Exon creation and establishment in human genes (2008)
Corvelo, André, Eyras, Eduardo
Abstract Background A large proportion of species-specific exons are alternatively spliced. In primates, Alu elements play a crucial role in the process of exon creation but many new exons have...
EGASP: the human ENCODE Genome Annotation Assessment Project (2006)
Guigó, Roderic, Flicek, Paul, Abril, Josep F, Reymond, Alexandre, Lagarde, Julien, Denoeud, France, ...
Abstract Background We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence....
Abstract Background Alternatively spliced exons play an important role in the diversification of gene function in most metazoans and are highly regulated by conserved motifs in exons and introns. Two...
Gene finding in the chicken genome (2005)
Eyras, Eduardo, Reymond, Alexandre, Castelo, Robert, Bye, Jacqueline M, Camara, Francisco, Flicek, Paul, ...
Abstract Background Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is...
Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line (2004)
Wahl, Matthias B, Caldwell, Randolph B, Kierzek, Andrzej M, Arakawa, Hiroshi, Eyras, Eduardo, Hubner, Nina, ...
Abstract Background The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures,...
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...
The Spacetime Life of a Non-BPS D-particle (2000)
Eyras, Eduardo, Panda, Sudhakar
We investigate the classical geometry generated by a stable non-BPS D-particle. We consider the boundary state of a stable non-BPS D-particle in the covariant formalism in the type IIB theory...
T-duality and actions for non-BPS D-branes (2000)
Eyras, Eduardo, Wit, Tim C. De, Roo, Mees De, Bergshoeff, Eric A., Panda, Sudhakar
We employ T-duality to restrict the tachyon dependence of effective actions for non-BPS D-branes. For the Born-Infeld part the criteria of T-duality and supersymmetry are satisfied by a simple...
Stable D8-branes and Tachyon Condensation in Type 0 Open String Theory (1999)
We consider non-BPS D8 (and D7) branes in type 0 open string theory and describe under which circumstances these branes are stable. We find stable non-BPS D7 and D8 in type 0 with and without...
Exotic Branes and Nonperturbative Seven Branes (1999)
Eyras, Eduardo, Lozano, Yolanda
We construct the effective action of certain exotic branes in the Type II theories which are not predicted by their spacetime supersymmetry algebras. We analyze in detail the case of the NS-7B brane,...
Kaluza-Klein Monopole and 5-brane Effective Actions (1999)
Eyras, Eduardo, Lozano, Yolanda
We review the construction of the Kaluza-Klein monopole of the Type IIA theory in the most general case of a massive background, as well as its relation via T-duality with the Type IIB NS-5-brane....
Brane Actions and String Dualities (1998)
Eyras, Eduardo, Lozano, Yolanda
An effective action for the M9-brane is proposed. We study its relation with other branes via dualities. Among these, we find actions for branes which are not suggested by the central charges of the...
The Kaluza-Klein Monopole in a Massive IIA Background (1998)
Eyras, Eduardo, Lozano, Yolanda
We construct the effective action of the KK-monopole in a massive Type IIA background. We follow two approaches. First we construct a massive M-theory KK-monopole from which the IIA monopole is...
5-branes, KK-monopoles and T-duality (1998)
Eyras, Eduardo, Janssen, Bert, Lozano, Yolanda
We construct the explicit worldvolume effective actions of the type IIB NS-5-brane and KK-monopole. These objects are obtained through a T-duality transformation from the IIA KK-monopole and the IIA...
The Massive Kaluza-Klein Monopole (1998)
Bergshoeff, Eric, Eyras, Eduardo, Lozano, Yolanda
We construct the (bosonic) effective worldvolume action of an M-theory Kaluza-Klein monopole in a background given by the bosonic sector of eleven-dimensional massive supergravity, i.e. a "massive...
The massive Kaluza-Klein monopole (1998)
Eyras, Eduardo, Bergshoeff, Eric, Lozano, Yolanda
We construct the (bosonic) effective worldvolume action of an M-theory Kaluza–Klein monopole in a background given by the bosonic sector of eleven-dimensional massive supergravity, i.e. a...
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...
Birney, Ewan, Andrews, T. Daniel, Bevan, Paul, Caccamo, Mario, Chen, Yuan, Clarke, Laura, ...
Ensembl (http://www.ensembl.org/) is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of...
The Ensembl Automatic Gene Annotation System
Curwen, Val, Eyras, Eduardo, Andrews, T. Daniel, Clarke, Laura, Mongin, Emmanuel, Searle, Steven M.J., ...
As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables...
ESTGenes: Alternative Splicing From ESTs in Ensembl
Eyras, Eduardo, Caccamo, Mario, Curwen, Val, Clamp, Michele
We describe a novel algorithm for deriving the minimal set of nonredundant transcripts compatible with the splicing structure of a set of ESTs mapped on a genome. Sets of ESTs with compatible...
Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line
Wahl, Matthias B, Caldwell, Randolph B, Kierzek, Andrzej M, Arakawa, Hiroshi, Eyras, Eduardo, Hubner, Nina, ...
Castelo, Robert, Reymond, Alexandre, Wyss, Carine, Câmara, Francisco, Parra, Genís, Antonarakis, Stylianos E., ...
The recent availability of the chicken genome sequence poses the question of whether there are human protein-coding genes conserved in chicken that are currently not included in the human gene...
Gene finding in the chicken genome
Eyras, Eduardo, Reymond, Alexandre, Castelo, Robert, Bye, Jacqueline M, Camara, Francisco, Flicek, Paul, ...
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...
Birney, Ewan, Andrews, T. Daniel, Bevan, Paul, Caccamo, Mario, Chen, Yuan, Clarke, Laura, ...
Ensembl (http://www.ensembl.org/) is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of...
The Ensembl Automatic Gene Annotation System
Curwen, Val, Eyras, Eduardo, Andrews, T. Daniel, Clarke, Laura, Mongin, Emmanuel, Searle, Steven M.J., ...
As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables...
ESTGenes: Alternative Splicing From ESTs in Ensembl
Eyras, Eduardo, Caccamo, Mario, Curwen, Val, Clamp, Michele
We describe a novel algorithm for deriving the minimal set of nonredundant transcripts compatible with the splicing structure of a set of ESTs mapped on a genome. Sets of ESTs with compatible...
Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line
Wahl, Matthias B, Caldwell, Randolph B, Kierzek, Andrzej M, Arakawa, Hiroshi, Eyras, Eduardo, Hubner, Nina, ...
Castelo, Robert, Reymond, Alexandre, Wyss, Carine, Câmara, Francisco, Parra, Genís, Antonarakis, Stylianos E., ...
The recent availability of the chicken genome sequence poses the question of whether there are human protein-coding genes conserved in chicken that are currently not included in the human gene...
Gene finding in the chicken genome
Eyras, Eduardo, Reymond, Alexandre, Castelo, Robert, Bye, Jacqueline M, Camara, Francisco, Flicek, Paul, ...
EGASP: the human ENCODE Genome Annotation Assessment Project
Guigó, Roderic, Flicek, Paul, Abril, Josep F, Reymond, Alexandre, Lagarde, Julien, Denoeud, France, ...
Lyle, Robert, Prandini, Paola, Osoegawa, Kazutoyo, Ten Hallers, Boudewijn, Humphray, Sean, Zhu, Baoli, ...
The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p),...
Schwartz, Schraga, Silva, João, Burstein, David, Pupko, Tal, Eyras, Eduardo, Ast, Gil
Introns are among the hallmarks of eukaryotic genes. Splicing of introns is directed by three main splicing signals: the 5′ splice site (5′ss), the branch site (BS), and the polypyrimdine...