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Masatoshi Nei

Research Profile

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Evolution, Molecular

Genes & Molecular Sequences

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TOP 3
Masafumi Nozawa; Sayaka Miura; Masatoshi Nei
Origins and evolution of microRNA genes in plant species.
Masatoshi Nei; Masafumi Nozawa
Roles of mutation and selection in speciation: from Hugo de Vries to the modern genomic era.
Sayaka Miura; Masafumi Nozawa; Masatoshi Nei
Evolutionary changes of the target sites of two microRNAs encoded in the Hox gene cluster of Drosophila and other insect species.

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All Publications

2012: Masafumi Nozawa; Sayaka Miura; Masatoshi Nei
Origins and evolution of microRNA genes in plant species.
Genome biology and evolution 2012;4(3):230-9.
2011: Masatoshi Nei; Masafumi Nozawa
Roles of mutation and selection in speciation: from Hugo de Vries to the modern genomic era.
Genome biology and evolution 2011;3():812-29.
2011: Sayaka Miura; Masafumi Nozawa; Masatoshi Nei
Evolutionary changes of the target sites of two microRNAs encoded in the Hox gene cluster of Drosophila and other insect species.
Genome biology and evolution 2011;3():129-39.
2010: Masatoshi Nei; Yoshiyuki Suzuki; Masafumi Nozawa
The neutral theory of molecular evolution in the genomic era.
Annual review of genomics and human genetics 2010;11():265-89.
2010: Masafumi Nozawa; Yoshiyuki Suzuki; Masatoshi Nei
Is positive selection responsible for the evolution of a duplicate UV-sensitive opsin gene in Heliconius butterflies?
Proceedings of the National Academy of Sciences of the United States of America 2010;107(23):E96; author reply E97.
2010: Naoko Takezaki; Masatoshi Nei; Koichiro Tamura
POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface.
Molecular biology and evolution 2010;27(4):747-52.
2010: Masafumi Nozawa; Sayaka Miura; Masatoshi Nei
Origins and evolution of microRNA genes in Drosophila species.
Genome biology and evolution 2010;2():180-9.
2009: Naoko Takezaki; Masatoshi Nei
Genomic drift and evolution of microsatellite DNAs in human populations.
Molecular biology and evolution 2009;26(8):1835-40.
2009: Masafumi Nozawa; Yoshiyuki Suzuki; Masatoshi Nei
Reliabilities of identifying positive selection by the branch-site and the site-prediction methods.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(16):6700-5.
2008: Masatoshi Nei; Yoshihito Niimura; Masafumi Nozawa
The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity.
Nature reviews. Genetics 2008;9(12):951-63.
2008: Dimitra Chalkia; Nikolas Nikolaidis; Wojciech Makalowski; Jan Klein; Masatoshi Nei
Origins and evolution of the formin multigene family that is involved in the formation of actin filaments.
Molecular biology and evolution 2008;25(12):2717-33.
2008: Sabyasachi Das; Nikolas Nikolaidis; Jan Klein; Masatoshi Nei
Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(43):16647-52.
2008: Sudhir Kumar; Masatoshi Nei; Joel Dudley; Koichiro Tamura
MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences.
Briefings in bioinformatics 2008;9(4):299-306.
2008: Zhenguo Lin; Zhenguo Lin; Masatoshi Nei
Ultraconserved coding regions outside the homeobox of mammalian Hox genes.
BMC evolutionary biology 2008;8():260.
2008: Naoko Takezaki; Masatoshi Nei
Empirical tests of the reliability of phylogenetic trees constructed with microsatellite DNA.
Genetics 2008;178(1):385-92.
2008: Sabyasachi Das; Masafumi Nozawa; Jan Klein; Masatoshi Nei
Evolutionary dynamics of the immunoglobulin heavy chain variable region genes in vertebrates.
Immunogenetics 2008;60(1):47-55.
2007: Masafumi Nozawa; Yoshihiro Kawahara; Masatoshi Nei
Genomic drift and copy number variation of sensory receptor genes in humans.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(51):20421-6.
2007: Koichiro Tamura; Joel Dudley; Masatoshi Nei; Sudhir Kumar
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
Molecular biology and evolution 2007;24(8):1596-9.
2007: Masatoshi Nei
The new mutation theory of phenotypic evolution.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(30):12235-42.
2007: Masafumi Nozawa; Masatoshi Nei
Evolutionary dynamics of olfactory receptor genes in Drosophila species.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(17):7122-7.
2007: Zhenguo Lin; Masatoshi Nei; Zhenguo Lin
The origins and early evolution of DNA mismatch repair genes--multiple horizontal gene transfers and co-evolution.
Nucleic acids research 2007;35(22):7591-603.
2007: Yoshihito Niimura; Masatoshi Nei
Extensive gains and losses of olfactory receptor genes in mammalian evolution.
PloS one 2007;2(8):e708.
2006: Zhenguo Lin; Hongzhi Kong; Masatoshi Nei; Zhenguo Lin
Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(27):10328-33.
2006: Li Hao; Jan Klein; Masatoshi Nei
Heterogeneous but conserved natural killer receptor gene complexes in four major orders of mammals.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(9):3192-7.
2006: Yoshihito Niimura; Masatoshi Nei
Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates.
Journal of human genetics 2006;51(6):505-17.
2005: Masatoshi Nei
Selectionism and neutralism in molecular evolution.
Molecular biology and evolution 2005;22(12):2318-42.
2005: Jongmin Nam; Masatoshi Nei
Evolutionary change of the numbers of homeobox genes in bilateral animals.
Molecular biology and evolution 2005;22(12):2386-94.
2005: Masatoshi Nei
Bottlenecks, genetic polymorphism and speciation.
Genetics 2005;170(1):1-4.
2005: Yoshihito Niimura; Masatoshi Nei
Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(17):6039-44.
2005: Nikolas Nikolaidis; Jan Klein; Masatoshi Nei
Origin and evolution of the Ig-like domains present in mammalian leukocyte receptors: insights from chicken, frog, and fish homologues.
Immunogenetics 2005;57(1-2):151-7.
2005: Nikolas Nikolaidis; Izabela Makalowska; Dimitra Chalkia; Wojciech Makalowski; Jan Klein; Masatoshi Nei
Origin and evolution of the chicken leukocyte receptor complex.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(11):4057-62.
2005: Li Hao; Masatoshi Nei
Rapid expansion of killer cell immunoglobulin-like receptor genes in primates and their coevolution with MHC Class I genes.
Gene 2005;347(2):149-59.
2005: Yoshihito Niimura; Masatoshi Nei
Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice.
Gene 2005;346():13-21.
2005: Yoshihito Niimura; Masatoshi Nei
Evolutionary changes of the number of olfactory receptor genes in the human and mouse lineages.
Gene 2005;346():23-8.
2005: Galina V Glazko; Vamsi Veeramachaneni; Masatoshi Nei; Wojciech Makałowski
Eighty percent of proteins are different between humans and chimpanzees.
Gene 2005;346():215-9.
2005: Masatoshi Nei; Alejandro P Rooney
Concerted and birth-and-death evolution of multigene families.
Annual review of genetics 2005;39():121-52.
2005: Jongmin Nam; Kerstin Kaufmann; Günter Theissen; Masatoshi Nei
A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes.
Nucleic acids research 2005;33(2):e12.
2004: Li Hao; Masatoshi Nei
Genomic organization and evolutionary analysis of Ly49 genes encoding the rodent natural killer cell receptors: rapid evolution by repeated gene duplication.
Immunogenetics 2004;56(5):343-54.
2004: Koichiro Tamura; Masatoshi Nei; Sudhir Kumar
Prospects for inferring very large phylogenies by using the neighbor-joining method.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(30):11030-5.
2004: Sudhir Kumar; Koichiro Tamura; Masatoshi Nei
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.
Briefings in bioinformatics 2004;5(2):150-63.
2004: Yoshiyuki Suzuki; Masatoshi Nei
False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus.
Molecular biology and evolution 2004;21(5):914-21.
2004: Nikolas Nikolaidis; Masatoshi Nei
Concerted and nonconcerted evolution of the Hsp70 gene superfamily in two sibling species of nematodes.
Molecular biology and evolution 2004;21(3):498-505.
2004: Jongmin Nam; Joonyul Kim; Shinyoung Lee; Gynheung An; Hong Ma; Masatoshi Nei
Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(7):1910-5.
2003: Yoshihito Niimura; Masatoshi Nei
Evolution of olfactory receptor genes in the human genome.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(21):12235-40.
2003: Jongmin Nam; Claude W dePamphilis; Hong Ma; Masatoshi Nei
Antiquity and evolution of the MADS-box gene family controlling flower development in plants.
Molecular biology and evolution 2003;20(9):1435-47.
2003: Helen Piontkivska; Masatoshi Nei
Birth-and-death evolution in primate MHC class I genes: divergence time estimates.
Molecular biology and evolution 2003;20(4):601-9.
2003: Galina V Glazko; Masatoshi Nei
Estimation of divergence times for major lineages of primate species.
Molecular biology and evolution 2003;20(3):424-34.
2003: Kazuharu Misawa; Masatoshi Nei
Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees.
Journal of molecular evolution 2003;57 Suppl 1():S290-6.
2002: Yoshiyuki Suzuki; Galina V Glazko; Masatoshi Nei
Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(25):16138-43.
2002: Yoshiyuki Suzuki; Masatoshi Nei
Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites.
Molecular biology and evolution 2002;19(11):1865-9.
2002: Takeshi Itoh; William Martin; Masatoshi Nei
Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(20):12944-8.
2002: Masatoshi Nei; Galina V Glazko
The Wilhelmine E. Key 2001 Invitational Lecture. Estimation of divergence times for a few mammalian and several primate species.
The Journal of heredity 2002;93(3):157-64.
2002: Helen Piontkivska; Alejandro P Rooney; Masatoshi Nei
Purifying selection and birth-and-death evolution in the histone H4 gene family.
Molecular biology and evolution 2002;19(5):689-97.
2002: Yoshiyuki Suzuki; Masatoshi Nei
Origin and evolution of influenza virus hemagglutinin genes.
Molecular biology and evolution 2002;19(4):501-9.
2002: Chen Su; Viet Khong Nguyen; Masatoshi Nei
Adaptive evolution of variable region genes encoding an unusual type of immunoglobulin in camelids.
Molecular biology and evolution 2002;19(3):205-15.
2002: Alejandro P Rooney; Helen Piontkivska; Masatoshi Nei
Molecular evolution of the nontandemly repeated genes of the histone 3 multigene family.
Molecular biology and evolution 2002;19(1):68-75.
2001: Yoshiyuki Suzuki; Masatoshi Nei
Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites.
Molecular biology and evolution 2001;18(12):2179-85.
2001: Chen Su; Masatoshi Nei
Evolutionary dynamics of the T-cell receptor VB gene family as inferred from the human and mouse genomic sequences.
Molecular biology and evolution 2001;18(4):503-13.
2001: Masatoshi Nei; P Xu; Galina V Glazko
Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(5):2497-502.
2000: Masatoshi Nei; Igor Rogozin; Helen Piontkivska
Purifying selection and birth-and-death evolution in the ubiquitin gene family.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(20):10866-71.
2000: K Takahashi; Masatoshi Nei
Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used.
Molecular biology and evolution 2000;17(8):1251-8.
2000: K Takahashi; Alejandro P Rooney; Masatoshi Nei
Origins and divergence times of mammalian class II MHC gene clusters.
The Journal of heredity 2000;91(3):198-204.
2000: Alejandro P Rooney; Jian Zhang; Masatoshi Nei
An unusual form of purifying selection in a sperm protein.
Molecular biology and evolution 2000;17(2):278-83.
2000: T Ota; T Sitnikova; Masatoshi Nei
Evolution of vertebrate immunoglobulin variable gene segments.
Current topics in microbiology and immunology 2000;248():221-45.
1999: Chen Su; Ingrid Jakobsen; X Gu; Masatoshi Nei
Diversity and evolution of T-cell receptor variable region genes in mammals and birds.
Immunogenetics 1999;50(5-6):301-8.
1999: C Su; Masatoshi Nei
Fifty-million-year-old polymorphism at an immunoglobulin variable region gene locus in the rabbit evolutionary lineage.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(17):9710-5.
1999: X Gu; Masatoshi Nei
Locus specificity of polymorphic alleles and evolution by a birth-and-death process in mammalian MHC genes.
Molecular biology and evolution 1999;16(2):147-56.
1998: Masatoshi Nei; jianzhi zhang
Molecular origin of species.
Science (New York, N.Y.) 1998;282(5393):1428-9.
1998: Masatoshi Nei; Sudhir Kumar; K Takahashi
The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(21):12390-7.
1998: Jian Zhang; H F Rosenberg; Masatoshi Nei
Positive Darwinian selection after gene duplication in primate ribonuclease genes.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(7):3708-13.
1998: T Sitnikova; Masatoshi Nei
Evolution of immunoglobulin kappa chain variable region genes in vertebrates.
Molecular biology and evolution 1998;15(1):50-60.
1997: Masatoshi Nei; X Gu; T Sitnikova
Evolution by the birth-and-death process in multigene families of the vertebrate immune system.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(15):7799-806.
1997: Masatoshi Nei; Jian Zhang; S Yokoyama
Color vision of ancestral organisms of higher primates.
Molecular biology and evolution 1997;14(6):611-8.
1997: Jian Zhang; Masatoshi Nei
Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods.
Journal of molecular evolution 1997;44 Suppl 1():S139-46.
1996: N Takezaki; Masatoshi Nei
Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA.
Genetics 1996;144(1):389-99.
1996: C A Russo; N Takezaki; Masatoshi Nei
Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny.
Molecular biology and evolution 1996;13(3):525-36.
1996: jianzhi zhang; Masatoshi Nei
Evolution of Antennapedia-class homeobox genes.
Genetics 1996;142(1):295-303.
1996: Masatoshi Nei; N Takezaki
The root of the phylogenetic tree of human populations.
Molecular biology and evolution 1996;13(1):170-7.
1995: Z Yang; Sudhir Kumar; Masatoshi Nei
A new method of inference of ancestral nucleotide and amino acid sequences.
Genetics 1995;141(4):1641-50.
1995: N Takezaki; Andrey Rzhetsky; Masatoshi Nei
Phylogenetic test of the molecular clock and linearized trees.
Molecular biology and evolution 1995;12(5):823-33.
1995: Masatoshi Nei
Motoo Kimura (1924-1994).
Molecular biology and evolution 1995;12(5):719-22.
1995: Masatoshi Nei
Genetic support for the out-of-Africa theory of human evolution.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(15):6720-2.
1995: C A Russo; N Takezaki; Masatoshi Nei
Molecular phylogeny and divergence times of drosophilid species.
Molecular biology and evolution 1995;12(3):391-404.
1995: T Sitnikova; Andrey Rzhetsky; Masatoshi Nei
Interior-branch and bootstrap tests of phylogenetic trees.
Molecular biology and evolution 1995;12(2):319-33.
1995: Masatoshi Nei; N Takezaki; T Sitnikova
Assessing molecular phylogenies.
Science (New York, N.Y.) 1995;267(5195):253-4; author reply 255-6.
1995: T Ota; Masatoshi Nei
Evolution of immunoglobulin VH pseudogenes in chickens.
Molecular biology and evolution 1995;12(1):94-102.
1995: Andrey Rzhetsky; Sudhir Kumar; Masatoshi Nei
Four-cluster analysis: a simple method to test phylogenetic hypotheses.
Molecular biology and evolution 1995;12(1):163-7.
1995: Andrey Rzhetsky; Masatoshi Nei
Tests of applicability of several substitution models for DNA sequence data.
Molecular biology and evolution 1995;12(1):131-51.
1994: N Takezaki; Masatoshi Nei
Inconsistency of the maximum parsimony method when the rate of nucleotide substitution is constant.
Journal of molecular evolution 1994;39(2):210-8.
1994: T Ota; Masatoshi Nei
Variance and covariances of the numbers of synonymous and nonsynonymous substitutions per site.
Molecular biology and evolution 1994;11(4):613-9.
1994: Andrey Rzhetsky; Masatoshi Nei
METREE: a program package for inferring and testing minimum-evolution trees.
Computer applications in the biosciences : CABIOS 1994;10(4):409-12.
1994: T Ota; Masatoshi Nei
Divergent evolution and evolution by the birth-and-death process in the immunoglobulin VH gene family.
Molecular biology and evolution 1994;11(3):469-82.
1994: Sudhir Kumar; K Tamura; Masatoshi Nei
MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers.
Computer applications in the biosciences : CABIOS 1994;10(2):189-91.
1994: Y Tateno; N Takezaki; Masatoshi Nei
Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site.
Molecular biology and evolution 1994;11(2):261-77.
1994: Andrey Rzhetsky; Masatoshi Nei
Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites.
Journal of molecular evolution 1994;38(3):295-9.
1993: Masatoshi Nei; A K Roychoudhury
Evolutionary relationships of human populations on a global scale.
Molecular biology and evolution 1993;10(5):927-43.
1993: Andrey Rzhetsky; Masatoshi Nei
Theoretical foundation of the minimum-evolution method of phylogenetic inference.
Molecular biology and evolution 1993;10(5):1073-95.
1993: Masatoshi Nei; N Takahata
Effective population size, genetic diversity, and coalescence time in subdivided populations.
Journal of molecular evolution 1993;37(3):240-4.
1993: K Tamura; Masatoshi Nei
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
Molecular biology and evolution 1993;10(3):512-26.
1993: Austin Hughes; Masatoshi Nei
Evolutionary relationships of the classes of major histocompatibility complex genes.
Immunogenetics 1993;37(5):337-46.
1992: Andrey Rzhetsky; Masatoshi Nei
Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference.
Journal of molecular evolution 1992;35(4):367-75.