in the fish Astyanax fasciatus. FEBS Lett. 334: 27-31.
• Yokoyama, S., Starmer, W. T. and Yokoyama, R. (1993)
  Paralogous origin of the red- and green-sensitive visual pigment genes in vertebrates. Mol. Biol. Evol. 10:527-538.
• Kawamura, S. and Yokoyama, S. (1993)
  Molecular characterization of the red visual pigment gene of the American chameleon (Anolis carolinensis). FEBS Lett. 323: 247-251.
• Yokoyama, R. and Yokoyama, S. (1990)
  Convergent evolution of the red- and green- like visual pigment genes in fish, Astyanax fasciatus, and human. Proc. Natl. Acad. Sci. USA 87: 9315-9318.
• Yokoyama, R, and Yokoyama, S. (1990)
  Isolation, DNA sequence and evolution of a color visual pigment gene of the blind cave fish Astyanax fasciatus. Vision Res. 30: 807-816.
• Yokoyama, S. and Yokoyama, R. (1989)
  Molecular evolution of human visual pigment genes. Mol. Biol. Evol. 6: 186-197.
• Yokoyama, S. and Yokoyama, R. (1987)
  Molecular evolution of mammalian class I alcohol dehydrogenase. Mol. Biol. Evol. 4: 504-513.

Quantum chemistry

• Sekharan, S., Yokoyama, S. and Morokuma, K. (2012)
  QM/MM Structure, Enantioselectivity, Spectroscopy of A3- and A4-Retinals in Visual Pigments: Implications for Insect Vision. J. Phys. Chem. B (in press).
• Altun, A., Morokuma, K. and Yokoyama, S. (2011)
  Hydrogen-bond network around retinal regulates the evolution of ultraviolet and violet vision. ACS Chemical Biology 6, 775-780.
• Watanabe, H. C., Mori, Y., Tada, T., Yokoyama, S. and Yamato, T. (2010)
  Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin. Biophysics 6: 67-78.
• Altun, A., Yokoyama, S. and Morokuma, K. (2009)
  Color tuning in short wavelength- sensitive human and mouse visual pigments: Ab initio quantum mechanics/ molecular mechanicks studies. J. Phys. Chem. A 113: 11685-11692.
• Altun, A., Yokoyama, S. and Morokuma, K. (2008)
  Mechanism of spectral tuning going from retinal in vacuo to bovine rhodopsin and its mutants: Multireference ab initio Quantum Mechanics/Molecular Mechanics studies. J. Phys. Chem. B. 112: 16883-16890.
• Altun, A., Yokoyama, S. and Morokuma, K. (2008)
  Quantum Mechanical/Molecular Mechanical studies on spectral tuning mechanisms of visual pigments and other photoactive proteins. Photochem. Photobiol. 84: 845-854.
• Altun, A., Yokoyama, S. and Morokuma, K. (2008)
  Spectral tuning in visual pigments: An ONIOM(QM:MM) study on bovine rhodopsin and its mutants. J. Phys. Chem. B 112: 6814-6827.

Molecular evolution

• Yokoyama, S. (2005)
  Molecules, biodiversity and adaptive evolution. J. Hered. 96: 169- 170. (Editorial introduction for a symposium volume.)
• Yokoyama, S. and Starmer, W. T. (1992)
  Phylogeny and evolutionary rates of G protein subunit genes. J. Mol. Evol. 35: 230-238.
• Yokoyama, S. (1991)
  Molecular evolution of the HIV and related viruses. in Evolution at the Molecular Level, R. K. Selander, A. G. Clark and T. S. Whittam (eds.), pp. 96-111, Sinauer, Sunderland.
• Gojobori, T., Moriyama, E. N., Shimizu, N., Ina, Y., Ikeo, K., Miura, T., Tsujimoto, H.,
• Hayami, M. and Yokoyama, S. (1990)
  Evolutionary origin of human and simian immunodeficiency viruses. Proc. Natl. Acad. Sci. USA 87: 4108-4111.
• Yokoyama, S., Yokoyama, R., Kinlaw, C. S. and Harry, D. E. (1990)
  Molecular evolution of the zinc-containing long-chain alcohol dehydrogenase genes. Mol. Biol . Evol. 7: 143-154.
• Yokoyama, S. and Yokoyama, R. (1990)
  Molecular evolution of visual pigment genes and other G-protein-coupled receptor genes. in Population Biology of Genes and Molecules, N. Takahata and J. F. Crow (eds.), pp. 307-322, Baifukan, Tokyo.
• Yokoyama, S., Isenberg, K. E. and Wright, A. F. (1989)
  Adaptive evolution of G protein coupled receptor genes. Mol. Biol. Evol. 6: 342-353.
• Yokoyama, S., Chung, L. and Gojobori, T. (1988)
  Molecular evolution of the human immunodeficiency and related viruses. Mol. Biol. Evol. 5: 237-251.
• Yokoyama, S. (1988)
  Molecular evolution of the human and simian immunodeficiency viruses. Mol. Biol. Evol. 5: 645-659.
• Gojobori, T. and Yokoyama, S. (1987)
  Molecular evolutionary rates of oncogenes. J. Mol. Evol. 26: 148-156.
• Gojobori, T., Moriyama, E. N. and Yokoyama, S. (1987)
  Molecular evolution of oncogenes. Jpn. J. Genet. 62: 163-177.
• Yokoyama, S. and Gojobori, T. (1987)
  Molecular evolution and phylogeny of the human AIDS viruses LAV, HTLV-III, and ARV. J. Mol. Evol. 24: 330-336.
• Yokoyama, S., Moriyama, E. N. and Gojobori, T. (1987)
  Molecular phylogeny of the human immunodeficiency and related viruses. Proc. Japan Acad. 63: 147-150.
• Gojobori, T. and Yokoyama, S. (1985)
  Rates of evolution of the retroviral oncogene of Moloney murine sarcoma virus and of its cellular homologues. Proc. Natl. Acad. Sci. USA 82: 4198-4201.
• Hall, B. G., Yokoyama, S. and Calhoun, D. H. (1983)
  Role of cryptic genes in microbial evolution. Mol. Biol. Evol. 1: 109-124.

Human genetics

• Yokoyama, S., Matsuo, Y., Ramsbotham, R. and Yokoyama, R. (1994)
  Molecular characterization of a class IV human alcohol dehydrogenase gene (ADH7). FEBS Lett. 351: 411-415.
• Yokoyama, S. and Harry, D. E. (1993)
  Molecular phylogeny and evolutionary rates of alcohol dehydrogenases in vertebrates and plants. Mol. Biol. Evol. 10: 1215-1226.
• Yokoyama, S., Matsuo, Y., Rajasekharan, S. and Yokoyama, R. (1992)
  Molecular structure of the human alcohol dehydrogenase 3 gene. Jpn. J. Genet. 67: 167-171.
• Matsuo, Y. and Yokoyama, S. (1990)
  Cloning and sequencing of a processed pseudogene derived from the human class III alcohol dehydrogenase gene. Am. J. Hum. Genet. 46: 85-91.
• Matsuo, Y. and Yokoyama, S. (1989)
  Molecular structure of the human alcohol dehydrogenase 1 gene. FEBS Lett. 243: 57-60.
• Matsuo, Y., Yokoyama, R. and Yokoyama, S. (1989)
  The genes for human alcohol dehydrogenases β1 and β2 differ by only one nucleotide. Eur. J. Biochem. 183: 317-320.
• Yokoyama, S. (1988)
  Evolution by social selection. Evol. Biol. 23: 85-126.
• Yokoyama, S. and Yokoyama, R. (1987)
  Molecular evolution of mammalian class I alcohol dehydrogenase. Mol. Biol. Evol. 4: 504-513.
• Yokoyama, S., Yokoyama, R. and Rotwein, P. (1987)
  Molecular characterization of cDNA clones encoding the human alcohol dehydrogenase β1 and the evolutionary relationship to the other class I subunits α and γ. Jpn. J. Genet. 62: 241-256.
• Yokoyama, S. (1987)
  Social selection in human populations: Protected polymorphism of deleterious alleles with incomplete penetrance. Genetic Epidemiology 4: 223-231.
• Yokoyama, S. (1986)
  Deterministic behavior of HLA haplotypes under symmetric overdominant selection. Jpn. J. Genet. 61: 61-70.
• Rotwein, P., Yokoyama, S., Didier, D. K. and Chirgwin J. M. (1986)
  Genetic analysis of the hypervariable region flanking the human insulin gene. Am. J. Hum. Genet. 39: 291-299.
• Yokoyama, S. (1986)
  The effect of social selection on the frequencies of genetic diseases. in Recent Trends in Medical Genetics. K. M. Marimuthu and P. M. Gopinath (eds), Pp. 207-216, Pergamon Press, Oxford.
• Yokoyama, S. (1985)
  DNA polymorphism and the susceptability to diseases. Am. J. Med. Genet. 21: 649-654.
• Yokoyama, S. (1985)
  Social selection in human populations: Sufficient conditions for protection of deleterious alleles in a subdivided population. J. Theor. Biol. 115: 455-465.
• Yokoyama, S. (1984)
  Social selection in human populations: Differential modification of the fitness by the sex of an affected parent. J. Theor. Biol. 109: 453-459.
• Yokoyama, S. and Ward, R. H. (1984)
  Age structure and the distribution of rare genetic diseases. Am. J. Med. Genet. 19: 65-79.
• Yokoyama, S. (1984)
  Comments on "The sociobiology of sex and sexes today" by M. Blute. Current Anthropology 25: 206-207.
• Yokoyama, S. (1983)
  Equilibrium frequencies of α-globin genes. J. Theor. Biol. 100: 173-180.
• Yokoyama, S. (1983)
  Selection for the α-thalassemia genes. Genetics 103: 143-148.
• Yokoyama, S. (1983)
  Polymorphism in the 5'-flanking region of the human insulin gene and the incidence of diabetes. Am. J. Hum. Genet. 35: 193-200.
• Yokoyama, S. (1983)
  Social selection in human populations: Fitness modification of offspring by an affected parent at two loci. Am. J. Hum. Genet. 35: 675-686.
• Yokoyama, S. (1983)
  Social selection and evolution of human diseases. Am. J. Phys. Anthrop. 62: 61-66.
• Yokoyama, S. (1983
  Theories of social selection in human populations. Am. J. Hum. Genet. 35: 362-375.
• Yokoyama, S. (1983)
  Social selection in human populations: Fitness interaction among sibs. Am. Nat. 122: 433-443.
• Yokoyama, S. and Rice, J. P. (1983)
  Social selection in human populations: Deterministic analyses on the modification of the fitness of offspring by affected parents. Social Biol. 30: 181-188.
• Yokoyama, S. (1983)
  Social selection and evolution of human diseases. in Genetics, Evolution, and Diseases. D. H. O'Rouke, G. M. Peterson, and F. E. Johnson (eds), Alan R. Liss, Inc., New York. (Also appeared as American Journal of Physical Anthropology, Vol. 62, No. 1)
• Cloninger, C. R., Reich, T. and Yokoyama, S. (1983)
  Genetic diversity, genome organization, and investigation of the etiology of psychiatric diseases. Psychiatric Development 3: 225-246.
• Yokoyama, S. and Templeton, R. (1982)
  Effect of cultural inheritance of reproductive compensation on the incidence of a sex-linked lethal disease. J. Theor. Biol. 99: 389-395.
• Yokoyama, S. (1981)
  Social selection in human populations: I. Modification of the fitness of offspring by an affected parent. Am. J. Hum. Genet. 33: 407-417.
• Yokoyama, S. (1981)
  Family size and evolution of Rh polymorphism. J. Theor. Biol. 92: 119-125.
• Yokoyama, S. (1981)
  Concept of genetic and evolutionary fitness and hereditary polyposis coli. Am. J. Hum. Genet. 33: 995-998.
• Yokoyama, S. (1981)
  Cultural inheritance of the desire for having male offspring and the incidence of a sex-linked lethal disease. Social Biol. 28: 315-327.
• Nei, M. and Yokoyama, S. (1981)
  Estimation of fitness reduction due to a chronic disease in man. Ann. Hum. Genet. 45 :261-265.
• Yokoyama, S., Reich, T. and Morgan, K. (1981)
  Inbreeding and the genetic control of nondisjunction. Human Genet. 59: 125-128.
• Yokoyama, S. (1980)
  The effect of social selection on population dynamics of rare deleterious genes. Heredity 45: 271-280.
• Yokoyama, S. (1980)
  The effect of variable progeny size and social selection on the population dynamics of rare lethal genes. Social Biol. 27: 70-78.
• Yokoyama, S. and Templeton, A. (1980)
  The effect of social selection on the population dynamics of Huntington's disease. Ann. Hum. Genet. 43: 413-417.
• Templeton, A. and Yokoyama, S. (1980)
  Effect of reproductive compensation and the desire to have male offspring on the incidence of a sex-linked lethal disease. Am. J. Hum. Genet. 32: 575-581.
• Yokoyama, S., Rice, J. P. and Yokoyama, R. W. (1980)
  The effect of social selection due to familial mental retardation on the marriage frequency of normal individuals. Social Biol. 27: 194-198.
• Yokoyama, S. (1979)
  Role of genetic drift in the high frequency of Tay-Sachs disease among Ashkenazic Jews. Ann. Hum. Genet. 43: 133-136.

Theoretical population genetics

• Yokoyama, S. and Schaal, B. (1986)
  Population dynamics of mutant alleles under maternal effect in plant populations. J. Hered. 77: 256-260.
• Yokoyama, S. and Schaal, B. (1985)
  A note on multiple-niche polymorphisms in plant populations. Am. Nat. 125: 158-163.
• Yokoyama, S. and Hetherington, L. E. (1982)
  The expected number of self- incompatibility alleles in finite plant populations. Heredity 48: 299-303.
• Yokoyama, S. and Nei, M. (1979)
  Population dynamics of sex-determining alleles in honey-bees and self-incompatibility alleles in plants. Genetics 91: 609-626.
• Yokoyama, S. (1979)
  The rate of allelism of lethal genes in a geographically structured population. Genetics 93: 245-262.
• Chakraborty, R. and Yokoyama, S. (1978)
  Heterozygosity and monomorphism reconsidered. Heredity 41: 327-333.
• Yokoyama, S. and Felsenstein, J. (1978)
  A model of kin selection for an altruistic trait considered as a quantitative character. Proc. Natl. Acad. Sci. USA 75: 420-422.
• Felsenstein, J. and Yokoyama, S. (1976)
  The evolutionary advantage of recombination. II. Individual selection for recombination. Genetics 83: 845-859.
• Yokoyama, S. (1977)
  Theoretical studies of the distribution of rare deleterious alleles in natural and human populations. Ph. D. Dissertation, University of Washington.
• Nei, M and Yokoyama, S. (1976)
  Effects of random fluctuation of selection intensity on genetic variability in a finite population. Japan. J. Genetics. 51: 355-369.

Developmental biology

• Yao, M.-C., Choi, J., Yokoyama, S., Austerberry, C. F. and Yao, C.-H. (1984)
  DNA elimination in tetrahymena: A developmental process involving extensive breakage and rejoining of DNA at defined sites. Cell 36: 433-440.