Identification of genes expressed in the hermaphrodite germ line of C. elegansusing SAGE (2009)
Wang, Xin, Zhao, Yongjun, Wong, Kim, Ehlers, Peter, Kohara, Yuji, Jones, Steven J, ...
Abstract Background Germ cells must progress through elaborate developmental stages from an undifferentiated germ cell to a fully differentiated gamete. Some of these stages include exiting mitosis...
Sato, Kazuhiro, Shin-I, Tadasu, Seki, Motoaki, Shinozaki, Kazuo, Yoshida, Hideya, Takeda, Kazuyoshi, ...
A collection of 5006 full-length (FL) cDNA sequences was developed in barley. Fifteen mRNA samples from various organs and treatments were pooled to develop a cDNA library using the CAP trapper...
The amphioxus genome and the evolution of the chordate karyotype (2008)
Putnam, Nicholas H., Butts, Thomas, Ferrier, David E. K., Furlong, Rebecca F., Hellsten, Uffe, Kawashima, Takeshi, ...
Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly...
UTGB/medaka: genomic resource database for medaka biology (2008)
Ahsan, Budrul, Kobayashi, Daisuke, Yamada, Tomoyuki, Kasahara, Masahiro, Sasaki, Shin, Saito, Taro L., ...
Medaka (Oryzias latipes) is a small egg-laying freshwater teleost native to East Asia that has become an excellent model system for developmental genetics and evolutionary biology. The draft medaka...
NEXTDB: The Expression Pattern Map Database for (2007)
C. Elegans, Tadasu Shin-i, Yuji Kohara
The nematode Caenorhabditis elegans (C. elegans) is a good model system to study functional genomics with respect to animal development, nervous system and behavior at the level of single cells....
NEXTDB: The Expression Pattern Map Database for (2007)
C Elegans, Tadasu Shin-i, Yuji Kohara
The nematode Caenorhabditis elegans (C. elegans) is a good model system to study functional genomics with respect to animal development, nervous system and behavior at the level of single cells....
Kato, Yuzuru, Kaneda, Masahiro, Hata, Kenichiro, Kumaki, Kenji, Hisano, Mizue, Kohara, Yuji, ...
DNA methylation is an important epigenetic modification regulating various biological phenomena, including genomic imprinting and transposon silencing. It is known that methylation of the...
Nakatani, Yoichiro, Takeda, Hiroyuki, Kohara, Yuji, Morishita, Shinichi
Although several vertebrate genomes have been sequenced, little is known about the genome evolution of early vertebrates and how large-scale genomic changes such as the two rounds of whole-genome...
Retrotransposon Silencing by DNA Methylation Can Drive Mammalian Genomic Imprinting (2007)
Shunsuke Suzuki, Ryuichi Ono, Takanori Narita, Andrew J. Pask, Geoffrey Shaw, Changshan Wang, ...
Among mammals, only eutherians and marsupials are viviparous and have genomic imprinting that leads to parent-of-origin-specific differential gene expression. We used comparative analysis to...
MATSUNO, Tetsuya, TOMINAGA, Nobuaki, ARIZONO, Koji, IGUCHI, Taisen, KOHARA, Yuji
Activity patterns of metabolic subnetworks, each of which can be regarded as a biological function module, were focused on in order to clarify biological meanings of observed deviation patterns of...
Lazakovitch, Elena, Kalb, John M, Matsumoto, Reiko, Hirono, Keiko, Kohara, Yuji, Gronostajski, Richard M
Abstract Background The Nuclear Factor I (one) (NFI) family of transcription/replication factors plays essential roles in mammalian gene expression and development and in adenovirus DNA replication....
Kunitomo, Hirofumi, Uesugi, Hiroko, Kohara, Yuji, Iino, Yuichi
Abstract It is not always easy to apply microarray technology to small numbers of cells because of the difficulty in selectively isolating mRNA from such cells. We report here the preparation of mRNA...
Kijimoto, Teiya, Watanabe, Masakatsu, Fujimura, Koji, Nakazawa, Masumi, Murakami, Yasunori, Kuratani, Shigeru, ...
Lake Victoria cichlid fishes are excellent examples of explosive adaptive radiation. Although Lake Victoria cichlids are believed to have arisen during a short period (∼14,000 years), they have...
Kijimoto, Teiya, Watanabe, Masakatsu, Fujimura, Koji, Nakazawa, Masumi, Murakami, Yasunori, Kuratani, Shigeru, ...
Lake Victoria cichlid fishes are excellent examples of explosive adaptive radiation. Although Lake Victoria cichlids are believed to have arisen during a short period (∼14,000 years), they have...
Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis (2005)
Shoguchi, Eiichi, Kawashima, Takeshi, Satou, Yutaka, Hamaguchi, Makoto, Sin-I, Tadasu, Kohara, Yuji, ...
The draft genome (∼160 Mb) of the urochordate ascidian Ciona intestinalis has been sequenced by the whole-genome shotgun method and should provide important insights into the origin and evolution...
Kijimoto, Teiya, Watanabe, Masakatsu, Fujimura, Koji, Nakazawa, Masumi, Murakami, Yasunori, Kuratani, Shigeru, ...
Lake Victoria cichlid fishes are excellent examples of explosive adaptive radiation. Although Lake Victoria cichlids are believed to have arisen during a short period (∼14,000 years), they have...
Minakuchi, Yohei, Ito, Masahiro, Kohara, Yuji
Motivation: A comprehensive gene expression database is essential for computer modeling and simulation of biological phenomena, including development. Development is a four-dimensional (4D; 3D...
Wakoh, Takeshi, Ikeda, Makoto, Uchino, Ryuji, Azumi, Kaoru, Nonaka, Masaru, Kohara, Yuji, ...
The immunity provided by ascidian hemocytes represents one prototype of innate immune function in vertebrates. However, there are currently no molecular markers of ascidian hemocytes. We accumulated...
Analyses of cDNAs from growth and slug stages of Dictyostelium discoideum (2004)
Urushihara, Hideko, Morio, Takahiro, Saito, Tamao, Kohara, Yuji, Koriki, Eiko, Ochiai, Hiroshi, ...
Dictyostelium is a favored model for studying problems in cell and developmental biology. To comprehend the genetic potential and networks that direct growth and multicellular development, we are...
Minakuchi, Yohei, Ito, Masahiro, Kohara, Yuji
Motivation: A comprehensive gene expression database is essential for computer modeling and simulation of biological phenomena, including development. Development is a four-dimensional (4D; 3D...
Yagi, Kasumi, Satou, Yatuka, Mazet, Francoise, Shimeld, Sebastian M., Degnan, Bernard M., Rokhsar, Daniel S., ...
A survey against the draft genome sequence and the cDNA/EST database of Ciona intestinalis identified a number of genes encoding transcription factors regulating a variety of processes including...
Yagi, Kasumi, Satou, Yatuka, Mazet, Francoise, Shimeld, Sebastian M., Degnan, Bernard M., Rokhsar, Daniel S., ...
A survey against the draft genome sequence and the cDNA/EST database of Ciona intestinalis identified a number of genes encoding transcription factors regulating a variety of processes including...
Yagi, Kasumi, Satou, Yatuka, Mazet, Francoise, Shimeld, Sebastian M., Degnan, Bernard M., Rokhsar, Daniel S., ...
A survey against the draft genome sequence and the cDNA/EST database of Ciona intestinalis identified a number of genes encoding transcription factors regulating a variety of processes including...
Ohta, Niji, Matsuzaki, Motomichi, Misumi, Osami, Miyagishima, Shin-ya, Nozaki, Hisayoshi, Tanaka, Kan, ...
The complete nucleotide sequence of the plastid genome of the unicellular primitive red alga Cyanidioschyzon merolae 10D (Cyanidiophyceae) was determined. The genome is a circular DNA composed of...
Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags (2002)
Kawashima, Takeshi, Kawashima, Shuichi, Kohara, Yuji, Kanehisa, Minoru, Makabe, Kazuhiro W.
MAGEST is a database for maternal gene expression information for an ascidian, Halocynthia roretzi. The ascidian has become an animal model in developmental biological research because it shows a...
Naito, Morihiro, Kohara, Yuji, Kurosawa, Yoshikazu
Using two primers corresponding to helix 1 and helix 3 regions in the homeodomain, we subjected genomic DNA from Caenorhabditis elegans to amplification by the polymerase chain reaction. Sequence...
Choi, Yong-Lark, Kawase, Shido, Nishida, Tohru, Sakai, Hiroshi, Komano, Tohru, Kawamukai, Makoto, ...
Kohara, Yuji, Tohdoh, Naoki, Jiang, Xiao-Wang, Okazaki, Tuneko
RNA-linked DNA molecules were obtained from E. coli dnaCts cells synchronously initiating a new round of chromosome replication. The deoxynucleotides at the transition from primer RNA to DNA were...
Mochii, Makoto, Yoshida, Satoru, Morita, Kiyokazu, Kohara, Yuji, Ueno, Naoto
Members of the transforming growth factor-β family play critical roles in body patterning, in both vertebrates and invertebrates. One transforming growth factor-β-related gene, dbl-1, has been...
Fields, Stanley, Kohara, Yuji, Lockhart, David J.
Complete genome sequences are providing a framework to allow the investigation of biological processes by the use of comprehensive approaches. Genome analysis also is having a dramatic impact on...
Hanazawa, Momoyo, Mochii, Makoto, Ueno, Naoto, Kohara, Yuji, Iino, Yuichi
Caenorhabditis elegans is an ideal organism for the study of the molecular basis of fundamental biological processes such as germ-line development, especially because of availability of the whole...
Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags
Kawashima, Takeshi, Kawashima, Shuichi, Kohara, Yuji, Kanehisa, Minoru, Makabe, Kazuhiro W.
MAGEST is a database for maternal gene expression information for an ascidian, Halocynthia roretzi. The ascidian has become an animal model in developmental biological research because it shows a...
Morita, Kiyokazu, Flemming, Anthony J., Sugihara, Yukiko, Mochii, Makoto, Suzuki, Yo, Yoshida, Satoru, ...
Using cDNA-based array analysis combined with double-stranded RNA interference (dsRNAi), we have identified yk298h6 as a target gene of Caenorhabditis elegans TGF-β signaling. Worms overexpressing...
Nishiyama, Tomoaki, Fujita, Tomomichi, Shin-I, Tadasu, Seki, Motoaki, Nishide, Hiroyo, Uchiyama, Ikuo, ...
The mosses and flowering plants diverged >400 million years ago. The mosses have haploid-dominant life cycles, whereas the flowering plants are diploid-dominant. The common ancestors of land plants...
Analyses of cDNAs from growth and slug stages of Dictyostelium discoideum
Urushihara, Hideko, Morio, Takahiro, Saito, Tamao, Kohara, Yuji, Koriki, Eiko, Ochiai, Hiroshi, ...
Dictyostelium is a favored model for studying problems in cell and developmental biology. To comprehend the genetic potential and networks that direct growth and multicellular development, we are...
Lazakovitch, Elena, Kalb, John M, Matsumoto, Reiko, Hirono, Keiko, Kohara, Yuji, Gronostajski, Richard M
Kunitomo, Hirofumi, Uesugi, Hiroko, Kohara, Yuji, Iino, Yuichi
An mRNA-tagging method was used to selectively isolate mRNA from a small number of cells for subsequent cDNA microarray analysis. The approach was used to identify genes specifically expressed in...
Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis
Shoguchi, Eiichi, Kawashima, Takeshi, Satou, Yutaka, Hamaguchi, Makoto, Sin-I, Tadasu, Kohara, Yuji, ...
The draft genome (∼160 Mb) of the urochordate ascidian Ciona intestinalis has been sequenced by the whole-genome shotgun method and should provide important insights into the origin and evolution...
Mochii, Makoto, Yoshida, Satoru, Morita, Kiyokazu, Kohara, Yuji, Ueno, Naoto
Members of the transforming growth factor-β family play critical roles in body patterning, in both vertebrates and invertebrates. One transforming growth factor-β-related gene, dbl-1, has been...
Fields, Stanley, Kohara, Yuji, Lockhart, David J.
Complete genome sequences are providing a framework to allow the investigation of biological processes by the use of comprehensive approaches. Genome analysis also is having a dramatic impact on...
Hanazawa, Momoyo, Mochii, Makoto, Ueno, Naoto, Kohara, Yuji, Iino, Yuichi
Caenorhabditis elegans is an ideal organism for the study of the molecular basis of fundamental biological processes such as germ-line development, especially because of availability of the whole...
Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags
Kawashima, Takeshi, Kawashima, Shuichi, Kohara, Yuji, Kanehisa, Minoru, Makabe, Kazuhiro W.
MAGEST is a database for maternal gene expression information for an ascidian, Halocynthia roretzi. The ascidian has become an animal model in developmental biological research because it shows a...
Morita, Kiyokazu, Flemming, Anthony J., Sugihara, Yukiko, Mochii, Makoto, Suzuki, Yo, Yoshida, Satoru, ...
Using cDNA-based array analysis combined with double-stranded RNA interference (dsRNAi), we have identified yk298h6 as a target gene of Caenorhabditis elegans TGF-β signaling. Worms overexpressing...
Nishiyama, Tomoaki, Fujita, Tomomichi, Shin-I, Tadasu, Seki, Motoaki, Nishide, Hiroyo, Uchiyama, Ikuo, ...
The mosses and flowering plants diverged >400 million years ago. The mosses have haploid-dominant life cycles, whereas the flowering plants are diploid-dominant. The common ancestors of land plants...
Analyses of cDNAs from growth and slug stages of Dictyostelium discoideum
Urushihara, Hideko, Morio, Takahiro, Saito, Tamao, Kohara, Yuji, Koriki, Eiko, Ochiai, Hiroshi, ...
Dictyostelium is a favored model for studying problems in cell and developmental biology. To comprehend the genetic potential and networks that direct growth and multicellular development, we are...
Kunitomo, Hirofumi, Uesugi, Hiroko, Kohara, Yuji, Iino, Yuichi
An mRNA-tagging method was used to selectively isolate mRNA from a small number of cells for subsequent cDNA microarray analysis. The approach was used to identify genes specifically expressed in...
Lazakovitch, Elena, Kalb, John M, Matsumoto, Reiko, Hirono, Keiko, Kohara, Yuji, Gronostajski, Richard M
Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis
Shoguchi, Eiichi, Kawashima, Takeshi, Satou, Yutaka, Hamaguchi, Makoto, Sin-I, Tadasu, Kohara, Yuji, ...
The draft genome (∼160 Mb) of the urochordate ascidian Ciona intestinalis has been sequenced by the whole-genome shotgun method and should provide important insights into the origin and evolution...
Retrotransposon Silencing by DNA Methylation Can Drive Mammalian Genomic Imprinting
Suzuki, Shunsuke, Ono, Ryuichi, Narita, Takanori, Pask, Andrew J, Shaw, Geoffrey, Wang, Changshan, ...
Among mammals, only eutherians and marsupials are viviparous and have genomic imprinting that leads to parent-of-origin-specific differential gene expression. We used comparative analysis to...
Yamato, Katsuyuki T., Ishizaki, Kimitsune, Fujisawa, Masaki, Okada, Sachiko, Nakayama, Shigeki, Fujishita, Mariko, ...
Y chromosomes are different from other chromosomes because of a lack of recombination. Until now, complete sequence information of Y chromosomes has been available only for some primates, although...
UTGB/medaka: genomic resource database for medaka biology
Ahsan, Budrul, Kobayashi, Daisuke, Yamada, Tomoyuki, Kasahara, Masahiro, Sasaki, Shin, Saito, Taro L., ...
Medaka (Oryzias latipes) is a small egg-laying freshwater teleost native to East Asia that has become an excellent model system for developmental genetics and evolutionary biology. The draft medaka...
Nakatani, Yoichiro, Takeda, Hiroyuki, Kohara, Yuji, Morishita, Shinichi
Although several vertebrate genomes have been sequenced, little is known about the genome evolution of early vertebrates and how large-scale genomic changes such as the two rounds of whole-genome...
Development of 5006 Full-Length CDNAs in Barley: A Tool for Accessing Cereal Genomics Resources
Sato, Kazuhiro, Shin-I, Tadasu, Seki, Motoaki, Shinozaki, Kazuo, Yoshida, Hideya, Takeda, Kazuyoshi, ...
A collection of 5006 full-length (FL) cDNA sequences was developed in barley. Fifteen mRNA samples from various organs and treatments were pooled to develop a cDNA library using the CAP trapper...
Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE
Wang, Xin, Zhao, Yongjun, Wong, Kim, Ehlers, Peter, Kohara, Yuji, Jones, Steven J, ...
Hashimoto, Hisashi, Miyamoto, Rieko, Watanabe, Naoki, Shiba, Dai, Ozato, Kenjiro, Inoue, Chikako, ...
Polycystic kidney disease (PKD) is a common hereditary disease in humans. Recent studies have shown an increasing number of ciliary genes that are involved in the pathogenesis of PKD. In this study,...