Integrating biological data – the Distributed Annotation System (2008)
Jenkinson, Andrew M, Albrecht, Mario, Birney, Ewan, Blankenburg, Hagen, Down, Thomas, Finn, Robert D, ...
Abstract Background The Distributed Annotation System (DAS) is a widely adopted protocol for dynamically integrating a wide range of biological data from geographically diverse sources. DAS continues...
Optimising oligonucleotide array design for ChIP-on-chip (2007)
Nielsen, Fiona, Graef, Stefan, Zhang, Xinmin, Kurtz, Stefan, Denissov, Sergei, Green, Roland, ...
No abstract available.
Reactome - a knowledgebase of human biological pathways (2007)
Peter D'Eustachio, David Croft, Bernard De Bono, Gopal Gopinath, Marc Gillespie, Bijay Jassal, ...
Pathway curation is a powerful tool for systematically associating gene products with functions. Reactome (www.reactome.org) is a manually curated human pathway knowledgebase describing a wide range...
In Vivo Validation of a Computationally Predicted Conserved Ath5 Target Gene Set (2007)
Filippo Del Bene, Laurence Ettwiller, Dorota Skowronska-Krawczyk, Herwig Baier, Jean-Marc Matter, Ewan Birney, ...
So far, the computational identification of transcription factor binding sites is hampered by the complexity of vertebrate genomes. Here we present an in silico procedure to predict target sites of a...
In vivo Validation of a Computationally Predicted Conserved Ath5 Target Gene Set (2007)
Filippo Del Bene, Laurence Ettwiller, Dorota Skowronska-Krawczyk, Herwig Baier, Jean-Marc Matter, Ewan Birney, ...
So far the computational identification of transcription factor binding sites was hampered by the complexity of vertebrate genomes. Here we present an in silico procedure to predict target sites of a...
Reactome: a knowledge base of biologic pathways and processes (2007)
Vastrik, Imre, D'Eustachio, Peter, Schmidt, Esther, Joshi-Tope, Geeta, Gopinath, Gopal, Croft, David, ...
Abstract Reactome http://www.reactome.org , an online curated resource for human pathway data, provides infrastructure for computation across the biologic reaction network. We use Reactome to infer...
Update of the Anopheles gambiaePEST genome assembly (2007)
Sharakhova, Maria V, Hammond, Martin P, Lobo, Neil F, Krzywinski, Jaroslaw, Unger, Maria F, Hillenmeyer, Maureen E, ...
Abstract Background The genome of Anopheles gambiae , the major vector of malaria, was sequenced and assembled in 2002. This initial genome assembly and analysis made available to the scientific...
Reactome: An integrated expert model of human molecular processes and access toolkit (2007)
De Bono, Bernard, Vastrik, Imre, D´Eustachio, Peter, Schmidt, Esther, Gopinath, Gopal, Croft, David, ...
The behaviour of pervasive molecular processes in human biology can be studied through the large-scale modeling of the molecular events that define them. Constructing detailed models of such extent...
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....
Ettwiller, Laurence, Paten, Benedict, Souren, Marcel, Loosli, Felix, Wittbrodt, Jochen, Birney, Ewan
Abstract We have developed several new methods to investigate transcriptional motifs in vertebrates. We developed a specific alignment tool appropriate for regions involved in transcription control,...
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...
Automated generation of heuristics for biological sequence comparison (2005)
Abstract Background Exhaustive methods of sequence alignment are accurate but slow, whereas heuristic approaches run quickly, but their complexity makes them more difficult to implement. We introduce...
Guigo, Roderic, Birney, Ewan, Brent, Michael, Dermitzakis, Emmanouil, Pachter, Lior, Crollius, Hugues Roest, ...
With the sponsorship of ``Fundacio La Caixa'' we met in Barcelona, November 21st and 22nd, to analyze the reasons why, after the completion of the human genome sequence, the identification all...
James A. Cuff, Ewan Birney, Michele E. Clamp, Geoffrey J. Barton
Motivation: An automatic sequence searching method (ProtEST) is described which constructs multiple protein sequence alignments from protein sequences and translated expressed sequence tags (ESTs)....
Representación gráfica de la secuencia del genoma humano en los 23 pares de cromosomas de los seres humanos. Se trata de un material acompañante al vol. 431, no. 7011 de la revista Nature (21 de...
Representación gráfica de la secuencia del genoma humano en los 23 pares de cromosomas de los seres humanos. Se trata de un material acompañante al vol. 431, no. 7011 de la revista Nature (21 de...
The Pfam Protein Families Database (2002)
Alex Bateman, Ewan Birney, Lorenzo Cerruti, Richard Durbin, Laurence Etwiller, Sean R. Eddy, ...
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in...
The Pfam Protein Families Database (2001)
Alex Bateman, Ewan Birney, Lorenzo Cerruti, Richard Durbin, Laurence Etwiller, Sean R. Eddy, ...
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in...
The Pfam Protein Families Database (2000)
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at http://www.sanger.ac.uk/Software/Pfam/ , in Sweden at...
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn
Pfam is a collection of multiple alignments and profile hidden Markov models of protein domain families. Release 3.1 is a major update of the Pfam database and contains 1313 families which are...
Studies in Probabilistic Sequence Alignment and Evolution (1998)
Ian Holmes, Ewan Birney, Bill Bruno, Richard Durbin, Sean Eddy, David Haussler, ...
The complete sequencing of whole genomes presents opportunities for detailed study of molecular evolution. This thesis combines theoretical developments of Bayesian approaches in bioinformatics with...
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. (1998)
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Robert D. Finn, Erik L. L
Pfam is a collection of multiple alignments and profile hidden Markov models of protein domain families. Release 3.1 is a major update of the Pfam database and contains 1313 families which are...
1 We have developed a code generating language, called Dynamite, specialised for the production and subsequent manipulation of complex dynamic programming methods for biological sequence comparison....
Pfam: Multiple Sequence Alignments and HMM-Profiles of Protein Domains (1997)
Sean R. Eddy, Ewan Birney, Alex Bateman
Pfam contains multiple alignments and hidden Markov model based profiles (HMM-profiles) of complete protein domains. The definition of domain boundaries, family members and alignment is done...
Pfam: Multiple Sequence Alignments and HMM-Profiles of Protein Domains (1997)
Sean R. Eddy, Ewan Birney, Alex Bateman, Richard Durbin
Pfam contains multiple alignments and hidden Markov model based profiles (HMM-profiles) of complete protein domains. The definition of domain boundaries, family members, and alignment is done...
The Pfam Protein Families Database (1970)
Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Kevin L. Howe, Erik L. L
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in...
The Pfam Protein Families Database
Bateman, Alex, Birney, Ewan, Cerruti, Lorenzo, Durbin, Richard, Etwiller, Laurence, Eddy, Sean R., ...
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in...
The Pfam Protein Families Database
Bateman, Alex, Birney, Ewan, Durbin, Richard, Eddy, Sean R., Howe, Kevin L., Sonnhammer, Erik L. L.
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at http://www.sanger.ac.uk/Software/Pfam/ , in Sweden at...
The European Bioinformatics Institute's data resources
Brooksbank, Catherine, Camon, Evelyn, Harris, Midori A., Magrane, Michele, Martin, Maria Jesus, Mulder, Nicola, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
The Bioperl Toolkit: Perl Modules for the Life Sciences
Stajich, Jason E., Block, David, Boulez, Kris, Brenner, Steven E., Chervitz, Stephen A., Dagdigian, Chris, ...
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of...
Comparative Analysis of Noncoding Regions of 77 Orthologous Mouse and Human Gene Pairs
Jareborg, Niclas, Birney, Ewan, Durbin, Richard
A data set of 77 genomic mouse/human gene pairs has been compiled from the EMBL nucleotide database, and their corresponding features determined. This set was used to analyze the degree of...
Using GeneWise in the Drosophila Annotation Experiment
The GeneWise method for combining gene prediction and homology searches was applied to the 2.9-Mb region from Drosophila melanogaster. The results from the Genome Annotation Assessment Project (GASP)...
EnsMart: A Generic System for Fast and Flexible Access to Biological Data
Kasprzyk, Arek, Keefe, Damian, Smedley, Damian, London, Darin, Spooner, William, Melsopp, Craig, ...
The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools....
Discovering Novel cis-Regulatory Motifs Using Functional Networks
Ettwiller, Laurence M., Rung, Johan, Birney, Ewan
We combined functional information such as protein–protein interactions or metabolic networks with genome information in Saccaromyces cerevisiae to predict cis-regulatory motifs in the upstream...
Dermitzakis, Emmanouil T., Kirkness, Ewen, Schwarz, Scott, Birney, Ewan, Reymond, Alexandre, Antonarakis, Stylianos E.
The analysis of conservation between the human and mouse genomes resulted in the identification of a large number of conserved nongenic sequences (CNGs). The functional significance of this nongenic...
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 Core Software Libraries
Stabenau, Arne, McVicker, Graham, Melsopp, Craig, Proctor, Glenn, Clamp, Michele, Birney, Ewan
Systems for managing genomic data must store a vast quantity of information. Ensembl stores these data in several MySQL databases. The core software libraries provide a practical and effective means...
Sockeye: A 3D Environment for Comparative Genomics
Montgomery, Stephen B., Astakhova, Tamara, Bilenky, Mikhail, Birney, Ewan, Fu, Tony, Hassel, Maik, ...
Comparative genomics techniques are used in bioinformatics analyses to identify the structural and functional properties of DNA sequences. As the amount of available sequence data steadily increases,...
Birney, Ewan, Clamp, Michele, Durbin, Richard
We present two algorithms in this paper: GeneWise, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and...
Hubbard, Simon J., Grafham, Darren V., Beattie, Kevin J., Overton, Ian M., McLaren, Stuart R., Croning, Michael D.R., ...
We present an analysis of the chicken (Gallus gallus) transcriptome based on the full insert sequences for 19,626 cDNAs, combined with 485,337 EST sequences. The cDNA data set has been functionally...
A survey of homozygous deletions in human cancer genomes
Cox, Charles, Bignell, Graham, Greenman, Chris, Stabenau, Arne, Warren, William, Stephens, Philip, ...
Homozygous deletions of recessive cancer genes and fragile sites are known to occur in human cancers. We identified 281 homozygous deletions in 636 cancer cell lines. Of these deletions, 86 were...
Gene finding in the chicken genome
Eyras, Eduardo, Reymond, Alexandre, Castelo, Robert, Bye, Jacqueline M, Camara, Francisco, Flicek, Paul, ...
Ettwiller, Laurence, Paten, Benedict, Souren, Marcel, Loosli, Felix, Wittbrodt, Jochen, Birney, Ewan
Several new methods and a specific alignment tool for investigating transcriptional motifs in vertebrates were used to identify all possible 12mers involved in transcription. Active instances of...
The Pfam Protein Families Database
Bateman, Alex, Birney, Ewan, Cerruti, Lorenzo, Durbin, Richard, Etwiller, Laurence, Eddy, Sean R., ...
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in...
The Pfam Protein Families Database
Bateman, Alex, Birney, Ewan, Durbin, Richard, Eddy, Sean R., Howe, Kevin L., Sonnhammer, Erik L. L.
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at http://www.sanger.ac.uk/Software/Pfam/ , in Sweden at...
The European Bioinformatics Institute's data resources
Brooksbank, Catherine, Camon, Evelyn, Harris, Midori A., Magrane, Michele, Martin, Maria Jesus, Mulder, Nicola, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
The Bioperl Toolkit: Perl Modules for the Life Sciences
Stajich, Jason E., Block, David, Boulez, Kris, Brenner, Steven E., Chervitz, Stephen A., Dagdigian, Chris, ...
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of...
Comparative Analysis of Noncoding Regions of 77 Orthologous Mouse and Human Gene Pairs
Jareborg, Niclas, Birney, Ewan, Durbin, Richard
A data set of 77 genomic mouse/human gene pairs has been compiled from the EMBL nucleotide database, and their corresponding features determined. This set was used to analyze the degree of...
Using GeneWise in the Drosophila Annotation Experiment
The GeneWise method for combining gene prediction and homology searches was applied to the 2.9-Mb region from Drosophila melanogaster. The results from the Genome Annotation Assessment Project (GASP)...
EnsMart: A Generic System for Fast and Flexible Access to Biological Data
Kasprzyk, Arek, Keefe, Damian, Smedley, Damian, London, Darin, Spooner, William, Melsopp, Craig, ...
The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools....
Discovering Novel cis-Regulatory Motifs Using Functional Networks
Ettwiller, Laurence M., Rung, Johan, Birney, Ewan
We combined functional information such as protein–protein interactions or metabolic networks with genome information in Saccaromyces cerevisiae to predict cis-regulatory motifs in the upstream...
Dermitzakis, Emmanouil T., Kirkness, Ewen, Schwarz, Scott, Birney, Ewan, Reymond, Alexandre, Antonarakis, Stylianos E.
The analysis of conservation between the human and mouse genomes resulted in the identification of a large number of conserved nongenic sequences (CNGs). The functional significance of this nongenic...
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 Core Software Libraries
Stabenau, Arne, McVicker, Graham, Melsopp, Craig, Proctor, Glenn, Clamp, Michele, Birney, Ewan
Systems for managing genomic data must store a vast quantity of information. Ensembl stores these data in several MySQL databases. The core software libraries provide a practical and effective means...
Sockeye: A 3D Environment for Comparative Genomics
Montgomery, Stephen B., Astakhova, Tamara, Bilenky, Mikhail, Birney, Ewan, Fu, Tony, Hassel, Maik, ...
Comparative genomics techniques are used in bioinformatics analyses to identify the structural and functional properties of DNA sequences. As the amount of available sequence data steadily increases,...
Birney, Ewan, Clamp, Michele, Durbin, Richard
We present two algorithms in this paper: GeneWise, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and...
Hubbard, Simon J., Grafham, Darren V., Beattie, Kevin J., Overton, Ian M., McLaren, Stuart R., Croning, Michael D.R., ...
We present an analysis of the chicken (Gallus gallus) transcriptome based on the full insert sequences for 19,626 cDNAs, combined with 485,337 EST sequences. The cDNA data set has been functionally...
A survey of homozygous deletions in human cancer genomes
Cox, Charles, Bignell, Graham, Greenman, Chris, Stabenau, Arne, Warren, William, Stephens, Philip, ...
Homozygous deletions of recessive cancer genes and fragile sites are known to occur in human cancers. We identified 281 homozygous deletions in 636 cancer cell lines. Of these deletions, 86 were...
Gene finding in the chicken genome
Eyras, Eduardo, Reymond, Alexandre, Castelo, Robert, Bye, Jacqueline M, Camara, Francisco, Flicek, Paul, ...
Ettwiller, Laurence, Paten, Benedict, Souren, Marcel, Loosli, Felix, Wittbrodt, Jochen, Birney, Ewan
Several new methods and a specific alignment tool for investigating transcriptional motifs in vertebrates were used to identify all possible 12mers involved in transcription. Active instances of...
VectorBase: a home for invertebrate vectors of human pathogens
Lawson, Daniel, Arensburger, Peter, Atkinson, Peter, Besansky, Nora J., Bruggner, Robert V., Butler, Ryan, ...
VectorBase () is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for...