Ioannis Iliopoulos, Sophia Tsoka, Miguel A. Andrade, Anton J. Enright, Mark Carroll, Patrick Poullet, ...
BIOINFORMATICS Motivation: Genome-wide functional annotation either by manual or automatic means has raised considerable concerns regarding the accuracy of assignments and the reproducibility of...
Parantu K Shah, Carolina Perez-iratxeta, Peer Bork, Miguel A Andrade
Information extractionfull text articlekeywordgene namedata miningtext mining Background: To date, many of the methods for information extraction of biological information from scientific articles...
Sánchez-Pulido, Luis, Andrade, Miguel A.
This article is available from: http://www.biomedcentral.com/1471-2091/8/23
Reynaud, Emmanuel G, Andrade, Miguel A, Bonneau, Fabien, Ly, Thi, Knop, Michael, Scheffzek, Klaus, ...
Abstract Background Compartmentalization is a key feature of eukaryotic cells, but its evolution remains poorly understood. GTPases are the oldest enzymes that use nucleotides as substrates and they...
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...
Ranking the whole MEDLINE database according to a large training set using text indexing (2005)
Suomela, Brian P, Andrade, Miguel A
Abstract Background The MEDLINE database contains over 12 million references to scientific literature, with about 3/4 of recent articles including an abstract of the publication. Retrieval of entries...
with the evolution of compartmentalization (2005)
Emmanuel G Reynaud, Miguel A Andrade, Fabien Bonneau, Thi Bach, Nga Ly, Michael Knop, ...
Human Lsg1 defines a family of essential GTPases that correlates
BMC Bioinformatics BioMed Central Correspondence (2005)
Carolina Perez-iratxeta, Miguel A Andrade
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background: DNA microarray probes are designed to match particular mRNA...
ACRATA: a novel electron transfer domain associated to apoptosis and cancer (2004)
Sanchez-Pulido, Luis, Rojas, Ana M, Valencia, Alfonso, Martinez-A, Carlos, Andrade, Miguel A
Abstract Background Recently, several members of a vertebrate protein family containing a six trans-membrane (6TM) domain and involved in apoptosis and cancer (e.g. STEAP, STAMP1, TSAP6), have been...
ACRATA: a novel electron transfer domain associated to apoptosis and cancer (2004)
Sánchez-Pulido, Luis, Rojas, Ana Mª., Valencia, Alfonso, Martínez-Alonso, Carlos, Andrade, Miguel A.
This article is available from: http://www.biomedcentral.com/1471-2407/4/98
Gene annotation from scientific literature using mappings between keyword systems (2004)
Pérez, Antonio J., Perez-Iratxeta, Carolina, Bork, Peer, Thode, Guillermo, Andrade, Miguel A.
Motivation: The description of genes in databases by keywords helps the non-specialist to quickly grasp the properties of a gene and increases the efficiency of computational tools that are applied...
Gene annotation from scientific literature using mappings between keyword systems (2004)
Pérez, Antonio J., Perez-Iratxeta, Carolina, Bork, Peer, Thode, Guillermo, Andrade, Miguel A.
Motivation: The description of genes in databases by keywords helps the non-specialist to quickly grasp the properties of a gene and increases the efficiency of computational tools that are applied...
Gene annotation from scientific literature using mappings between keyword systems (2004)
Pérez, Antonio J., Perez-Iratxeta, Carolina, Bork, Peer, Thode, Guillermo, Andrade, Miguel A.
Motivation: The description of genes in databases by keywords helps the non-specialist to quickly grasp the properties of a gene and increases the efficiency of computational tools that are applied...
Brian P Suomela, Miguel A Andrade, Brian P Suomela, Miguel A Andrade
set using text indexing
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...
Genome sequences and great expectations (2000)
Iliopoulos, Ioannis, Tsoka, Sophia, Andrade, Miguel A, Janssen, Paul, Audit, Benjamin, Tramontano, Anna, ...
Abstract To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern...
Open letter Genome sequences and great expectations (2000)
Ioannis Iliopoulos, Sophia Tsoka, Miguel A Andrade, Paul Janssen, Benjamin Audit, Anna Tramontano, ...
The electronic version of this article is the complete one and can be
NAIL--Network Analysis Interface for Linking HMMER results (2000)
Sánchez-Pulido, Luis, Yuan, Yan P., Andrade, Miguel A., Bork, Peer
Summary: Network Analysis Interface for Linking HMMER results (NAIL) is a web-based tool for the analysis of results from a HMMER protein database-search. NAIL facilitates the selection of protein...
Dandekar, Thomas, Huynen, Martijn, Regula, Jörg Thomas, Ueberle, Barbara, Zimmermann, Carl Ulrich, Andrade, Miguel A., ...
Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10...
Christian Blaschke, Miguel A. Andrade, Christos Ouzounis, Alfonso Valencia
We describe the basic design of a system for automatic detection of protein--protein interactions extracted from scientific abstracts. By restricting the problem domain and imposing a number of...
Position-Specific Annotation of Protein Function Based on Multiple Homologs (1999)
In this work I present an algorithm for deriving position-specific protein functional annotations. The input is based on the results of a sequence similarity search of a query sequence against a...
Adaptation of protein surfaces to subcellular location (1998)
Miguel A. Andrade, Seaân I. O'donoghue, Burkhard Rost, European Bioinformatics
For over 30 years, researchers have sought to discover the principles that determine the fold of globular proteins in aqueous environments. The goals of this research effort are to predict tertiary
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames
Dandekar, Thomas, Huynen, Martijn, Regula, Jörg Thomas, Ueberle, Barbara, Zimmermann, Carl Ulrich, Andrade, Miguel A., ...
Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10...
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...
Genome sequences and great expectations
Iliopoulos, Ioannis, Tsoka, Sophia, Andrade, Miguel A, Janssen, Paul, Audit, Benjamin, Tramontano, Anna, ...
To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern is that...
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...
ACRATA: a novel electron transfer domain associated to apoptosis and cancer
Sanchez-Pulido, Luis, Rojas, Ana M, Valencia, Alfonso, Martinez-A, Carlos, Andrade, Miguel A
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
Reynaud, Emmanuel G, Andrade, Miguel A, Bonneau, Fabien, Ly, Thi Bach Nga, Knop, Michael, Scheffzek, Klaus, ...
Netzel, Rebecca, Perez-Iratxeta, Carolina, Bork, Peer, Andrade, Miguel A.
Country-specific variations of the English language in the biomedical literature
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames
Dandekar, Thomas, Huynen, Martijn, Regula, Jörg Thomas, Ueberle, Barbara, Zimmermann, Carl Ulrich, Andrade, Miguel A., ...
Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10...
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...
Genome sequences and great expectations
Iliopoulos, Ioannis, Tsoka, Sophia, Andrade, Miguel A, Janssen, Paul, Audit, Benjamin, Tramontano, Anna, ...
To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern is that...
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...
ACRATA: a novel electron transfer domain associated to apoptosis and cancer
Sanchez-Pulido, Luis, Rojas, Ana M, Valencia, Alfonso, Martinez-A, Carlos, Andrade, Miguel A
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
Reynaud, Emmanuel G, Andrade, Miguel A, Bonneau, Fabien, Ly, Thi Bach Nga, Knop, Michael, Scheffzek, Klaus, ...
Netzel, Rebecca, Perez-Iratxeta, Carolina, Bork, Peer, Andrade, Miguel A.
Country-specific variations of the English language in the biomedical literature