Rooting the eutherian tree: the power and pitfalls of phylogenomics (2007)
Nishihara, Hidenori, Okada, Norihiro, Hasegawa, Masami
Abstract Background Ongoing genome sequencing projects have led to a phylogenetic approach based on genome-scale data (phylogenomics), which is beginning to shed light on longstanding unresolved...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
An international team has systematically validated and annotated just over 21,000 human genes using full-length cDNA, thereby providing a valuable new resource for the human genetics community.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
Abstract Background Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian...
Combining Multiple Datasets in a Likelihood Analysis: Which Models are Best? (2002)
Tal Pupko, Dorothe Huchon, Ying Cao, Norihiro Okada, Masami Hasegawa
Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single gene. Given the vast number of gene sequences now available, phylogenetic studies are now based on...
Nikaido, Masato, Rooney, Alejandro P., Okada, Norihiro
Insertion analysis of short and long interspersed elements is a powerful method for phylogenetic inference. In a previous study of short interspersed element data, it was found that cetaceans,...
Nikaido, Masato, Matsuno, Fumio, Hamilton, Healy, Brownell, Robert L., Cao, Ying, Ding, Wang, ...
SINE (short interspersed element) insertion analysis elucidates contentious aspects in the phylogeny of toothed whales and dolphins (Odontoceti), especially river dolphins. Here, we characterize 25...
Terai, Yohey, Mayer, Werner E., Klein, Jan, Tichy, Herbert, Okada, Norihiro
In East African Lake Victoria >200 endemic species of haplochromine fishes have been described on the basis of morphological and behavioral differences. Yet molecular analysis has failed to reveal...
Terai, Yohey, Morikawa, Naoko, Kawakami, Koichi, Okada, Norihiro
The adaptive radiation of cichlid fishes in the lakes of East Africa is a prime example of speciation. The choice of cichlid mates on the basis of a variety of coloration represents a potential basis...
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
The first comprehensive analysis of human processed pseudogenes (PPs) using all known human genes as queries is presented. The data suggest a nearly simultaneous burst of PP and Alu formation in the...
Okada, Norihiro, Nishimura, Susumu
The Q* nucleosides isolated from rabbit liver tRNA are known to have sugars (mannose or galactose) linked to their cyclopentene diol moiety. A Q* nucleoside containing mannose (manQ) was synthesized...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Segawa, Takahiro, Miyamoto, Koji, Ushida, Kazunari, Agata, Kiyokazu, Okada, Norihiro, Kohshima, Shiro
The bacterial flora and biomass in mountain snow from the Tateyama Mountains, Toyama Prefecture, Japan, one of the heaviest snowfall regions in the world, were analyzed by amplified ribosomal DNA...
Sugawara, Tohru, Terai, Yohey, Imai, Hiroo, Turner, George F., Koblmüller, Stephan, Sturmbauer, Christian, ...
Many examples of the appearance of similar traits in different lineages are known during the evolution of organisms. However, the underlying genetic mechanisms have been elucidated in very few cases....
Solution structure of an RNA stem–loop derived from the 3′ conserved region of eel LINE UnaL2
BABA, SEIKI, KAJIKAWA, MASAKI, OKADA, NORIHIRO, KAWAI, GOTA
The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3′ tail containing a stem–loop that is critical for their retrotransposition....
Ogiwara, Ikuo, Miya, Masaki, Ohshima, Kazuhiko, Okada, Norihiro
We have identified a new superfamily of vertebrate short interspersed repetitive elements (SINEs), designated V-SINEs, that are widespread in fishes and frogs. Each V-SINE includes a central...
Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2
Nomura, Yusuke, Kajikawa, Masaki, Baba, Seiki, Nakazato, Shinta, Imai, Takayuki, Sakamoto, Taiichi, ...
The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3′ tail that is critical for their retrotransposition. The predicted secondary...
Iwashita, Motoko, Watanabe, Masakatsu, Ishii, Masaru, Chen, Tim, Johnson, Stephen L, Kurachi, Yoshihisa, ...
Many animals have a variety of pigment patterns, even within a species, and these patterns may be one of the driving forces of speciation. Recent molecular genetic studies on zebrafish have revealed...
Nikaido, Masato, Rooney, Alejandro P., Okada, Norihiro
Insertion analysis of short and long interspersed elements is a powerful method for phylogenetic inference. In a previous study of short interspersed element data, it was found that cetaceans,...
Nikaido, Masato, Matsuno, Fumio, Hamilton, Healy, Brownell, Robert L., Cao, Ying, Ding, Wang, ...
SINE (short interspersed element) insertion analysis elucidates contentious aspects in the phylogeny of toothed whales and dolphins (Odontoceti), especially river dolphins. Here, we characterize 25...
Terai, Yohey, Mayer, Werner E., Klein, Jan, Tichy, Herbert, Okada, Norihiro
In East African Lake Victoria >200 endemic species of haplochromine fishes have been described on the basis of morphological and behavioral differences. Yet molecular analysis has failed to reveal...
Ogiwara, Ikuo, Miya, Masaki, Ohshima, Kazuhiko, Okada, Norihiro
We have identified a new superfamily of vertebrate short interspersed repetitive elements (SINEs), designated V-SINEs, that are widespread in fishes and frogs. Each V-SINE includes a central...
Terai, Yohey, Morikawa, Naoko, Kawakami, Koichi, Okada, Norihiro
The adaptive radiation of cichlid fishes in the lakes of East Africa is a prime example of speciation. The choice of cichlid mates on the basis of a variety of coloration represents a potential basis...
Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
The first comprehensive analysis of human processed pseudogenes (PPs) using all known human genes as queries is presented. The data suggest a nearly simultaneous burst of PP and Alu formation in the...
Okada, Norihiro, Nishimura, Susumu
The Q* nucleosides isolated from rabbit liver tRNA are known to have sugars (mannose or galactose) linked to their cyclopentene diol moiety. A Q* nucleoside containing mannose (manQ) was synthesized...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Segawa, Takahiro, Miyamoto, Koji, Ushida, Kazunari, Agata, Kiyokazu, Okada, Norihiro, Kohshima, Shiro
The bacterial flora and biomass in mountain snow from the Tateyama Mountains, Toyama Prefecture, Japan, one of the heaviest snowfall regions in the world, were analyzed by amplified ribosomal DNA...
Sugawara, Tohru, Terai, Yohey, Imai, Hiroo, Turner, George F., Koblmüller, Stephan, Sturmbauer, Christian, ...
Many examples of the appearance of similar traits in different lineages are known during the evolution of organisms. However, the underlying genetic mechanisms have been elucidated in very few cases....
Solution structure of an RNA stem–loop derived from the 3′ conserved region of eel LINE UnaL2
BABA, SEIKI, KAJIKAWA, MASAKI, OKADA, NORIHIRO, KAWAI, GOTA
The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3′ tail containing a stem–loop that is critical for their retrotransposition....
Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2
Nomura, Yusuke, Kajikawa, Masaki, Baba, Seiki, Nakazato, Shinta, Imai, Takayuki, Sakamoto, Taiichi, ...
The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3′ tail that is critical for their retrotransposition. The predicted secondary...
Iwashita, Motoko, Watanabe, Masakatsu, Ishii, Masaru, Chen, Tim, Johnson, Stephen L, Kurachi, Yoshihisa, ...
Many animals have a variety of pigment patterns, even within a species, and these patterns may be one of the driving forces of speciation. Recent molecular genetic studies on zebrafish have revealed...
Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions
Nishihara, Hidenori, Hasegawa, Masami, Okada, Norihiro
Despite the recent large-scale efforts dedicated to comprehensive phylogenetic analyses using mitochondrial and nuclear DNA sequences, several relationships among mammalian orders remain...
Functional noncoding sequences derived from SINEs in the mammalian genome
Nishihara, Hidenori, Smit, Arian F.A., Okada, Norihiro
Recent comparative analyses of mammalian sequences have revealed that a large number of nonprotein-coding genomic regions are under strong selective constraint. Here, we report that some of these...
Divergent Selection on Opsins Drives Incipient Speciation in Lake Victoria Cichlids
Terai, Yohey, Seehausen, Ole, Sasaki, Takeshi, Takahashi, Kazuhiko, Mizoiri, Shinji, Sugawara, Tohru, ...
Divergent natural selection acting on ecological traits, which also affect mate choice, is a key element of ecological speciation theory, but has not previously been demonstrated at the molecular...
Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts
Ichiyanagi, Kenji, Nakajima, Ryo, Kajikawa, Masaki, Okada, Norihiro
Autonomous non-long-terminal-repeat retrotransposons (NLRs) proliferate by retrotransposition via coordinated reactions of target DNA cleavage and reverse transcription by a mechanism called...
Spot pattern of leopard Danio is caused by mutation in the zebrafish connexin41.8 gene
Watanabe, Masakatsu, Iwashita, Motoko, Ishii, Masaru, Kurachi, Yoshihisa, Kawakami, Atsushi, Kondo, Shigeru, ...
Leopard, a well-known zebrafish mutant that has a spotted skin pattern instead of stripes, is a model for the study of pigment patterning. To understand the mechanisms underlying stripe formation, as...
Xue, Bingye, Rooney, Alejandro P., Kajikawa, Masaki, Okada, Norihiro, Roelofs, Wendell L.
The biosynthesis of female moth sex pheromone blends is controlled by a number of different enzymes, many of which are encoded by members of multigene families. One such multigene family, the...
Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals
Piskurek, Oliver, Okada, Norihiro
Poxviruses (Poxviridae) are a family of double-stranded DNA viruses with no RNA stage. Members of the genus Orthopoxvirus (OPV) are highly invasive and virulent. It was recently shown that the...
A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids
Babushok, Daria V., Ohshima, Kazuhiko, Ostertag, Eric M., Chen, Xinsheng, Wang, Yanfeng, Mandal, Prabhat K., ...
Most new genes arise by duplication of existing gene structures, after which relaxed selection on the new copy frequently leads to mutational inactivation of the duplicate; only rarely will a new...
Rooting the eutherian tree: the power and pitfalls of phylogenomics
Nishihara, Hidenori, Okada, Norihiro, Hasegawa, Masami
In an attempt to root the eutherian tree using genome-scale data with the maximum likelihood method, a concatenate analysis supports a putatively wrong tree, whereas separate analyses of different...