A simple method for studying the molecular mechanisms of ultraviolet and violet reception in vertebrates

Adaptive evolutionary paths from UV reception to sensing violet light by epistatic interactions

(2015) S. Yokoyama et al.   Science Advances

Spectral tuning in vertebrate short wavelength-sensitive 1 (SWS1) visual pigments: Can wavelength sensitivity be inferred from sequence data?

(2014) Frances E. Hauser et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

(2014) Marco Biasini et al.   NUCLEIC ACIDS RESEARCH

The spectral transmission of ocular media suggests ultraviolet sensitivity is widespread among mammals

(2014) R. H. Douglas et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Epistatic Adaptive Evolution of Human Color Vision

(2014) Shozo Yokoyama et al.   PLoS Genetics

The phylogenetic distribution of ultraviolet sensitivity in birds

(2013) Anders Ödeen et al.   BMC EVOLUTIONARY BIOLOGY

Synthetic Biology of Phenotypic Adaptation in Vertebrates: The Next Frontier

(2013) S. Yokoyama   MOLECULAR BIOLOGY AND EVOLUTION

The missense of smell: functional variability in the human odorant receptor repertoire

(2013) Joel D Mainland et al.   NATURE NEUROSCIENCE

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

(2013) Michael J. Harms et al.   NATURE REVIEWS GENETICS

Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors

(2013) M. J. Harms et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin

(2013) C. Natarajan et al.   SCIENCE

Functional Evolution of Mammalian Odorant Receptors

(2012) Kaylin A. Adipietro et al.   PLoS Genetics

Evolution of Minimal Specificity and Promiscuity in Steroid Hormone Receptors

(2012) Geeta N. Eick et al.   PLoS Genetics

H-Bond Network around Retinal Regulates the Evolution of Ultraviolet and Violet Vision

(2011) Ahmet Altun et al.   ACS Chemical Biology

The Neutral Theory of Molecular Evolution in the Genomic Era

(2010) Masatoshi Nei et al.   Annual Review of Genomics and Human Genetics

Analyzing protein structure and function using ancestral gene reconstruction

(2010) Michael J Harms et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Is positive selection responsible for the evolution of a duplicate UV-sensitive opsin gene in Heliconius butterflies?

(2010) M. Nozawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shedding Light on Serpent Sight: The Visual Pigments of Henophidian Snakes

(2009) W. L. Davies et al.   JOURNAL OF NEUROSCIENCE

Color Tuning in Short Wavelength-Sensitive Human and Mouse Visual Pigments: Ab initio Quantum Mechanics/Molecular Mechanics Studies

(2009) Ahmet Altun et al.   JOURNAL OF PHYSICAL CHEMISTRY A

In defense of statistical methods for detecting positive selection

(2009) Z. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Response to Yang et al.: Problems with Bayesian methods of detecting positive selection at the DNA sequence level

(2009) M. Nozawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary replacement of UV vision by violet vision in fish

(2009) T. Tada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic functional evolution of an odorant receptor for sex-steroid-derived odors in primates

(2009) Hanyi Zhuang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

(2009) M. Nozawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Dim-Light and Color Vision Pigments

(2008) Shozo Yokoyama   Annual Review of Genomics and Human Genetics

Molecular Basis of Spectral Tuning in the Red- and Green-Sensitive (M/LWS) Pigments in Vertebrates

(2008) S. Yokoyama et al.   GENETICS

The origin of adaptive phenotypes

(2008) A. L. Hughes   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

(2008) S. Yokoyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cone visual pigments in two marsupial species: the fat-tailed dunnart (Sminthopsis crassicaudata) and the honey possum (Tarsipes rostratus)

(2008) J. A Cowing et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES