Tenhaken, Raimund, Doerks, Tobias, Bork, Peer
Abstract Background Recognition of microbial pathogens by plants triggers the hypersensitive reaction , a common form of programmed cell death in plants. These dying cells generate signals that...
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...
SMART 4.0: towards genomic data integration (2004)
Letunic, Ivica, Copley, Richard R., Schmidt, Steffen, Ciccarelli, Francesca D., Doerks, Tobias, Schultz, Jörg, ...
SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of...
Proteome Analysis Based on Motif Statistics (2003)
Cnrs Genopole Evry, Tobias Doerks, Martin Vingron
Motivation: Even for the amino acid motifs collected in the Prosite database there may be chance occurences as opposed to those occurences where the motif is involved in fold or function of a...
Recent improvements to the SMART domain-based sequence annotation resource (2002)
Letunic, Ivica, Goodstadt, Leo, Dickens, Nicholas J., Doerks, Tobias, Schultz, Joerg, Mott, Richard, ...
SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with...
Annotation und Klassifkation nuklearer Domänen / (2001)
Frankfurt (Main), Universiẗat, Diss., 2003 (Nicht für den Austausch).
SMART: a web-based tool for the study of genetically mobile domains (2000)
Schultz, Jörg, Copley, Richard R., Doerks, Tobias, Ponting, Chris P., Bork, Peer
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://SMART.embl-heidelberg.de )....
Recent improvements to the SMART domain-based sequence annotation resource
Letunic, Ivica, Goodstadt, Leo, Dickens, Nicholas J., Doerks, Tobias, Schultz, Joerg, Mott, Richard, ...
SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with...
SMART: a web-based tool for the study of genetically mobile domains
Schultz, Jörg, Copley, Richard R., Doerks, Tobias, Ponting, Chris P., Bork, Peer
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://SMART.embl-heidelberg.de )....
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...
SMART 4.0: towards genomic data integration
Letunic, Ivica, Copley, Richard R., Schmidt, Steffen, Ciccarelli, Francesca D., Doerks, Tobias, Schultz, Jörg, ...
SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of...
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
Doerks, Tobias, Von Mering, Christian, Bork, Peer
Three integrated genomic context methods were used to annotate uncharacterized proteins in 102 bacterial genomes. Of 7853 orthologous groups with unknown function containing 45 110 proteins, 1738...
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...
Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins
Suyama, Mikita, Doerks, Tobias, Braun, Isabelle C., Sattler, Michael, Izaurralde, Elisa, Bork, Peer
Vertebrate TAP is a nuclear mRNA export factor homologous to yeast Mex67p. The middle domain of TAP binds directly to p15, a protein related to the nuclear transport factor 2 (NTF2), whereas its...
Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions
Doerks, Tobias, Copley, Richard R., Schultz, Jörg, Ponting, Chris P., Bork, Peer
A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of...
Recent improvements to the SMART domain-based sequence annotation resource
Letunic, Ivica, Goodstadt, Leo, Dickens, Nicholas J., Doerks, Tobias, Schultz, Joerg, Mott, Richard, ...
SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with...
SMART: a web-based tool for the study of genetically mobile domains
Schultz, Jörg, Copley, Richard R., Doerks, Tobias, Ponting, Chris P., Bork, Peer
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://SMART.embl-heidelberg.de )....
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...
Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions
Doerks, Tobias, Copley, Richard R., Schultz, Jörg, Ponting, Chris P., Bork, Peer
A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of...
SMART 4.0: towards genomic data integration
Letunic, Ivica, Copley, Richard R., Schmidt, Steffen, Ciccarelli, Francesca D., Doerks, Tobias, Schultz, Jörg, ...
SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of...
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
Doerks, Tobias, Von Mering, Christian, Bork, Peer
Three integrated genomic context methods were used to annotate uncharacterized proteins in 102 bacterial genomes. Of 7853 orthologous groups with unknown function containing 45 110 proteins, 1738...
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...
Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins
Suyama, Mikita, Doerks, Tobias, Braun, Isabelle C., Sattler, Michael, Izaurralde, Elisa, Bork, Peer
Vertebrate TAP is a nuclear mRNA export factor homologous to yeast Mex67p. The middle domain of TAP binds directly to p15, a protein related to the nuclear transport factor 2 (NTF2), whereas its...
Behm-Ansmant, Isabelle, Rehwinkel, Jan, Doerks, Tobias, Stark, Alexander, Bork, Peer, Izaurralde, Elisa
MicroRNAs (miRNAs) silence the expression of target genes post-transcriptionally. Their function is mediated by the Argonaute proteins (AGOs), which colocalize to P-bodies with mRNA degradation...
STRING 7—recent developments in the integration and prediction of protein interactions
Von Mering, Christian, Jensen, Lars J., Kuhn, Michael, Chaffron, Samuel, Doerks, Tobias, Krüger, Beate, ...
Information on protein–protein interactions is still mostly limited to a small number of model organisms, and originates from a wide variety of experimental and computational techniques. The...
eggNOG: automated construction and annotation of orthologous groups of genes
Jensen, Lars Juhl, Julien, Philippe, Kuhn, Michael, Von Mering, Christian, Muller, Jean, Doerks, Tobias, ...
The identification of orthologous genes forms the basis for most comparative genomics studies. Existing approaches either lack functional annotation of the identified orthologous groups, hampering...
Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing
Eulalio, Ana, Rehwinkel, Jan, Stricker, Mona, Huntzinger, Eric, Yang, Schu-Fee, Doerks, Tobias, ...
microRNAs (miRNAs) silence gene expression by suppressing protein production and/or by promoting mRNA decay. To elucidate how silencing is accomplished, we screened an RNA interference library for...