K2D2: Estimation of protein secondary structure from circular dichroism spectra (2008)
Perez-Iratxeta, Carolina, Andrade-Navarro, Miguel A
Abstract Background Circular dichroism spectroscopy is a widely used technique to analyze the secondary structure of proteins in solution. Predictive methods use the circular dichroism spectra from...
Gene function in early mouse embryonic stem cell differentiation (2007)
Sene, Kagnew, Porter, Christopher J, Palidwor, Gareth, Perez-Iratxeta, Carolina, Muro, Enrique M, Campbell, Pearl A, ...
Abstract Background Little is known about the genes that drive embryonic stem cell differentiation. However, such knowledge is necessary if we are to exploit the therapeutic potential of stem cells....
Gene function in early mouse embryonic stem cell differentiation (2007)
Sene, Kagnew, Porter, Christopher J, Palidwor, Gareth, Perez-Iratxeta, Carolina, Muro, Enrique M, Campbell, Pearl A, ...
Abstract Background Little is known about the genes that drive embryonic stem cell differentiation. However, such knowledge is necessary if we are to exploit the therapeutic potential of stem cells....
Amplification of the Gene Ontology annotation of Affymetrix probe sets (2006)
Muro, Enrique M, Perez-Iratxeta, Carolina, Andrade-Navarro, Miguel A
Abstract Background The annotations of Affymetrix DNA microarray probe sets with Gene Ontology terms are carefully selected for correctness. This results in very accurate but incomplete annotations...
G2D: a tool for mining genes associated with disease (2005)
Perez-Iratxeta, Carolina, Wjst, Matthias, Bork, Peer, Andrade, Miguel A
Abstract Background Human inherited diseases can be associated by genetic linkage with one or more genomic regions. The availability of the complete sequence of the human genome allows examining...
Inconsistencies over time in 5% of NetAffx probe-to-gene annotations (2005)
Perez-Iratxeta, Carolina, Andrade, Miguel A
Abstract Background DNA microarray probes are designed to match particular mRNA transcripts, often based on expressed sequences like ESTs, or cDNAs, many times incomplete. As a result, the relations...
Systematic Association of Genes to Phenotypes by Genome and Literature Mining (2005)
Jan O. Korbel, Tobias Doerks, Lars J. Jensen, Carolina Perez-Iratxeta, Szymon Kaczanowski, Sean D. Hooper, ...
The combination of text mining and comparative genomics is shown to be a powerful approach to predicting phenotypes that are associated with particular genes in bacterial genomes.
Systematic Association of Genes to Phenotypes by Genome and Literature Mining (2005)
Jan O. Korbel, Tobias Doerks, Lars J. Jensen, Carolina Perez-Iratxeta, Szymon Kaczanowski, Sean D. Hooper, ...
One of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. So far no global analysis has attempted to explore those connections in the light of...
Information extraction from full text scientific articles: Where are the keywords? (2003)
Shah, Parantu K, Perez-Iratxeta, Carolina, Bork, Peer, Andrade, Miguel A
Abstract Background To date, many of the methods for information extraction of biological information from scientific articles are restricted to the abstract of the article. However, full text...
Andrade, Miguel A, Ciccarelli, Francesca D, Perez-Iratxeta, Carolina, Bork, Peer
Abstract Background Iron uptake from the host is essential for bacteria that infect animals. To find potential targets for drugs active against pathogenic bacteria, we have searched all completely...
Andrade, Miguel A, Ciccarelli, Francesca D, Perez-Iratxeta, Carolina, Bork, Peer
Iron uptake from the host is essential for bacteria that infect animals. A protein domain has been identified that appears in variable copy number in bacterial genes that are usually in the vicinity...
Information extraction from full text scientific articles: Where are the keywords?
Shah, Parantu K, Perez-Iratxeta, Carolina, Bork, Peer, Andrade, Miguel A
Update on XplorMed: a web server for exploring scientific literature
Perez-Iratxeta, Carolina, Pérez, Antonio J., Bork, Peer, Andrade, Miguel A.
As scientific literature databases like MEDLINE increase in size, so does the time required to search them. Scientists must frequently inspect long lists of references manually, often just reading...
Systematic Association of Genes to Phenotypes by Genome and Literature Mining
Korbel, Jan O, Doerks, Tobias, Jensen, Lars J, Perez-Iratxeta, Carolina, Kaczanowski, Szymon, Hooper, Sean D, ...
One of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. So far no global analysis has attempted to explore those connections in the light of...
G2D: a tool for mining genes associated with disease
Perez-Iratxeta, Carolina, Wjst, Matthias, Bork, Peer, Andrade, Miguel A
Netzel, Rebecca, Perez-Iratxeta, Carolina, Bork, Peer, Andrade, Miguel A.
Country-specific variations of the English language in the biomedical literature
Amplification of the Gene Ontology annotation of Affymetrix probe sets
Muro, Enrique M, Perez-Iratxeta, Carolina, Andrade-Navarro, Miguel A
Tiffin, Nicki, Adie, Euan, Turner, Frances, Brunner, Han G., Van Driel, Marc A., Oti, Martin, ...
Genome-wide experimental methods to identify disease genes, such as linkage analysis and association studies, generate increasingly large candidate gene sets for which comprehensive empirical...
Andrade, Miguel A, Ciccarelli, Francesca D, Perez-Iratxeta, Carolina, Bork, Peer
Iron uptake from the host is essential for bacteria that infect animals. A protein domain has been identified that appears in variable copy number in bacterial genes that are usually in the vicinity...
Information extraction from full text scientific articles: Where are the keywords?
Shah, Parantu K, Perez-Iratxeta, Carolina, Bork, Peer, Andrade, Miguel A
Update on XplorMed: a web server for exploring scientific literature
Perez-Iratxeta, Carolina, Pérez, Antonio J., Bork, Peer, Andrade, Miguel A.
As scientific literature databases like MEDLINE increase in size, so does the time required to search them. Scientists must frequently inspect long lists of references manually, often just reading...
Systematic Association of Genes to Phenotypes by Genome and Literature Mining
Korbel, Jan O, Doerks, Tobias, Jensen, Lars J, Perez-Iratxeta, Carolina, Kaczanowski, Szymon, Hooper, Sean D, ...
One of the major challenges of functional genomics is to unravel the connection between genotype and phenotype. So far no global analysis has attempted to explore those connections in the light of...
G2D: a tool for mining genes associated with disease
Perez-Iratxeta, Carolina, Wjst, Matthias, Bork, Peer, Andrade, Miguel A
Netzel, Rebecca, Perez-Iratxeta, Carolina, Bork, Peer, Andrade, Miguel A.
Country-specific variations of the English language in the biomedical literature
Amplification of the Gene Ontology annotation of Affymetrix probe sets
Muro, Enrique M, Perez-Iratxeta, Carolina, Andrade-Navarro, Miguel A
Tiffin, Nicki, Adie, Euan, Turner, Frances, Brunner, Han G., Van Driel, Marc A., Oti, Martin, ...
Genome-wide experimental methods to identify disease genes, such as linkage analysis and association studies, generate increasingly large candidate gene sets for which comprehensive empirical...
Gene function in early mouse embryonic stem cell differentiation
Sene, Kagnew Hailesellasse, Porter, Christopher J, Palidwor, Gareth, Perez-Iratxeta, Carolina, Muro, Enrique M, Campbell, Pearl A, ...
Oct4 Targets Regulatory Nodes to Modulate Stem Cell Function
Campbell, Pearl A., Perez-Iratxeta, Carolina, Andrade-Navarro, Miguel A., Rudnicki, Michael A.
Stem cells are characterized by two defining features, the ability to self-renew and to differentiate into highly specialized cell types. The POU homeodomain transcription factor Oct4 (Pou5f1) is an...
Update of the G2D tool for prioritization of gene candidates to inherited diseases
Perez-Iratxeta, Carolina, Bork, Peer, Andrade-Navarro, Miguel A.
G2D (genes to diseases) is a web resource for prioritizing genes as candidates for inherited diseases. It uses three algorithms based on different prioritization strategies. The input to the server...
Genes to Diseases (G2D) Computational Method to Identify Asthma Candidate Genes
Tremblay, Karine, Lemire, Mathieu, Potvin, Camille, Tremblay, Alexandre, Hunninghake, Gary M., Raby, Benjamin A., ...
Asthma is a complex trait for which different strategies have been used to identify its environmental and genetic predisposing factors. Here, we describe a novel methodological approach to select...