N. Okada

发表

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

Kanako O. Koyanagi, Michael A. Thomas, H. Mewes, 2004, PLoS Biology.

Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders

S. Pääbo, P. Waddell, M. Hasegawa, 1998, Journal of Molecular Evolution.

Seasonal Change in Bacterial Flora and Biomass in Mountain Snow from the Tateyama Mountains, Japan, Analyzed by 16S rRNA Gene Sequencing and Real-Time PCR

S. Kohshima, N. Okada, K. Agata, 2005, Applied and Environmental Microbiology.

Implication of a new function of human tDNAs in chromatin organization

K. Kurokawa, T. Ikemura, Y. Iwasaki, 2020, Scientific Reports.

Natural selection of the rhodopsin gene during the adaptive radiation of East African Great Lakes cichlid fishes.

N. Okada, T. Sugawara, Y. Terai, 2002, Molecular biology and evolution.

The effect of selection on a long wavelength-sensitive (LWS) opsin gene of Lake Victoria cichlid fishes

J. Klein, N. Okada, Y. Terai, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons.

M. Nishida, N. Okada, K. Takahashi, 2001, Molecular biology and evolution.

Spot pattern of leopard Danio is caused by mutation in the zebrafish connexin41.8 gene

Masaru Ishii, Masakatsu Watanabe, Yoshihisa Kurachi, 2006, EMBO reports.

Mechanisms of T-DNA transfer and integration into plant chromosomes: role of vir B , vir D4 and vir E2 and a short interspersed repetitive element (SINE) from tobacco

N. Okada, Kenzo Nakamura, Y. Machida, 1994 .

A microsatellite-based genetic linkage map and putative sex-determining genomic regions in Lake Victoria cichlids.

N. Okada, Kohta Yoshida, K. Kikuchi, 2015, Gene.

Construction of Chromosome Markers from the Lake Victoria Cichlid Paralabidochromis chilotes and Their Application to Comparative Mapping

Y. Matsuda, N. Okada, A. Kuroiwa, 2013, Cytogenetic and Genome Research.

The complete mitochondrial genomes of deep-sea squid (Bathyteuthis abyssicola), bob-tail squid (Semirossia patagonica) and four giant cuttlefish (Sepia apama, S. latimanus, S. lycidas and S. pharaonis), and their application to the phylogenetic analysis of Decapodiformes.

N. Okada, K. Tsuchiya, S. Segawa, 2013, Molecular phylogenetics and evolution.

Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

Shigenori Maruyama, N. Okada, Hidenori Nishihara, 2009, Proceedings of the National Academy of Sciences.

First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea.

N. Okada, M. Nikaido, Takeshi Sasaki, 2004, Molecular biology and evolution.

SINEs of speciation: tracking lineages with retroposons.

N. Okada, A. Shedlock, Kazuhiko Takahashi, 2004, Trends in ecology & evolution.

Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales.

N Okada, N. Okada, A. Rooney, 1999, Proceedings of the National Academy of Sciences of the United States of America.

SINE insertions: powerful tools for molecular systematics.

N Okada, N. Okada, A. Shedlock, 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

Rooting the eutherian tree: the power and pitfalls of phylogenomics

Masami Hasegawa, M. Hasegawa, N. Okada, 2007, Genome Biology.

Combining multiple data sets in a likelihood analysis: which models are the best?

Tal Pupko, Masami Hasegawa, Dorothée Huchon, 2002, Molecular biology and evolution.

Correction: Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

Kanako O. Koyanagi, Michael A. Thomas, Gopal R. Gopinath, 2004, PLoS biology.

The 3′ ends of tRNA-derived SINEs originated from the 3’ ends of LINEs: A new example from the bovine genome

N. Okada, M. Hamada, Mitsuhiro Hamada, 2009, Journal of Molecular Evolution.

Phylogenetic Relationships Among East African Haplochromine Fish as Revealed by Short Interspersed Elements (SINEs)

J. Klein, N. Takahata, N. Takezaki, 2003, Journal of Molecular Evolution.

Genetically distinct coelacanth population off the northern Tanzanian coast

Wen-Hsiung Li, J. J. Emerson, N. Okada, 2011, Proceedings of the National Academy of Sciences.

The genomic substrate for adaptive radiation in African cichlid fish

Eric S. Lander, Chris P. Ponting, Francis Galibert, 2014, Nature.

The evolution of the pro-domain of bone morphogenetic protein 4 (Bmp4) in an explosively speciated lineage of East African cichlid fishes.

N. Okada, Y. Terai, N. Morikawa, 2002, Molecular biology and evolution.

Evolutionary Gain of Dbx1 Expression Drives Subplate Identity in the Cerebral Cortex.

H. Okano, C. Dehay, A. Pierani, 2019, Cell reports.

Distinct functions of two olfactory marker protein genes derived from teleost-specific whole genome duplication

N. Okada, K. Hagino-Yamagishi, M. Nikaido, 2015, BMC Evolutionary Biology.

Construction of a BAC library for Haplochromis chilotes, a cichlid fish from Lake Victoria.

A. Fujiyama, Masakatsu Watanabe, N. Okada, 2003, Genes & genetic systems.

Acquisition of endonuclease specificity during evolution of L1 retrotransposon.

N. Okada, K. Ichiyanagi, D. Duvernell, 2007, Molecular biology and evolution.

A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons

V. Tarabykin, A. Pierani, M. Hirakawa, 2011, PloS one.

mRNA retrotransposition coupled with 5' inversion as a possible source of new genes.

N. Okada, K. Kojima, 2009, Molecular biology and evolution.

A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids.

E. Ostertag, H. Kazazian, N. Okada, 2007, Genome research.

Molecular developmental mechanism in polypterid fish provides insight into the origin of vertebrate lungs

N. Okada, M. Okabe, Koji Fujimura, 2016, Scientific Reports.

Evolution of the active sequences of the HpaI short interspersed elements

N. Okada, S. Murata, Y. Kido, 1995, Journal of Molecular Evolution.

SINEs as Credible Signs to Prove Common Ancestry in the Tree of Life: A Brief Review of Pioneering Case Studies in Retroposon Systematics

N. Okada, M. Nikaido, Hidenori Nishihara, 2022, Genes.

Characterization of species-specifically amplified SINEs in three salmonid species—Chum salmon, pink salmon, and kokanee: The local environment of the genome may be important for the generation of a dominant source gene at a newly retroposed locus

N. Okada, M. Kaeriyama, A. Gharrett, 1996, Journal of Molecular Evolution.

Low dependency of retrotransposition on the ORF1 protein of the zebrafish LINE, ZfL2-1.

N. Okada, Tomohiro Sugano, M. Kajikawa, 2012, Gene.

Self-Interaction, Nucleic Acid Binding, and Nucleic Acid Chaperone Activities Are Unexpectedly Retained in the Unique ORF1p of Zebrafish LINE

N. Okada, Mitsuhiro Nakamura, M. Kajikawa, 2011, Molecular and Cellular Biology.

Integrated mechanism for the generation of the 5′ junctions of LINE inserts

N. Okada, K. Yamaguchi, M. Kajikawa, 2014, Nucleic acids research.

SINEs involved in the microevolution and macroevolution of mammals

N. Okada, Hidenori Nishihara, 2013 .

Lineage-Specific Expansion of Vomeronasal Type 2 Receptor-Like (OlfC) Genes in Cichlids May Contribute to Diversification of Amino Acid Detection Systems

A. Fujiyama, A. Toyoda, T. Kocher, 2013, Genome biology and evolution.

Phylogeny of Galactolipid Synthase Homologs Together with their Enzymatic Analyses Revealed a Possible Origin and Divergence Time for Photosynthetic Membrane Biogenesis

H. Ohta, N. Okada, M. Shimojima, 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.

A new mechanism to ensure integration during LINE retrotransposition: a suggestion from analyses of the 5' extra nucleotides.

N. Okada, K. Yamaguchi, M. Kajikawa, 2012, Gene.

Intra- and Interfamily Relationships of Vespertilionidae Inferred by Various Molecular Markers Including SINE Insertion Data

M. Hasegawa, N. Okada, Liang-kong Lin, 2002, Journal of Molecular Evolution.

Bone development in the jaw of Nile tilapia Oreochromis niloticus (Pisces: Cichlidae)

N. Okada, Koji Fujimura, 2008, Development, growth & differentiation.

Protein phylogeny of translation elongation factor EF-1α suggests microsporidians are extremely ancient eukaryotes

M. Hasegawa, N. Okada, T. Hashimoto, 1996, Journal of Molecular Evolution.

Mitochondrial phylogenetics and evolution of mysticete whales.

Masami Hasegawa, Hidehiro Kato, Healy Hamilton, 2005, Systematic biology.

Pigment Pattern in jaguar/obelix Zebrafish Is Caused by a Kir7.1 Mutation: Implications for the Regulation of Melanosome Movement

Stephen L. Johnson, M. Ishii, Masakatsu Watanabe, 2006, PLoS genetics.

Molecular evidence from retroposons that whales form a clade within even-toed ungulates

N. Okada, H. Kato, K. Ohshima, 1997, Nature.

Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins

M. Hasegawa, N. Okada, R. Brownell, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals

N. Okada, O. Piskurek, 2007, Proceedings of the National Academy of Sciences.

Phylogenetic analysis of diprotodontian marsupials based on complete mitochondrial genomes.

M. Hasegawa, N. Okada, S. Donnellan, 2006, Genes & genetic systems.

Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs.

N. Okada, S. Kojima, K. Ohshima, 1993, Proceedings of the National Academy of Sciences of the United States of America.

Close phylogenetic relationship between vestimentifera (tube worms) and annelida revealed by the amino acid sequence of elongation factor-lα

M. Hasegawa, N. Okada, T. Hashimoto, 1993, Journal of Molecular Evolution.

B Chromosomes Have a Functional Effect on Female Sex Determination in Lake Victoria Cichlid Fishes

Masakatsu Watanabe, Y. Matsuda, N. Okada, 2011, PLoS genetics.

A SINE that acquired a role in signal transduction during evolution.

N. Okada, K. Ohshima, M. Nikaido, 1998, Molecular biology and evolution.

Retropositional parasitism of SINEs on LINEs: identification of SINEs and LINEs in elasmobranchs.

N Okada, M. Miya, N. Okada, 1999, Molecular biology and evolution.

Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2

Gota Kawai, Takayuki Imai, Masaki Kajikawa, 2006, Nucleic acids research.

Patterns of genomic differentiation between two Lake Victoria cichlid species, Haplochromis pyrrhocephalus and H. sp. ‘macula’

N. Okada, S. Takuno, A. Sato, 2019, BMC Evolutionary Biology.

Determining the Position of Storks on the Phylogenetic Tree of Waterbirds by Retroposon Insertion Analysis

N. Okada, Hidenori Nishihara, M. Watanabe, 2015, Genome biology and evolution.

The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis.

N. Okada, O. Piskurek, Hidenori Nishihara, 2009, Gene.

Genomic alterations upon integration of zebrafish L1 elements revealed by the TANT method.

N. Okada, K. Ichiyanagi, 2006, Gene.

Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions.

M. Hasegawa, N. Okada, Hidenori Nishihara, 2006, Proceedings of the National Academy of Sciences of the United States of America.

The rise and fall of the CR1 subfamily in the lineage leading to penguins.

H. Inoko, D. Mindell, N. Okada, 2006, Gene.

Retroposons: genetic footprints on the evolutionary paths of life.

N. Okada, Hidenori Nishihara, 2008, Methods in molecular biology.

MyrSINEs: a novel SINE family in the anteater genomes.

N. Okada, M. Nikaido, Hidenori Nishihara, 2007, Gene.

A retroposon analysis of Afrotherian phylogeny.

J. Thewissen, M. Stanhope, N. Okada, 2005, Molecular biology and evolution.

Ancient SINEs from African endemic mammals.

N. Okada, M. Nikaido, Hidenori Nishihara, 2003, Molecular biology and evolution.

Towards resolving the interordinal relationships of placental mammals.

P. Waddell, M. Hasegawa, N. Okada, 1999, Systematic biology.

Functional noncoding sequences derived from SINEs in the mammalian genome.

A. Smit, N. Okada, Hidenori Nishihara, 2006, Genome research.

Intron retention as a new pre-symptomatic marker of aging and its recovery to the normal state by a traditional Japanese multi-herbal medicine.

A. Nishi, Masahiro Yamamoto, Y. Iwasaki, 2021, Gene.

Intron retention as a new pre-symptomatic marker of aging and its recovery to the normal state by a traditional Japanese multi-herbal medicine

A. Nishi, Masahiro Yamamoto, Y. Iwasaki, 2020, bioRxiv.

herbal medicine 2 3 Running title : Recovery of alternative splicing from the senescence to healthy type by 4 an herbal medicine 5 6 7

A. Nishi, Masahiro Yamamoto, Y. Iwasaki, 2020 .

Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates

Yoshiyuki Sakaki, Takashi Gojobori, Masahira Hattori, 2003, Genome Biology.

V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit.

M. Miya, N. Okada, K. Ohshima, 2002, Genome research.

The 3' ends of tRNA-derived short interspersed repetitive elements are derived from the 3' ends of long interspersed repetitive elements

N. Okada, K. Ohshima, Y. Terai, 1996, Molecular and cellular biology.

Unique mammalian tRNA-derived repetitive elements in dermopterans: the t-SINE family and its retrotransposition through multiple sources.

N. Okada, M. Baba, Boeadi, 2003, Molecular biology and evolution.

In Vitro Screening for Compounds That Enhance Human L1 Mobilization

H. Kazazian, N. Okada, J. Goodier, 2013, PloS one.

Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla.

M. Hasegawa, N. Okada, Ying Cao, 2003, Molecular phylogenetics and evolution.

Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data.

M. Hasegawa, N. Okada, Ying Cao, 2000, Gene.

Sensory drive speciation and patterns of variation at selectively neutral genes

N. Okada, H. Tachida, Y. Terai, 2014, Evolutionary Ecology.

Sauria SINEs: Novel Short Interspersed Retroposable Elements That Are Widespread in Reptile Genomes

N. Okada, C. Austin, O. Piskurek, 2006, Journal of Molecular Evolution.

Possible involvement of SINEs in mammalian-specific brain formation

N. Saitou, T. Shimogori, Mikiko Tanaka, 2008, Proceedings of the National Academy of Sciences.

Determination of the entire sequence of turtle CR1: the first open reading frame of the turtle CR1 element encodes a protein with a novel zinc finger motif.

N. Okada, K. Ohshima, M. Kajikawa, 1997, Molecular biology and evolution.

Distinct functions of two olfactory marker protein genes derived from teleost-specific whole genome duplication

N. Okada, K. Hagino-Yamagishi, M. Nikaido, 2015, BMC Evolutionary Biology.

SINEs and LINEs: symbionts of eukaryotic genomes with a common tail

N. Okada, K. Ohshima, Norihiro Okada, 2005, Cytogenetic and Genome Research.

Relationship among coelacanths, lungfishes, and tetrapods: A phylogenetic analysis based on mitochondrial cytochrome oxidase I gene sequences

M. Hasegawa, N. Okada, S. Yokobori, 1994, Journal of Molecular Evolution.

Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes.

M. Kanehisa, M. Hirakawa, N. Okada, 2009, Gene.

Isolation and characterization of retrotransposition-competent LINEs from zebrafish.

N. Okada, Tomohiro Sugano, M. Kajikawa, 2006, Gene.

Extensive morphological convergence and rapid radiation in the evolutionary history of the family Geoemydidae (old world pond turtles) revealed by SINE insertion analysis.

N. Okada, A. Shedlock, Takeshi Sasaki, 2006, Systematic biology.

SINE cousins: the 3'-end tails of the two oldest and distantly related families of SINEs are descended from the 3' ends of LINEs with the same genealogical origin.

N. Okada, K. Takahashi, Y. Terai, 1998, Molecular biology and evolution.

SINEs and LINEs share common 3' sequences: a review.

N. Okada, K. Ohshima, I. Ogiwara, 1997, Gene.

Isolation and characterization of active LINE and SINEs from the eel.

N. Okada, K. Ichiyanagi, Nozomu Tanaka, 2005, Molecular biology and evolution.

LINEs Mobilize SINEs in the Eel through a Shared 3′ Sequence

N. Okada, M. Kajikawa, 2002, Cell.

Characterization of a novel SINE superfamily from invertebrates: "Ceph-SINEs" from the genomes of squids and cuttlefish.

N. Okada, K. Tsuchiya, S. Segawa, 2010, Gene.

Existence of a bovine LINE repetitive insert that appears in the cDNA of bovine protein BCNT in ruminant, but not in human, genomes.

K. Hashimoto, T. Masui, N. Okada, 1998, Gene.

Coordinately Co-opted Multiple Transposable Elements Constitute an Enhancer for wnt5a Expression in the Mammalian Secondary Palate

V. Tarabykin, M. Hirakawa, K. Sumiyama, 2016, PLoS genetics.

A new system for analyzing LINE retrotransposition in the chicken DT40 cell line widely used for reverse genetics.

N. Okada, H. Koyama, T. Ono, 2007, Gene.

Chronology of the extant African elephant species and case study of the species identification of the small African elephant with the molecular phylogenetic method.

M. Hasegawa, N. Okada, Takahiro Yonezawa, 2009, Gene.

Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths.

Taro L. Saito, S. Sugano, Yutaka Suzuki, 2012, Gene.

Retroposon mapping in molecular systematics.

N. Okada, A. Shedlock, M. Nikaido, 2004, Methods in molecular biology.

SINE evolution, missing data, and the origin of whales.

N Okada, M. Milinkovitch, N. Okada, 2000, Systematic biology.

LINE retrotransposition and host DNA repair machinery

N. Okada, K. Yamaguchi, M. Kajikawa, 2015, Mobile genetic elements.

Mechanism by which a LINE protein recognizes its 3′ tail RNA

N. Okada, Takuma Matsumoto, M. Kajikawa, 2014, Nucleic acids research.

Retroposons of salmonoid fishes (Actinopterygii: Salmonoidei) and their evolution.

N. Okada, Vitaliy Matveev, 2009, Gene.

Mobility pathways for vertebrate L1, L2, CR1, and RTE clade retrotransposons.

N. Okada, K. Ichiyanagi, 2008, Molecular biology and evolution.

Novel SINE families from salmons validate Parahucho (Salmonidae) as a distinct genus and give evidence that SINEs can incorporate LINE-related 3'-tails of other SINEs.

N. Okada, Hidenori Nishihara, Vitaliy Matveev, 2007, Molecular biology and evolution.

Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts.

N. Okada, K. Ichiyanagi, M. Kajikawa, 2006, Genome research.

Afrotherian phylogeny as inferred from complete mitochondrial genomes.

M. Hasegawa, N. Okada, Ying Cao, 2003, Molecular phylogenetics and evolution.

The evolution of genes for pigmentation in African cichlid fishes.

N. Okada, Y. Terai, A. Sugie, 2004, Gene.

Visual adaptation in Lake Victoria cichlid fishes: depth-related variation of color and scotopic opsins in species from sand/mud bottoms

N. Okada, A. Sato, Y. Terai, 2017, BMC Evolutionary Biology.

Coelacanth genomes reveal signatures for evolutionary transition from water to land

T. Itoh, S. Sugano, Yutaka Suzuki, 2010, Genome research.

Newly discovered young CORE-SINEs in marsupial genomes.

N. Okada, S. Donnellan, C. Austin, 2008, Gene.

Genomic expansion of the Bov-A2 retroposon relating to phylogeny and breed management

N. Okada, M. Nikaido, H. Mannen, 2007, Mammalian Genome.

Toothed whale monophyly reassessed by SINE insertion analysis: the absence of lineage sorting effects suggests a small population of a common ancestral species.

N. Okada, O. Piskurek, M. Nikaido, 2007, Molecular phylogenetics and evolution.

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Baleen whale phylogeny and a past extensive radiation event revealed by SINE insertion analysis.

N. Okada, H. Hamilton, L. Pastene, 2006, Molecular biology and evolution.

Using SINEs to probe ancient explosive speciation: "hidden" radiation of African cichlids?

M. Nishida, N. Okada, Y. Terai, 2003, Molecular biology and evolution.

Characterization of novel Alu- and tRNA-related SINEs from the tree shrew and evolutionary implications of their origins.

N. Okada, Y. Terai, Hidenori Nishihara, 2002, Molecular biology and evolution.

Mosaic structure and retropositional dynamics during evolution of subfamilies of short interspersed elements in African cichlids.

N. Okada, Kazuhiko Takahashi, 2002, Molecular biology and evolution.

Evolution of CHR-2 SINEs in cetartiodactyl genomes: possible evidence for the monophyletic origin of toothed whales

Hideaki Abe, Healy Hamilton, N. Okada, 2001, Mammalian Genome.

Retroposition of the AFC Family of SINEs (Short Interspersed Repetitive Elements) Before and During the Adaptive Radiation of Cichlid Fishes in Lake Malawi and Related Inferences About Phylogeny

M. Nishida, N. Okada, M. Yuma, 2001, Journal of Molecular Evolution.

CetSINEs and AREs are not SINEs but are parts of cetartiodactyl L1

N. Okada, M. Nikaido, 2000, Mammalian Genome.

Monophyletic Origin of the Order Chiroptera and Its Phylogenetic Position Among Mammalia, as Inferred from the Complete Sequence of the Mitochondrial DNA of a Japanese Megabat, the Ryukyu Flying Fox (Pteropus dasymallus)

Masami Hasegawa, Masashi Harada, M. Hasegawa, 2000, Journal of Molecular Evolution.

Consistency of SINE insertion topology and flanking sequence tree: quantifying relationships among cetartiodactyls.

Hidetoshi Shimodaira, M. Hasegawa, N. Okada, 2000, Molecular biology and evolution.

Genealogy of families of SINEs in cetaceans and artiodactyls: the presence of a huge superfamily of tRNA(Glu)-derived families of SINEs.

N. Okada, K. Ohshima, H. Abe, 1999, Molecular biology and evolution.

Detection of the ongoing sorting of ancestrally polymorphic SINEs toward fixation or loss in populations of two species of charr during speciation.

N. Okada, J. Reist, M. Hamada, 1998, Genetics.

A novel family of short interspersed repetitive elements (SINEs) from cichlids: the patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fishes in Lake Tanganyika.

M. Nishida, N. Okada, K. Takahashi, 1998, Molecular biology and evolution.

The salmon SmaI family of short interspersed repetitive elements (SINEs): interspecific and intraspecific variation of the insertion of SINEs in the genomes of chum and pink salmon.

N. Okada, L. Park, M. Hamada, 1997, Genetics.

A newly isolated family of short interspersed repetitive elements (SINEs) in coregonid fishes (whitefish) with sequences that are almost identical to those of the SmaI family of repeats: possible evidence for the horizontal transfer of SINEs.

M. Hasegawa, N. Okada, J. Reist, 1997, Genetics.

Generality of the tRNA origin of short interspersed repetitive elements (SINEs). Characterization of three different tRNA-derived retroposons in the octopus.

N. Okada, K. Ohshima, 1994, Journal of molecular biology.

Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids.

N. Okada, S. Murata, L. Park, 1994, Proceedings of the National Academy of Sciences of the United States of America.

Amplification of distinct subfamilies of short interspersed elements during evolution of the Salmonidae.

N. Okada, M. Himberg, N. Takasaki, 1994, Journal of molecular biology.

A novel tRNA species as an origin of short interspersed repetitive elements (SINEs). Equine SINEs may have originated from tRNA(Ser).

N. Okada, K. Ohshima, H. Yasue, 1994, Journal of molecular biology.

Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution.

N. Okada, S. Murata, N. Takasaki, 1993, Proceedings of the National Academy of Sciences of the United States of America.

Several short interspersed repetitive elements (SINEs) in distant species may have originated from a common ancestral retrovirus: characterization of a squid SINE and a possible mechanism for generation of tRNA-derived retroposons.

N. Okada, K. Ohshima, R. Koishi, 1993, Proceedings of the National Academy of Sciences of the United States of America.

Shaping and reshaping of salmonid genomes by amplification of tRNA-derived retroposons during evolution.

K. Matsumoto, N. Okada, S. Murata, 1991, Proceedings of the National Academy of Sciences of the United States of America.

The phylogenetic relationships of insectivores with special reference to the lesser hedgehog tenrec as inferred from the complete sequence of their mitochondrial genome.

M. Hasegawa, N. Okada, Ying Cao, 2003, Genes & genetic systems.

MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals

N. Okada, Federico Plazzi, M. Passamonti, 2016, Genome biology and evolution.

Probing the secondary structure of salmon SmaI SINE RNA.

N. Okada, N. Nameki, Hiroko Kawagoe-Takaki, 2006, Gene.

Functional splice sites in a zebrafish LINE and their influence on zebrafish gene expression.

N. Okada, M. Kajikawa, Masato Tamura, 2007, Gene.

Integrated mechanism for the generation of the 5′ junctions of LINE inserts

N. Okada, K. Yamaguchi, M. Kajikawa, 2014, Nucleic acids research.

Details of retropositional genome dynamics that provide a rationale for a generic division: the distinct branching of all the pacific salmon and trout (Oncorhynchus) from the Atlantic salmon and trout (Salmo).

N. Okada, S. Murata, H. Tachida, 1996, Genetics.

Emergence of mammals by emergency: exaptation

Tomomi Shimogori, T. Shimogori, N. Okada, 2010, Genes to cells : devoted to molecular & cellular mechanisms.

Maximum Likelihood Analysis of the Complete Mitochondrial Genomes of Eutherians and a Reevaluation of the Phylogeny of Bats and Insectivores

Masami Hasegawa, Masashi Harada, Satoru Tomita, 2001, Journal of Molecular Evolution.

cimp1, a novel astacin family metalloproteinase gene from East African cichlids, is differentially expressed between species during growth.

Y. Kohara, T. Gojobori, Masakatsu Watanabe, 2005, Molecular biology and evolution.

Development of the embryo, larva and early juvenile of Nile tilapia Oreochromis niloticus (Pisces: Cichlidae). Developmental staging system

N. Okada, Koji Fujimura, 2007, Development, growth & differentiation.

Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish

N. Okada, G. Kawai, M. Otsu, 2017, Journal of Biochemistry (Tokyo).

Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2.

N. Okada, G. Kawai, S. Baba, 2004, RNA.

Balaenoptera omurai is a newly discovered baleen whale that represents an ancient evolutionary lineage.

Masami Hasegawa, Shiro Wada, M. Hasegawa, 2006, Molecular phylogenetics and evolution.

The status of the Japanese and East Asian bats of the genus Myotis (Vespertilionidae) based on mitochondrial sequences.

M. Hasegawa, N. Okada, Liang-kong Lin, 2003, Molecular phylogenetics and evolution.

Spot pattern of Leopard Danio is caused by the mutation in zebrafish connexin 41 . 8 gene

M. Ishii, Masakatsu Watanabe, N. Okada, 2006 .

Population structure of two closely related pelagic cichlids in Lake Victoria, Haplochromis pyrrhocephalus and H. laparogramma.

M. Nishida, N. Okada, H. Tachida, 2009, Gene.

Shaping of the lower jaw bone during growth of Nile tilapia Oreochromis niloticus and a Lake Victoria cichlid Haplochromis chilotes: A geometric morphometric approach

N. Okada, Koji Fujimura, 2008, Development, growth & differentiation.

Characterization of V1R receptor (ora) genes in Lake Victoria cichlids.

N. Okada, K. Hagino-Yamagishi, M. Nikaido, 2012, Gene.

Phylogenetic position of guinea pigs revisited.

N Okada, M. Hasegawa, N. Okada, 1997, Molecular biology and evolution.

Genomic Signatures for Species-Specific Adaptation in Lake Victoria Cichlids Derived from Large-Scale Standing Genetic Variation

T. Itoh, A. Toyoda, N. Okada, 2021, Molecular biology and evolution.

Multiple Episodic Evolution Events in V1R Receptor Genes of East-African Cichlids

N. Okada, Y. Satta, K. Hagino-Yamagishi, 2014, Genome biology and evolution.

Speciation through sensory drive in cichlid fish

M. Schneider, N. Okada, O. Seehausen, 2008, Nature.

High prevalence of non-synonymous substitutions in mtDNA of cichlid fishes from Lake Victoria.

N. Okada, H. Tachida, Y. Terai, 2014, Gene.

Heterotypy in the N-terminal region of growth/differentiation factor 5 (GDF5) mature protein during teleost evolution.

M. Miya, M. Nishida, N. Okada, 2008, Molecular biology and evolution.

Molecular evidence from short interspersed elements (SINEs) that Oncorhynchus masou (cherry salmon) is monophyletic

N. Okada, S. Murata, Takanori Kobayashi, 1998 .

Genetic variation and demographic history of the Haplochromis laparogramma group of Lake Victoria-An analysis based on SINEs and mitochondrial DNA.

N. Okada, O. Seehausen, H. Tachida, 2010, Gene.

Parallelism of amino acid changes at the RH1 affecting spectral sensitivity among deep-water cichlids from Lakes Tanganyika and Malawi.

G. Turner, N. Okada, T. Sugawara, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens

T. Abe, T. Gojobori, S. Tamaki, 2020, PLoS genetics.

Mitogenomic analysis for coelacanths (Latimeria chalumnae) caught in Tanzania.

N. Okada, B. Ngatunga, Tetsu Sato, 2007, Gene.

Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications.

M. Hasegawa, N. Okada, K. Tsuchiya, 2006, Molecular phylogenetics and evolution.

Genetic Evidence That the Non-Homologous End-Joining Repair Pathway Is Involved in LINE Retrotransposition

N. Okada, H. Koyama, N. Adachi, 2009, PLoS genetics.

Vertebrate rhodopsin adaptation to dim light via rapid meta-II intermediate formation.

N. Okada, T. Sugawara, H. Imai, 2010, Molecular biology and evolution.

Evolutionary Changes in Vertebrate Genome Signatures with Special Focus on Coelacanth

T. Abe, T. Ikemura, K. Wada, 2014, DNA research : an international journal for rapid publication of reports on genes and genomes.

magp4 gene may contribute to the diversification of cichlid morphs and their speciation.

Y. Kohara, T. Gojobori, K. Ikeo, 2006, Gene.

The complexity of alternative splicing of hagoromo mRNAs is increased in an explosively speciated lineage in East African cichlids

K. Kawakami, N. Okada, Y. Terai, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Molecular phylogenetic study on the origin and evolution of Mustelidae.

M. Hasegawa, N. Okada, Takahiro Yonezawa, 2007, Gene.

New candidate species most closely related to penguins.

Masami Hasegawa, Maiko Watanabe, M. Hasegawa, 2006, Gene.

Combining Multiple Datasets in a Likelihood Analysis: Which Models Are Best?

Tal Pupko, Masami Hasegawa, Dorothée Huchon, 2022 .

Evolution of Shh endoderm enhancers during morphological transition from ventral lungs to dorsal gas bladder

H. Kiyonari, N. Okada, K. Naruse, 2017, Nature Communications.

Molecularevidence from retroposonsthatwhales formacladewithin even-toedungulates

N. Okada, H. Kato, K. Ohshima, 2022 .

Reverse evolution in RH1 for adaptation of cichlids to water depth in Lake Tanganyika.

N. Okada, T. Sugawara, Y. Terai, 2011, Molecular biology and evolution.

Genetic Structure of Pelagic and Littoral Cichlid Fishes from Lake Victoria

N. Okada, H. Tachida, Y. Terai, 2013, PloS one.

Speciation of Cichlid Fishes by Sensory Drive

N. Okada, Y. Terai, 2011 .

Functional diversification of kir7.1 in cichlids accelerated by gene duplication.

Masakatsu Watanabe, N. Okada, Kazue Hiraide, 2007, Gene.

Divergent Selection on Opsins Drives Incipient Speciation in Lake Victoria Cichlids

Masakatsu Watanabe, N. Okada, O. Seehausen, 2006, PLoS biology.

Accelerated evolution of the surface amino acids in the WD-repeat domain encoded by the hagoromo gene in an explosively speciated lineage of East African cichlid fishes.

K. Kawakami, N. Okada, Y. Terai, 2002, Molecular biology and evolution.

Allometric growth of the trunk leads to the rostral shift of the pelvic fin in teleost fishes.

Y. Aita, Mikiko Tanaka, N. Okada, 2010, Developmental biology.

The complete mitochondrial DNA sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates.

P. Waddell, M. Hasegawa, N. Okada, 1998, Molecular biology and evolution.

Extensive analysis of EST sequences reveals that all cichlid species in Lake Victoria share almost identical transcript sets.

Y. Kohara, Masakatsu Watanabe, N. Okada, 2009, Gene.

Extensive analysis of ORF sequences from two different cichlid species in Lake Victoria provides molecular evidence for a recent radiation event of the Victoria species flock: identity of EST sequences between Haplochromis chilotes and Haplochromis sp. "Redtailsheller".

Y. Kohara, Y. Tateno, Masakatsu Watanabe, 2004, Gene.

Correlation between nuptial colors and visual sensitivities tuned by opsins leads to species richness in sympatric Lake Victoria cichlid fishes.

N. Okada, H. Tachida, T. Sugawara, 2012, Molecular biology and evolution.

PERMANENT GENETIC RESOURCES: Isolation and characterization of microsatellite loci in the cichlid fish in Lake Victoria, Haplochromis chilotes

M. Nishida, N. Okada, H. Takeshima, 2008, Molecular ecology resources.

A SINE-Derived Element Constitutes a Unique Modular Enhancer for Mammalian Diencephalic Fgf8

T. Shimogori, M. Hirakawa, K. Sumiyama, 2012, PloS one.

Special issue on phylogenomics and its future.

N. Okada, 2009, Gene.

A model for the mechanism of initial generation of short interspersed elements (SINEs)

N. Okada, K. Ohshima, 1993, Journal of Molecular Evolution.

A unique neurogenomic state emerges after aggressive confrontations in males of the fish Betta splendens.

Y. Iwasaki, N. Okada, K. Oshima, 2021, Gene.

A unique neurogenomic state emerges after aggressive confrontations in males of the fish Betta splendens

Y. Iwasaki, N. Okada, K. Oshima, 2020, bioRxiv.

Novel sex pheromone desaturases in the genomes of corn borers generated through gene duplication and retroposon fusion

N. Okada, A. Rooney, W. Roelofs, 2007, Proceedings of the National Academy of Sciences.

The Origin of Chlorarachniophyte Plastids, as Inferred from Phylogenetic Comparisons of Amino Acid Sequences of EF-Tu

M. Hasegawa, N. Okada, Ying Cao, 1997, Journal of Molecular Evolution.

Laterality is Universal Among Fishes but Increasingly Cryptic Among Derived Groups

Masaki Yasugi, N. Okada, Mifuyu Nakajima, 2017, Zoological Science.

Simple and complex SINEs: A brief critical comment.

N. Okada, O. Piskurek, 2006, Gene.

Conserved repertoire of orthologous vomeronasal type 1 receptor genes in ruminant species

K. Mogi, N. Okada, H. Okamura, 2009, BMC Evolutionary Biology.

Sensory drive speciation and patterns of variation at selectively neutral genes

N. Okada, H. Tachida, Y. Terai, 2014, Evolutionary Ecology.

SINEs: Short interspersed repeated elements of the eukaryotic genome.

N. Okada, N. Okada, 1991, Trends in ecology & evolution.

Patterns of genomic differentiation between two Lake Victoria cichlid species, Haplochromis pyrrhocephalus and H. sp. ‘macula’

N. Okada, A. Sato, Y. Terai, 2019, BMC Evolutionary Biology.

Data of RNA-seq transcriptomes in the brain associated with aggression in males of the fish Betta splendens

Y. Iwasaki, N. Okada, K. Oshima, 2021, Data in brief.

Identification of four Engrailed genes in the Japanese lamprey, Lethenteron japonicum

Mikiko Tanaka, N. Okada, S. Kuratani, 2008, Developmental dynamics : an official publication of the American Association of Anatomists.