Sequence-based feature prediction and annotation of proteins (2009)
Juncker, Agnieszka S, Jensen, Lars J, Pierleoni, Andrea, Bernsel, Andreas, Tress, Michael L, Bork, Peer, ...
Abstract A recent trend in computational methods for annotation of protein function is that many prediction tools are combined in complex workflows and pipelines to facilitate the analysis of feature...
STRING 8--a global view on proteins and their functional interactions in 630 organisms (2009)
Jensen, Lars J., Kuhn, Michael, Stark, Manuel, Chaffron, Samuel, Creevey, Chris, Muller, Jean, ...
Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data...
InterPro: the integrative protein signature database (2009)
Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse...
SMART 6: recent updates and new developments (2009)
Letunic, Ivica, Doerks, Tobias, Bork, Peer
Simple modular architecture research tool (SMART) is an online tool (http://smart.embl.de/) for the identification and annotation of protein domains. It provides a user-friendly platform for the...
Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution (2008)
Quijano, Carlos, Tomancak, Pavel, López-Marti, Jesús, Suyama, Mikita, Bork, Peer, Milán, Marco, ...
[Background] The physical organization and chromosomal localization of genes within genomes is known to play an important role in their function. Most genes arise by duplication and move along the...
Selective maintenance of Drosophilatandemly arranged duplicated genes during evolution (2008)
Quijano, Carlos, Tomancak, Pavel, Lopez-Marti, Jesus, Suyama, Mikita, Bork, Peer, Milan, Marco, ...
Abstract Background The physical organization and chromosomal localization of genes within genomes is known to play an important role in their function. Most genes arise by duplication and move along...
REVIEW Predicting Function: From Genes to Genomes (2008)
Peer Bork, Thomas D, E Diaz-lazcoz, Frank Eisenhaber, Martijn Huynen, ...
Genomes and function prediction Prediction of protein function using computational tools becomes more and more important as the gap between the increasing amount of sequences and the experimental...
Perotti, Christian, Liu, Ruixuan, Parusel, Christine T, Böcher, Nadine, Schultz, Jörg, Bork, Peer, ...
Abstract Introduction The prolactin-Janus-kinase-2-signal transducer and activator of transcription-5 (JAK2-STAT5) pathway is essential for the development and functional differentiation of the...
Korff, Sebastian, Woerner, Stefan M, Yuan, Yan P, Bork, Peer, Von Knebel Doeberitz, Magnus, Gebert, Johannes
Abstract Background Protein tyrosine phosphatases (PTPs) like their antagonizing protein tyrosine kinases are key regulators of signal transduction thereby assuring normal control of cellular growth...
Just-in-time assembly of cell-cycle protein complexes (2008)
Lars J. Jensen, Ulrik De Lichtenberg, Thomas S. Jensen, Søren Brunak, Peer Bork
Our comparative analysis of eukaryotic cell-cycle complexes reveals that the identity of the periodically expressed subunits differs significantly between organisms and is often mirrored by changes...
STRING and STITCH: known and predicted interactions between proteins and chemicals (2008)
Lars J. Jensen, Michael Kuhn, Manuel Stark, Samuel Chaffron, Christian Von Mering, Peer Bork
Information on protein-protein and protein-chemical interactions is essential for understanding cellular functions. The STRING and STITCH web resources integrate interaction evidence derived from...
Pallejà, Albert, Harrington, Eoghan D, Bork, Peer
Abstract Background Across the fully sequenced microbial genomes there are thousands of examples of overlapping genes. Many of these are only a few nucleotides long and are thought to function by...
Circular reasoning rather than cyclic expression (2008)
Jensen, Lars, De Lichtenberg, Ulrik, Jensen, Thomas, Brunak, Søren, Bork, Peer
A response to Combined analysis reveals a core set of cycling genes by Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden and Z Bar-Joseph. Genome Biol 2007, 8 :R146.
Non-random retention of protein-coding overlapping genes in Metazoa (2008)
Soldà, Giulia, Suyama, Mikita, Pelucchi, Paride, Boi, Silvia, Guffanti, Alessandro, Rizzi, Ermanno, ...
Abstract Background Although the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a...
BIOINFORMATICS Application Note Medusa: A simple tool for interaction graph analysis (2008)
Medusa is a java application for visualizing and manipulating graphs of interaction, such as data from the STRING database. It features an intuitive user interface developed with the help of...
Prodom Smart, Tigrfams The Consortium, Interpro An Integrated, The Interpro, Consortium Nicola, J. Mulder, ...
is a group of scientists responsible for the production and maintenance of InterPro
BIOINFORMATICS ORIGINAL PAPER Databases and ontologies (2008)
Parantu K. Shah, Peer Bork, Bioinformatics Online
doi:10.1093/bioinformatics/btk044
Ivica Letunic, Peer Bork, Joaquin Dopazo
Summary: Interactive Tree Of Life (iTOL) is a web based tool for the display, manipulation and annotation of phylogenetic trees. Trees can be interactively pruned and re-rooted. Various types of data...
The genome of the model beetle and pest Tribolium castaneum (2008)
Gibbs, Richard A, Weinstock, George M, Brown, Susan J, Denell, Robin, Beeman, Richard W, ...
Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural...
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans (2008)
King, Nicole, Westbrook, M. Jody, Young, Susan L., Kuo, Alan, Abedin, Monika, Chapman, Jarrod, ...
Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome...
Principia Scientia, Printed in USA AUTOMATED PAIR-WISE COMPARISONS OF MICROBIAL GENOMES (2008)
Arvind K. Bansal, Peer Bork, Peter J. Stuckey
ABSTRACT. In this paper, we describe a framework for an automated pair-wise comparison of complete microbial 2 genomes to derive putative orthologous genes � functionally equivalent counterparts of...
Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution (2008)
Quijano, Carlos, Tomancak, Pavel, Lopez-Marti, Jesus, Suyama, Mikita, Bork, Peer, Milan, Marco, ...
BACKGROUND: The physical organization and chromosomal localization of genes within genomes is known to play an important role in their function. Most genes arise by duplication and move along the...
constraints or mispredictions? (2008)
Bmc Genomics, Albert Pallejà, Eoghan D Harrington, Peer Bork, Biomed Central
Large gene overlaps in prokaryotic genomes: result of functional
Correspondence Circular reasoning rather than cyclic expression (2008)
Lars Juhl Jensen, Ulrik De Lichtenberg, Thomas Skøt Jensen, Søren Brunak, Peer Bork, A Combined, ...
The electronic version of this article is the complete one and can be
Protein-protein interactions: analysis and prediction (2008)
Frishman, Dmitrij, Albrecht, Mario, Blankenburg, Hagen, Bork, Peer, Harrington, Eoghan D., Hermjakob, Henning, ...
SuperTarget and Matador: resources for exploring drug-target relationships (2008)
Günther, Stefan, Kuhn, Michael, Dunkel, Mathias, Campillos, Monica, Senger, Christian, Petsalaki, Evangelia, ...
The molecular basis of drug action is often not well understood. This is partly because the very abundant and diverse information generated in the past decades on drugs is hidden in millions of...
eggNOG: automated construction and annotation of orthologous groups of genes (2008)
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...
NetworKIN: a resource for exploring cellular phosphorylation networks (2008)
Linding, Rune, Jensen, Lars Juhl, Pasculescu, Adrian, Olhovsky, Marina, Colwill, Karen, Bork, Peer, ...
Protein kinases control cellular responses by phosphorylating specific substrates. Recent proteome-wide mapping of protein phosphorylation sites by mass spectrometry has discovered thousands of in...
STITCH: interaction networks of chemicals and proteins (2008)
Kuhn, Michael, Von Mering, Christian, Campillos, Monica, Jensen, Lars Juhl, Bork, Peer
The knowledge about interactions between proteins and small molecules is essential for the understanding of molecular and cellular functions. However, information on such interactions is widely...
4DXpress: a database for cross-species expression pattern comparisons (2008)
Haudry, Yannick, Berube, Hugo, Letunic, Ivica, Weeber, Paul-Daniel, Gagneur, Julien, Girardot, Charles, ...
In the major animal model species like mouse, fish or fly, detailed spatial information on gene expression over time can be acquired through whole mount in situ hybridization experiments. In these...
Sircah: a tool for the detection and visualization of alternative transcripts (2008)
Harrington, Eoghan D., Bork, Peer
Summary: Sircah is a flexible tool for the detection, analysis and visualization of alternative transcripts. It takes as input gene models or spliced alignments and creates a database of alternative...
KEGG Atlas mapping for global analysis of metabolic pathways (2008)
Okuda, Shujiro, Yamada, Takuji, Hamajima, Masami, Itoh, Masumi, Katayama, Toshiaki, Bork, Peer, ...
KEGG Atlas is a new graphical interface to the KEGG suite of databases, especially to the systems information in the PATHWAY and BRITE databases. It currently consists of a single global map and an...
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...
Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing (2007)
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...
Update of the G2D tool for prioritization of gene candidates to inherited diseases (2007)
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...
Prediction of effective genome size in metagenomic samples (2007)
Raes, Jeroen, Korbel, Jan O, Lercher, Martin J, Von Mering, Christian, Bork, Peer
Abstract We introduce a novel computational approach to predict effective genome size (EGS; a measure that includes multiple plasmid copies, inserted sequences, and associated phages and viruses)...
Hooper, Sean D., Boué, Stephanie, Krause, Roland, Jensen, Lars J., Mason, Christopher E., Ghanim, Murad, ...
Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing (2007)
Eulalio, Anna, Rehwinkel, J., Stricker, M., Huntzinger, Eric, Young, S.F., Doerks, T., ...
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...
Hooper, Sean D ., Boué, Stephanie, Krause, Roland, Jensen, Lars J ., Mason, Christopher E., Ghanim, Murad, ...
Time-series analysis of whole-genome expression data during Drosophila melanogaster development indicates that up to 86% of its genes change their relative transcript level during embryogenesis. By...
Guillaume Bourque, Evgeny M. Zdobnov, Peer Bork, Pavel A. Pevzner, Glenn Tesler, Email Alerting, ...
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
Christian Von Mering, Lars J. Jensen, Michael Kuhn, Samuel Chaffron, Tobias Doerks, Beate Krüger, ...
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...
New developments in the interpro database (2007)
Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, ...
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE,
Jeroen Raes, Jan O Korbel, Martin J Lercher, Christian Von Mering, Peer Bork
The electronic version of this article is the complete one and can be
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation (2007)
Summary: Interactive Tree Of Life (iTOL) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. Trees can be interactively pruned and re-rooted. Various types of data...
New developments in the InterPro database (2007)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs,...
STRING 7--recent developments in the integration and prediction of protein interactions (2007)
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...
Fabiana Perocchi, Lars J. Jensen, Julien Gagneur, Uwe Ahting, Christian Von Mering, Peer Bork, ...
Mitochondria carry out specialized functions; compartmentalized, yet integrated into the metabolic and signaling processes of the cell. Although many mitochondrial proteins have been identified,...
Insights into social insects from the genome of the honeybee Apis mellifera (2006)
Robinson, Gene E, Gibbs, Richard A, Worley, Kim C, Evans, Jay D, Maleszka, Ryszard, ...
Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes,...
Mikita Suyama, Eoghan Harrington, Peer Bork, David Torrents
The identification and classification of genes and pseudogenes in duplicated regions still constitutes a challenge for standard automated genome annotation procedures. Using an integrated homology...
SMART 5: domains in the context of genomes and networks (2006)
Ivica Letunic, Richard R. Copley, Birgit Pils, Stefan Pinkert, Jörg Schultz, Peer Bork
The Simple Modular Architecture Research Tool 10 (SMART) is an online resource
SMART 5: domains in the context of genomes and networks (2006)
Ivica Letunic, Richard R. Copley, Birgit Pils, Stefan Pinkert, Jörg Schultz, Peer Bork
The Simple Modular Architecture Research Tool 10 (SMART) is an online resource
Identification and analysis of evolutionarily cohesive functional modules in protein networks (2006)
Campillos, Mónica, Von Mering, Christian, Jensen, Lars Juhl, Bork, Peer
The increasing number of sequenced genomes makes it possible to infer the evolutionary history of functional modules, i.e., groups of proteins that contribute jointly to the same cellular function in...
Suyama, Mikita, Torrents, David, Bork, Peer
PAL2NAL is a web server that constructs a multiple codon alignment from the corresponding aligned protein sequences. Such codon alignments can be used to evaluate the type and rate of nucleotide...
LSAT: learning about alternative transcripts in MEDLINE (2006)
Motivation: Generation of alternative transcripts from the same gene is an important biological event due to their contribution in creating functional diversity in eukaryotes. In this work, we choose...
Identification and analysis of evolutionarily cohesive functional modules in protein networks (2006)
Campillos, Mónica, Von Mering, Christian, Jensen, Lars Juhl, Bork, Peer
The increasing number of sequenced genomes makes it possible to infer the evolutionary history of functional modules, i.e., groups of proteins that contribute jointly to the same cellular function in...
Extraction of regulatory gene/protein networks from Medline (2006)
Saric, Jasmin, Jensen, Lars Juhl, Ouzounova, Rossitza, Rojas, Isabel, Bork, Peer
Motivation: We have previously developed a rule-based approach for extracting information on the regulation of gene expression in yeast. The biomedical literature, however, contains information on...
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...
SMART 5: domains in the context of genomes and networks (2006)
Letunic, Ivica, Copley, Richard R., Pils, Birgit, Pinkert, Stefan, Schultz, Jörg, Bork, Peer
The Simple Modular Architecture Research Tool (SMART) is an online resource (http://smart.embl.de/) used for protein domain identification and the analysis of protein domain architectures. Many new...
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...
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...
Büssow, Konrad, Scheich, Christoph, Sievert, Volker, Harttig, Ulrich, Schultz, Jörg, Simon, Bernd, ...
Abstract Background The availability of suitable recombinant protein is still a major bottleneck in protein structure analysis. The Protein Structure Factory, part of the international structural...
Extraction of Transcript Diversity from Scientific Literature (2005)
Parantu K Shah, Lars J Jensen, Stéphanie Boué, Peer Bork
Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and...
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...
Initial sequence of the chimpanzee genome and comparison with the human genome (2005)
Mikkelsen, Tarjei S., Hillier, LaDeana W., Eichler, Evan E., Zody, Michael C., Jaffe, David B., Yang, Shiaw-Pyng, ...
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences...
Büssow, Konrad, Scheich, Christoph, Sievert, Volker, Harttig, Ulrich, Schultz, Jörg, Simon, Bernd, ...
Background The availability of suitable recombinant protein is still a major bottleneck in protein structure analysis. The Protein Structure Factory, part of the international structural genomics...
Medusa: a simple tool for interaction graph analysis
Guillaume Bourque, Evgeny M. Zdobnov, Peer Bork, Pavel A. Pevzner, Glenn Tesler, Email Alerting, ...
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
InterPro, progress and status in 2005 (2005)
Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
InterPro, progress and status in 2005 (2005)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
Von Mering, Christian, Jensen, Lars J., Snel, Berend, Hooper, Sean D., Krupp, Markus, Foglierini, Mathilde, ...
A full description of a protein's function requires knowledge of all partner proteins with which it specifically associates. From a functional perspective, ‘association’ can mean direct physical...
Medusa: a simple tool for interaction graph analysis (2005)
Summary: Medusa is a Java application for visualizing and manipulating graphs of interaction, such as data from the STRING database. It features an intuitive user interface developed with the help of...
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets (2005)
REHWINKEL, JAN, LETUNIC, IVICA, RAES, JEROEN, BORK, PEER, IZAURRALDE, ELISA
Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades mRNAs containing nonsense codons, and regulates the expression of naturally occurring transcripts. While NMD is not...
Structural similarity to bridge sequence space: Finding new families on the bridges (2005)
Shah, Parantu K., Aloy, Patrick, Bork, Peer, Russell, Robert B.
Structures for protein domains have increased rapidly in recent years owing to advances in structural biology and structural genomics projects. New structures are often similar to those solved...
Bourque, Guillaume, Zdobnov, Evgeny M., Bork, Peer, Pevzner, Pavel A., Tesler, Glenn
Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the...
Complex genomic rearrangements lead to novel primate gene function (2005)
Ciccarelli, Francesca D., Von Mering, Christian, Suyama, Mikita, Harrington, Eoghan D., Izaurralde, Elisa, Bork, Peer
Orthologous genes that maintain a single-copy status in a broad range of species may indicate a selection against gene duplication. If this is the case, then duplicates of such genes that do survive...
The WHy domain mediates the response to desiccation in plants and bacteria (2005)
Ciccarelli, Francesca D., Bork, Peer
Motivation: The hypersensitive response (HR) is a process activated by plants after microbial infection. Its main phenotypic effects are both a programmed death of the plant cells near the infection...
Complex genomic rearrangements lead to novel primate gene function (2005)
Ciccarelli, Francesca D., Von Mering, Christian, Suyama, Mikita, Harrington, Eoghan D., Izaurralde, Elisa, Bork, Peer
Orthologous genes that maintain a single-copy status in a broad range of species may indicate a selection against gene duplication. If this is the case, then duplicates of such genes that do survive...
Extraction of regulatory gene/protein networks from Medline (2005)
Ari, Jasmin, Jensen, Lars Juhl, Ouzounova, Rossitza, Rojas, Isabel, Bork, Peer
Motivation: We have previously developed a rule based approach for extracting information on the regulation of gene expression in yeast. The biomedical literature, however, contains information on...
Medusa: a simple tool for interaction graph analysis (2005)
Summary: Medusa is a java application for visualizing and manipulating graphs of interaction, such as data from the STRING database. It features an intuitive user interface developed with the help of...
Zdobnov, Evgeny M., Campillos, Mónica, Harrington, Eoghan D., Torrents, David, Bork, Peer
We suggest an annotation strategy for genes encoded by retroviruses and transposable elements (RETRA genes) based on a set of marker protein domains. Usually RETRA genes are masked in vertebrate...
Comparative metagenomics of microbial communities (2004)
Tringe, Susannah Green, Von Mering, Christian, Kobayashi, Arthur, Salamov, Asaf A., Chen, Kevin, Chang, Hwai W., ...
The predicted proteins encoded in DNA isolated from environmental microbial community samples reveal habitat-specific metabolic demands.
Structure-based assembly of protein complexes in yeast (2004)
Böttcher, Bettina, Leutwein, Christina, Mellwig, Christian, Fischer, Susanne, ...
Images of entire cells are preceding atomic structures of the separate molecular machines that they contain. The resulting gap in knowledge can be partly bridged by protein-protein interactions,...
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...
Smart 4.0: towards genomic data integration (2004)
Ivica Letunic, Richard R. Copley, Steffen Schmidt, Francesca D. Ciccarelli, Tobias Doerks, Joè Rg Schultz, ...
SMART (Simple Modular Architecture Research Tool) is a web tool
Functional clues for hypothetical proteins based on genomic context analysis (2004)
Tobias Doerks, Christian Von Mering, Peer Bork
in prokaryotes
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...
Suyama, Mikita, Torrents, David, Bork, Peer
Summary: BLAST2GENE is a program that allows a detailed analysis of genomic regions containing completely or partially duplicated genes. From a BLAST (or BL2SEQ) comparison of a protein or nucleotide...
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...
Comparison of computational methods for the identification of cell cycle regulated genes (2004)
De Lichtenberg, Ulrik, Jensen, Lars Juhl, Fausbøll, Anders, Jensen, Thomas Skøt, Bork, Peer, Brunak, Søren
Motivation: DNA microarrays have been used extensively to study the cell cycle transcription programme in a number of model organisms. The Saccharomyces cerevisiae data in particular have been...
The WHy domain mediates the response to desiccation in plants and bacteria (2004)
Ciccarelli, Francesca D., Bork, Peer
Motivation: The Hypersensitive Response (HR) is a process activated by plants after microbial infection. Its main phenotypic effects are both a programmed death of the plant cells nearby the...
Jensen, Lars Juhl, Lagarde, Julien, Von Mering, Christian, Bork, Peer
DNA microarray experiments have provided vast amounts of data which can be used for inferring gene function. However, most methods for predicting functional associations between genes from expression...
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes (2004)
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...
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...
Bourque, Guillaume, Zdobnov, Evgeny M., Bork, Peer, Pevzner, Pavel A., Tesler, Glenn
Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the...
Suyama, Mikita, Torrents, David, Bork, Peer
Summary: BLAST2GENE is a program that allows a detailed analysis of genomic regions containing completely or partially duplicated genes. From a BLAST (or BL2SEQ) comparison of a protein or nucleotide...
Suyama, Mikita, Torrents, David, Bork, Peer
Summary: BLAST2GENE is a program that allows a detailed analysis of genomic regions containing completely or partially duplicated genes. From a BLAST (or BL2SEQ) comparison of a protein or nucleotide...
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...
Comparison of computational methods for the identification of cell cycle regulated genes (2004)
De Lichtenberg, Ulrik, Jensen, Lars Juhl, Fausbøll, Anders, Jensen, Thomas Skøt, Bork, Peer, Brunak, Søren
Motivation: DNA microarrays have been used extensively to study the cell cycle transcription programme in a number of model organisms. The Saccharomyces cerevisiae data in particular have been...
The WHy domain mediates the response to desiccation in plants and bacteria (2004)
Ciccarelli, Francesca D., Bork, Peer
Motivation: The Hypersensitive Response (HR) is a process activated by plants after microbial infection. Its main phenotypic effects are both a programmed death of the plant cells nearby the...
The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold (2003)
Ciccarelli, Francesca D, Izaurralde, Elisa, Bork, Peer
Abstract Background Multimeric protein complexes have a role in many cellular pathways and are highly interconnected with various other proteins. The characterization of their domain composition and...
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...
Increase of functional diversity by alternative splicing (2003)
Kriventseva,Evgenia V., Koch,Ina, Apweiler,Rolf, Vingron,Martin, Bork,Peer, Gelfand,Mikhail S., ...
A large-scale analysis of protein isoforms arising from alternative splicing shows that alternative splicing tends to insert or delete complete protein domains more frequently than expected by...
The InterPro Database, 2003 brings increased coverage and new features (2003)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
Increase of functional diversity by alternative splicing (2003)
Kriventseva, Evgenia V., Koch, Ina, Apweiler, Rolf, Vingron, Martin, Bork, Peer, Gelfand, Mikhail S., ...
A large-scale analysis of protein isoforms arising from alternative splicing shows that alternative splicing tends to insert or delete complete protein domains more frequently than expected by...
Impact of selection, mutation rate and genetic drift on human genetic variation (2003)
Shamil Sunyaev, Fyodor A. Kondrashov, Peer Bork, Vasily Ramensky
Copyright © 2003 Oxford University Press The accumulation of genome-wide information on single nucleotide polymorphisms in humans provides an unprecedented opportunity to detect the evolutionary...
Rune Linding, Christine Gemünd, Sophie Chabanis-davidson, Morten Mattingsdal, Scott Cameron, ...
Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line...
The InterPro Database, 2003 brings increased coverage and new features (2003)
Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
an all-alpha-helix fold (2003)
Francesca D Ciccarelli, Elisa Izaurralde, Peer Bork, Open Access
The PAM domain, a multi-protein complex-associated module with
Impact of selection, mutation rate and genetic drift on human genetic variation (2003)
Sunyaev, Shamil, Kondrashov, Fyodor A., Bork, Peer, Ramensky, Vasily
The accumulation of genome-wide information on single nucleotide polymorphisms in humans provides an unprecedented opportunity to detect the evolutionary forces responsible for heterogeneity of the...
Puntervoll, Pål, Linding, Rune, Gemünd, Christine, Chabanis-Davidson, Sophie, Mattingsdal, Morten, Cameron, Scott, ...
Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line...
Update on XplorMed: a web server for exploring scientific literature (2003)
Perez-Iratxeta, Carolina, Pérez, Antonio, Bork, Peer, Andrade, Miguel
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...
A Genome-Wide Survey of Human Pseudogenes (2003)
Torrents, David, Suyama, Mikita, Zdobnov, Evgeny, Bork, Peer
We screened all intergenic regions in the human genome to identify pseudogenes with a combination of homology searches and a functionality test using the ratio of silent to replacement nucleotide...
STRING: a database of predicted functional associations between proteins (2003)
Mering, Christian Von, Huynen, Martijn, Jaeggi, Daniel, Schmidt, Steffen, Bork, Peer, Snel, Berend
Functional links between proteins can often be inferred from genomic associations between the genes that encode them: groups of genes that are required for the same function tend to show similar...
The InterPro Database, 2003 brings increased coverage and new features (2003)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
Impact of selection, mutation rate and genetic drift on human genetic variation (2003)
Sunyaev, Shamil, Kondrashov, Fyodor A., Bork, Peer, Ramensky, Vasily
The accumulation of genome-wide information on single nucleotide polymorphisms in humans provides an unprecedented opportunity to detect the evolutionary forces responsible for heterogeneity of the...
Krause, Roland, Von Mering, Christian, Bork, Peer
Motivation: The analysis of protein–protein interactions allows for detailed exploration of the cellular machinery. The biochemical purification of protein complexes followed by identification of...
Impact of selection, mutation rate and genetic drift on human genetic variation (2003)
Sunyaev, Shamil, Kondrashov, Fyodor A., Bork, Peer, Ramensky, Vasily
The accumulation of genome-wide information on single nucleotide polymorphisms in humans provides an unprecedented opportunity to detect the evolutionary forces responsible for heterogeneity of the...
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...
Identification of attenuation and antitermination regulation in prokaryotes (2002)
Lathe, Warren C, Suyama, Mikita, Bork, Peer
Abstract Many operons of biochemical pathways in bacterial genomes are regulated by processes called attenuation and antitermination. Though the specific mechanism can be quite different, attenuation...
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...
Mulder, Nicola J., Apweiler, Rolf, Attwood, Terri K., Bairoch, Amos, Bateman, Alex, ...
The exponential increase in the submission of nucleotide sequences to the nucleotide sequence database by genome sequencing centres has resulted in a need for rapid, automatic methods for...
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,...
Comparative analysis of protein interaction networks (2002)
Recent advances in proteomics and computational biology have lead to a flood of protein interaction data and resulting interaction networks (e.g. (Gavin et al., 2002)). Here I first analyse the...
Common exon duplication in animals and its role in alternative splicing (2002)
Letunic, Ivica, Copley, Richard R., Bork, Peer
When searching the genomes of human, fly and worm for cases of exon duplication, we found that about 10% of all genes contain tandemly duplicated exons. In the course of the analyses, 2438...
Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions (2002)
Doerks, Tobias, Copley, Richard R., Schultz, Jörg, Ponting, Chris P., Bork, Peer
Iyer, Lakshminarayan M, Aravind, L, Bork, Peer, Hofmann, Kay, Mushegian, Arcady R, Zhulin, Igor B, ...
Abstract Background Computational predictions are critical for directing the experimental study of protein functions. Therefore it is paradoxical when an apparently erroneous computational prediction...
Eisenhaber, Birgit, Bork, Peer, Eisenhaber, Frank
To investigate the occurrence of glycosylphosphatidylinositol (GPI) lipid anchor modification in various taxonomic ranges, potential substrate proteins have been searched for in completely sequenced...
Huynen, Martijn A., Snel, Berend, Bork, Peer, Gibson, Toby J.
Much has been learned about the cellular pathology of Friedreich’s ataxia, a recessive neurodegenerative disease resulting from insufficient expression of the mitochondrial protein frataxin....
Prediction of deleterious human alleles (2001)
Sunyaev, Shamil, Ramensky, Vasily, Koch, Ina, Lathe III, Warren, Kondrashov, Alexey S., Bork, Peer
Single nucleotide polymorphisms (SNPs) constitute the bulk of human genetic variation, occurring with an average density of ∼1/1000 nucleotides of a genotype. SNPs are either neutral allelic...
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 )....
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...
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...
HGBASE: a database of SNPs and other variations in and around human genes (2000)
Brookes, Anthony J., Lehväslaiho, Heikki, Siegfried, Marianne, Boehm, Jana G., Yuan, Yan P., Sarkar, Chandra M., ...
Human genome polymorphism is expected to play a key role in defining the etiologic basis of phenotypic differences between individuals in aspects such as drug responses and common disease...
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...
Pathway alignment : application to the comparative analysis of glycolytic enzymes (1999)
Dandekar, Thomas, Schuster, Stefan, Snel, Berend, Huynen, Martijn, Bork, Peer
Comparative analysis of metabolic pathways in different genomes yields important information on their evolution, on pharmacological targets and on biotechnological applications. In this study on...
Ponting, Chris P., Schultz, Jörg, Milpetz, Frank, Bork, Peer
SMART is a simple modular architecture research tool and database that provides domain identification and annotation on the WWW (http://coot.embl-heidelberg.de/SMART ). The tool compares query...
Enzymes Thomas Dandekar, Thomas Dandekar, Stefan Schuster, Berend Snel, Martijn Huynen, Peer Bork
INTRODUCTION Sequence alignment is a well-established tool for investigating and comparing nucleic acids from di#erent species and for identifying characteristic gaps, insertions and dissimilarities....
Applying Logic Programming to Derive Novel Functional Information (1999)
of this work in other works must
The Sequence Alerting Server--a new WEB server (1997)
Hegyi, Hedvig, Lai, Jen-Mai, Bork, Peer
A Sequence Alteiling Server with a WWW inteiface is described which informs users with query sequences in database searches about new entries in protein databases related to their query....
Downloaded From, C. Ouzounis, P. Bork, G. Casari, C. Sander, Christos Ouzounis, ...
Article cited in:
Klassifizierung, Charakterisierung und Evolution extrazellulärer Proteinmodule / (1994)
Text engl. - Enth. 24 Sonderabdr. aus verschiedenen Zeitschr.
Erkennung und Nutzung von Eigenschaftsmustern in Proteinsequenzen. (1990)
Leipzig, Univ., Diss. A, 1990 (Nicht f.d. Austausch).
Dimopoulos, George, Casavant, Thomas L., Chang, Shereen, Scheetz, Todd, Roberts, Chad, Donohue, Micca, ...
Together with AIDS and tuberculosis, malaria is at the top of the list of devastating infectious diseases. However, molecular genetic studies of its major vector, Anopheles gambiae, are still quite...
Positionally cloned human disease genes: Patterns of evolutionary conservation and functional motifs
Mushegian, Arcady R., Bassett, Douglas E., Boguski, Mark S., Bork, Peer, Koonin, Eugene V.
Positional cloning has already produced the sequences of more than 70 human genes associated with specific diseases. In addition to their medical importance, these genes are of interest as a set of...
Huynen, Martijn A., Bork, Peer
The determination of complete genome sequences provides us with an opportunity to describe and analyze evolution at the comprehensive level of genomes. Here we compare nine genomes with respect to...
SMART, a simple modular architecture research tool: Identification of signaling domains
Schultz, Jörg, Milpetz, Frank, Bork, Peer, Ponting, Chris P.
Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows...
Iyer, Lakshminarayan M, Aravind, L, Bork, Peer, Hofmann, Kay, Mushegian, Arcady R, Zhulin, Igor B, ...
Herold, Andrea, Suyama, Mikita, Rodrigues, João P., Braun, Isabelle C., Kutay, Ulrike, Carmo-Fonseca, Maria, ...
Vertebrate TAP (also called NXF1) and its yeast orthologue, Mex67p, have been implicated in the export of mRNAs from the nucleus. The TAP protein includes a noncanonical RNP-type RNA binding domain,...
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 )....
HGBASE: a database of SNPs and other variations in and around human genes
Brookes, Anthony J., Lehväslaiho, Heikki, Siegfried, Marianne, Boehm, Jana G., Yuan, Yan P., Sarkar, Chandra M., ...
Human genome polymorphism is expected to play a key role in defining the etiologic basis of phenotypic differences between individuals in aspects such as drug responses and common disease...
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...
The identification of functional modules from the genomic association of genes
Snel, Berend, Bork, Peer, Huynen, Martijn A.
By combining the pairwise interactions between proteins, as predicted by the conserved co-occurrence of their genes in operons, we obtain protein interaction networks. Here we study the properties of...
Thomasová, Dana, Ton, Lucas Q., Copley, Richard R., Zdobnov, Evgeny M., Wang, Xuelan, Hong, Young S., ...
We have sequenced six overlapping clones from a library of bacterial artificial chromosome (BAC) clones derived from a laboratory strain of the mosquito, Anopheles gambiae, the major vector of human...
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...
Human non-synonymous SNPs: server and survey
Ramensky, Vasily, Bork, Peer, Sunyaev, Shamil
Human single nucleotide polymorphisms (SNPs) represent the most frequent type of human population DNA variation. One of the main goals of SNP research is to understand the genetics of the human...
Schell, Mark A., Karmirantzou, Maria, Snel, Berend, Vilanova, David, Berger, Bernard, Pessi, Gabriella, ...
Bifidobacteria are Gram-positive prokaryotes that naturally colonize the human gastrointestinal tract (GIT) and vagina. Although not numerically dominant in the complex intestinal microflora, they...
STRING: a database of predicted functional associations between proteins
Von Mering, Christian, Huynen, Martijn, Jaeggi, Daniel, Schmidt, Steffen, Bork, Peer, Snel, Berend
Functional links between proteins can often be inferred from genomic associations between the genes that encode them: groups of genes that are required for the same function tend to show similar...
The InterPro Database, 2003 brings increased coverage and new features
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
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...
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins
Puntervoll, Pål, Linding, Rune, Gemünd, Christine, Chabanis-Davidson, Sophie, Mattingsdal, Morten, Cameron, Scott, ...
Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line...
Nonsense-mediated mRNA decay in Drosophila:at the intersection of the yeast and mammalian pathways
Gatfield, David, Unterholzner, Leonie, Ciccarelli, Francesca D., Bork, Peer, Izaurralde, Elisa
The nonsense-mediated mRNA decay (NMD) pathway promotes the rapid degradation of mRNAs containing premature stop codons (PTCs). In Caenorhabditis elegans, seven genes (smg1–7) playing an essential...
Predicting Protein Cellular Localization Using a Domain Projection Method
Mott, Richard, Schultz, Jörg, Bork, Peer, Ponting, Chris P.
We investigate the co-occurrence of domain families in eukaryotic proteins to predict protein cellular localization. Approximately half (300) of SMART domains form a “small-world network”, linked...
Genome evolution reveals biochemical networks and functional modules
Von Mering, Christian, Zdobnov, Evgeny M., Tsoka, Sophia, Ciccarelli, Francesca D., Pereira-Leal, Jose B., Ouzounis, Christos A., ...
The analysis of completely sequenced genomes uncovers an astonishing variability between species in terms of gene content and order. During genome history, the genes are frequently rear-ranged,...
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...
Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences
Huynen, Martijn, Snel, Berend, Lathe, Warren, Bork, Peer
Various new methods have been proposed to predict functional interactions between proteins based on the genomic context of their genes. The types of genomic context that they use are Type I: the...
Forler, Daniel, Rabut, Gwénaël, Ciccarelli, Francesca D., Herold, Andrea, Köcher, Thomas, Niggeweg, Ricarda, ...
Metazoan NXF1-p15 heterodimers promote the nuclear export of bulk mRNA across nuclear pore complexes (NPCs). In vitro, NXF1-p15 forms a stable complex with the nucleoporin RanBP2/Nup358, a component...
A Genome-Wide Survey of Human Pseudogenes
Torrents, David, Suyama, Mikita, Zdobnov, Evgeny, Bork, Peer
We screened all intergenic regions in the human genome to identify pseudogenes with a combination of homology searches and a functionality test using the ratio of silent to replacement nucleotide...
ArrayProspector: a web resource of functional associations inferred from microarray expression data
Jensen, Lars Juhl, Lagarde, Julien, Von Mering, Christian, Bork, Peer
DNA microarray experiments have provided vast amounts of data which can be used for inferring gene function. However, most methods for predicting functional associations between genes from expression...
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...
Von Mering, Christian, Jensen, Lars J., Snel, Berend, Hooper, Sean D., Krupp, Markus, Foglierini, Mathilde, ...
A full description of a protein's function requires knowledge of all partner proteins with which it specifically associates. From a functional perspective, ‘association’ can mean direct physical...
InterPro, progress and status in 2005
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
Bourque, Guillaume, Zdobnov, Evgeny M., Bork, Peer, Pevzner, Pavel A., Tesler, Glenn
Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the...
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes
Zdobnov, Evgeny M., Campillos, Mónica, Harrington, Eoghan D., Torrents, David, Bork, Peer
We suggest an annotation strategy for genes encoded by retroviruses and transposable elements (RETRA genes) based on a set of marker protein domains. Usually RETRA genes are masked in vertebrate...
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...
A complex prediction: three-dimensional model of the yeast exosome
Aloy, Patrick, Ciccarelli, Francesca D., Leutwein, Christina, Gavin, Anne-Claude, Superti-Furga, Giulio, Bork, Peer, ...
We present a model of the yeast exosome based on the bacterial degradosome component polynucleotide phosphorylase (PNPase). Electron microscopy shows the exosome to resemble PNPase but with key...
The rhodanese/Cdc25 phosphatase superfamily: Sequence–structure–function relations
Rhodanese domains are ubiquitous structural modules occurring in the three major evolutionary phyla. They are found as tandem repeats, with the C-terminal domain hosting the properly structured...
Extraction of Transcript Diversity from Scientific Literature
Shah, Parantu K, Jensen, Lars J, Boué, Stéphanie, Bork, Peer
Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and...
G2D: a tool for mining genes associated with disease
Perez-Iratxeta, Carolina, Wjst, Matthias, Bork, Peer, Andrade, Miguel A
Büssow, Konrad, Scheich, Christoph, Sievert, Volker, Harttig, Ulrich, Schultz, Jörg, Simon, Bernd, ...
Netzel, Rebecca, Perez-Iratxeta, Carolina, Bork, Peer, Andrade, Miguel A.
Country-specific variations of the English language in the biomedical literature
SMART 5: domains in the context of genomes and networks
Letunic, Ivica, Copley, Richard R., Pils, Birgit, Pinkert, Stefan, Schultz, Jörg, Bork, Peer
The Simple Modular Architecture Research Tool (SMART) is an online resource () used for protein domain identification and the analysis of protein domain architectures. Many new features were...
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...
Complex genomic rearrangements lead to novel primate gene function
Ciccarelli, Francesca D., Von Mering, Christian, Suyama, Mikita, Harrington, Eoghan D., Izaurralde, Elisa, Bork, Peer
Orthologous genes that maintain a single-copy status in a broad range of species may indicate a selection against gene duplication. If this is the case, then duplicates of such genes that do survive...
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets
REHWINKEL, JAN, LETUNIC, IVICA, RAES, JEROEN, BORK, PEER, IZAURRALDE, ELISA
Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades mRNAs containing nonsense codons, and regulates the expression of naturally occurring transcripts. While NMD is not...
Suyama, Mikita, Harrington, Eoghan, Bork, Peer, Torrents, David
The identification and classification of genes and pseudogenes in duplicated regions still constitutes a challenge for standard automated genome annotation procedures. Using an integrated homology...
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
Suyama, Mikita, Torrents, David, Bork, Peer
PAL2NAL is a web server that constructs a multiple codon alignment from the corresponding aligned protein sequences. Such codon alignments can be used to evaluate the type and rate of nucleotide...
Identification and analysis of evolutionarily cohesive functional modules in protein networks
Campillos, Mónica, Von Mering, Christian, Jensen, Lars Juhl, Bork, Peer
The increasing number of sequenced genomes makes it possible to infer the evolutionary history of functional modules, i.e., groups of proteins that contribute jointly to the same cellular function in...
Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle
Perocchi, Fabiana, Jensen, Lars J, Gagneur, Julien, Ahting, Uwe, Von Mering, Christian, Bork, Peer, ...
Mitochondria carry out specialized functions; compartmentalized, yet integrated into the metabolic and signaling processes of the cell. Although many mitochondrial proteins have been identified,...
Environments shape the nucleotide composition of genomes
Foerstner, Konrad U, Von Mering, Christian, Hooper, Sean D, Bork, Peer
To test the impact of environments on genome evolution, we analysed the relative abundance of the nucleotides guanine and cytosine (‘GC content') of large numbers of sequences from four distinct...
Dimopoulos, George, Casavant, Thomas L., Chang, Shereen, Scheetz, Todd, Roberts, Chad, Donohue, Micca, ...
Together with AIDS and tuberculosis, malaria is at the top of the list of devastating infectious diseases. However, molecular genetic studies of its major vector, Anopheles gambiae, are still quite...
Positionally cloned human disease genes: Patterns of evolutionary conservation and functional motifs
Mushegian, Arcady R., Bassett, Douglas E., Boguski, Mark S., Bork, Peer, Koonin, Eugene V.
Positional cloning has already produced the sequences of more than 70 human genes associated with specific diseases. In addition to their medical importance, these genes are of interest as a set of...
Huynen, Martijn A., Bork, Peer
The determination of complete genome sequences provides us with an opportunity to describe and analyze evolution at the comprehensive level of genomes. Here we compare nine genomes with respect to...
SMART, a simple modular architecture research tool: Identification of signaling domains
Schultz, Jörg, Milpetz, Frank, Bork, Peer, Ponting, Chris P.
Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows...
Iyer, Lakshminarayan M, Aravind, L, Bork, Peer, Hofmann, Kay, Mushegian, Arcady R, Zhulin, Igor B, ...
Herold, Andrea, Suyama, Mikita, Rodrigues, João P., Braun, Isabelle C., Kutay, Ulrike, Carmo-Fonseca, Maria, ...
Vertebrate TAP (also called NXF1) and its yeast orthologue, Mex67p, have been implicated in the export of mRNAs from the nucleus. The TAP protein includes a noncanonical RNP-type RNA binding domain,...
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 )....
HGBASE: a database of SNPs and other variations in and around human genes
Brookes, Anthony J., Lehväslaiho, Heikki, Siegfried, Marianne, Boehm, Jana G., Yuan, Yan P., Sarkar, Chandra M., ...
Human genome polymorphism is expected to play a key role in defining the etiologic basis of phenotypic differences between individuals in aspects such as drug responses and common disease...
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...
The identification of functional modules from the genomic association of genes
Snel, Berend, Bork, Peer, Huynen, Martijn A.
By combining the pairwise interactions between proteins, as predicted by the conserved co-occurrence of their genes in operons, we obtain protein interaction networks. Here we study the properties of...
Thomasová, Dana, Ton, Lucas Q., Copley, Richard R., Zdobnov, Evgeny M., Wang, Xuelan, Hong, Young S., ...
We have sequenced six overlapping clones from a library of bacterial artificial chromosome (BAC) clones derived from a laboratory strain of the mosquito, Anopheles gambiae, the major vector of human...
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...
Human non-synonymous SNPs: server and survey
Ramensky, Vasily, Bork, Peer, Sunyaev, Shamil
Human single nucleotide polymorphisms (SNPs) represent the most frequent type of human population DNA variation. One of the main goals of SNP research is to understand the genetics of the human...
Schell, Mark A., Karmirantzou, Maria, Snel, Berend, Vilanova, David, Berger, Bernard, Pessi, Gabriella, ...
Bifidobacteria are Gram-positive prokaryotes that naturally colonize the human gastrointestinal tract (GIT) and vagina. Although not numerically dominant in the complex intestinal microflora, they...
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...
STRING: a database of predicted functional associations between proteins
Von Mering, Christian, Huynen, Martijn, Jaeggi, Daniel, Schmidt, Steffen, Bork, Peer, Snel, Berend
Functional links between proteins can often be inferred from genomic associations between the genes that encode them: groups of genes that are required for the same function tend to show similar...
The InterPro Database, 2003 brings increased coverage and new features
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
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...
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins
Puntervoll, Pål, Linding, Rune, Gemünd, Christine, Chabanis-Davidson, Sophie, Mattingsdal, Morten, Cameron, Scott, ...
Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line...
Nonsense-mediated mRNA decay in Drosophila:at the intersection of the yeast and mammalian pathways
Gatfield, David, Unterholzner, Leonie, Ciccarelli, Francesca D., Bork, Peer, Izaurralde, Elisa
The nonsense-mediated mRNA decay (NMD) pathway promotes the rapid degradation of mRNAs containing premature stop codons (PTCs). In Caenorhabditis elegans, seven genes (smg1–7) playing an essential...
Predicting Protein Cellular Localization Using a Domain Projection Method
Mott, Richard, Schultz, Jörg, Bork, Peer, Ponting, Chris P.
We investigate the co-occurrence of domain families in eukaryotic proteins to predict protein cellular localization. Approximately half (300) of SMART domains form a “small-world network”, linked...
Genome evolution reveals biochemical networks and functional modules
Von Mering, Christian, Zdobnov, Evgeny M., Tsoka, Sophia, Ciccarelli, Francesca D., Pereira-Leal, Jose B., Ouzounis, Christos A., ...
The analysis of completely sequenced genomes uncovers an astonishing variability between species in terms of gene content and order. During genome history, the genes are frequently rear-ranged,...
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...
Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences
Huynen, Martijn, Snel, Berend, Lathe, Warren, Bork, Peer
Various new methods have been proposed to predict functional interactions between proteins based on the genomic context of their genes. The types of genomic context that they use are Type I: the...
Forler, Daniel, Rabut, Gwénaël, Ciccarelli, Francesca D., Herold, Andrea, Köcher, Thomas, Niggeweg, Ricarda, ...
Metazoan NXF1-p15 heterodimers promote the nuclear export of bulk mRNA across nuclear pore complexes (NPCs). In vitro, NXF1-p15 forms a stable complex with the nucleoporin RanBP2/Nup358, a component...
A Genome-Wide Survey of Human Pseudogenes
Torrents, David, Suyama, Mikita, Zdobnov, Evgeny, Bork, Peer
We screened all intergenic regions in the human genome to identify pseudogenes with a combination of homology searches and a functionality test using the ratio of silent to replacement nucleotide...
ArrayProspector: a web resource of functional associations inferred from microarray expression data
Jensen, Lars Juhl, Lagarde, Julien, Von Mering, Christian, Bork, Peer
DNA microarray experiments have provided vast amounts of data which can be used for inferring gene function. However, most methods for predicting functional associations between genes from expression...
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...
Von Mering, Christian, Jensen, Lars J., Snel, Berend, Hooper, Sean D., Krupp, Markus, Foglierini, Mathilde, ...
A full description of a protein's function requires knowledge of all partner proteins with which it specifically associates. From a functional perspective, ‘association’ can mean direct physical...
InterPro, progress and status in 2005
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
Bourque, Guillaume, Zdobnov, Evgeny M., Bork, Peer, Pevzner, Pavel A., Tesler, Glenn
Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the...
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes
Zdobnov, Evgeny M., Campillos, Mónica, Harrington, Eoghan D., Torrents, David, Bork, Peer
We suggest an annotation strategy for genes encoded by retroviruses and transposable elements (RETRA genes) based on a set of marker protein domains. Usually RETRA genes are masked in vertebrate...
Complex genomic rearrangements lead to novel primate gene function
Ciccarelli, Francesca D., Von Mering, Christian, Suyama, Mikita, Harrington, Eoghan D., Izaurralde, Elisa, Bork, Peer
Orthologous genes that maintain a single-copy status in a broad range of species may indicate a selection against gene duplication. If this is the case, then duplicates of such genes that do survive...
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...
A complex prediction: three-dimensional model of the yeast exosome
Aloy, Patrick, Ciccarelli, Francesca D., Leutwein, Christina, Gavin, Anne-Claude, Superti-Furga, Giulio, Bork, Peer, ...
We present a model of the yeast exosome based on the bacterial degradosome component polynucleotide phosphorylase (PNPase). Electron microscopy shows the exosome to resemble PNPase but with key...
The rhodanese/Cdc25 phosphatase superfamily: Sequence–structure–function relations
Rhodanese domains are ubiquitous structural modules occurring in the three major evolutionary phyla. They are found as tandem repeats, with the C-terminal domain hosting the properly structured...
Extraction of Transcript Diversity from Scientific Literature
Shah, Parantu K, Jensen, Lars J, Boué, Stéphanie, Bork, Peer
Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and...
G2D: a tool for mining genes associated with disease
Perez-Iratxeta, Carolina, Wjst, Matthias, Bork, Peer, Andrade, Miguel A
Büssow, Konrad, Scheich, Christoph, Sievert, Volker, Harttig, Ulrich, Schultz, Jörg, Simon, Bernd, ...
Netzel, Rebecca, Perez-Iratxeta, Carolina, Bork, Peer, Andrade, Miguel A.
Country-specific variations of the English language in the biomedical literature
SMART 5: domains in the context of genomes and networks
Letunic, Ivica, Copley, Richard R., Pils, Birgit, Pinkert, Stefan, Schultz, Jörg, Bork, Peer
The Simple Modular Architecture Research Tool (SMART) is an online resource () used for protein domain identification and the analysis of protein domain architectures. Many new features were...
Environments shape the nucleotide composition of genomes
Foerstner, Konrad U, Von Mering, Christian, Hooper, Sean D, Bork, Peer
To test the impact of environments on genome evolution, we analysed the relative abundance of the nucleotides guanine and cytosine (‘GC content') of large numbers of sequences from four distinct...
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets
REHWINKEL, JAN, LETUNIC, IVICA, RAES, JEROEN, BORK, PEER, IZAURRALDE, ELISA
Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades mRNAs containing nonsense codons, and regulates the expression of naturally occurring transcripts. While NMD is not...
Identification and analysis of evolutionarily cohesive functional modules in protein networks
Campillos, Mónica, Von Mering, Christian, Jensen, Lars Juhl, Bork, Peer
The increasing number of sequenced genomes makes it possible to infer the evolutionary history of functional modules, i.e., groups of proteins that contribute jointly to the same cellular function in...
Suyama, Mikita, Harrington, Eoghan, Bork, Peer, Torrents, David
The identification and classification of genes and pseudogenes in duplicated regions still constitutes a challenge for standard automated genome annotation procedures. Using an integrated homology...
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
Suyama, Mikita, Torrents, David, Bork, Peer
PAL2NAL is a web server that constructs a multiple codon alignment from the corresponding aligned protein sequences. Such codon alignments can be used to evaluate the type and rate of nucleotide...
Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle
Perocchi, Fabiana, Jensen, Lars J, Gagneur, Julien, Ahting, Uwe, Von Mering, Christian, Bork, Peer, ...
Mitochondria carry out specialized functions; compartmentalized, yet integrated into the metabolic and signaling processes of the cell. Although many mitochondrial proteins have been identified,...
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...
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis
Hooper, Sean D, Boué, Stephanie, Krause, Roland, Jensen, Lars J, Mason, Christopher E, Ghanim, Murad, ...
Time-series analysis of whole-genome expression data during Drosophila melanogaster development indicates that up to 86% of its genes change their relative transcript level during embryogenesis. By...
Prediction of effective genome size in metagenomic samples
Raes, Jeroen, Korbel, Jan O, Lercher, Martin J, Von Mering, Christian, Bork, Peer
A novel computational approach shows a link between genome size and habitat from analysis of environmental metagenomic DNA reads.
New developments in the InterPro database
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs,...
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...
Comparative analysis of environmental sequences: potential and challenges
Foerstner, Konrad U, Von Mering, Christian, Bork, Peer
Environmental sequencing, also dubbed metagenomics, is increasingly being used to obtain insights into organismal communities in diverse habitats, and has a variety of potential applications...
4DXpress: a database for cross-species expression pattern comparisons
Haudry, Yannick, Berube, Hugo, Letunic, Ivica, Weeber, Paul-Daniel, Gagneur, Julien, Girardot, Charles, ...
In the major animal model species like mouse, fish or fly, detailed spatial information on gene expression over time can be acquired through whole mount in situ hybridization experiments. In these...
STITCH: interaction networks of chemicals and proteins
Kuhn, Michael, Von Mering, Christian, Campillos, Monica, Jensen, Lars Juhl, Bork, Peer
The knowledge about interactions between proteins and small molecules is essential for the understanding of molecular and cellular functions. However, information on such interactions is widely...
SuperTarget and Matador: resources for exploring drug-target relationships
Günther, Stefan, Kuhn, Michael, Dunkel, Mathias, Campillos, Monica, Senger, Christian, Petsalaki, Evangelia, ...
The molecular basis of drug action is often not well understood. This is partly because the very abundant and diverse information generated in the past decades on drugs is hidden in millions of...
NetworKIN: a resource for exploring cellular phosphorylation networks
Linding, Rune, Jensen, Lars Juhl, Pasculescu, Adrian, Olhovsky, Marina, Colwill, Karen, Bork, Peer, ...
Protein kinases control cellular responses by phosphorylating specific substrates. Recent proteome-wide mapping of protein phosphorylation sites by mass spectrometry has discovered thousands of in...
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...
Taxis, Christof, Keller, Philipp, Kavagiou, Zaharoula, Jensen, Lars Juhl, Colombelli, Julien, Bork, Peer, ...
Spindle pole bodies (SPBs) provide a structural basis for genome inheritance and spore formation during meiosis in yeast. Upon carbon source limitation during sporulation, the number of haploid...
Structural similarity to bridge sequence space: Finding new families on the bridges
Shah, Parantu K., Aloy, Patrick, Bork, Peer, Russell, Robert B.
Structures for protein domains have increased rapidly in recent years owing to advances in structural biology and structural genomics projects. New structures are often similar to those solved...
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...
Non-random retention of protein-coding overlapping genes in Metazoa
Soldà, Giulia, Suyama, Mikita, Pelucchi, Paride, Boi, Silvia, Guffanti, Alessandro, Rizzi, Ermanno, ...
A Novel Class of RanGTP Binding Proteins
Görlich, Dirk, Dabrowski, Marylena, Bischoff, F. Ralf, Kutay, Ulrike, Bork, Peer, Hartmann, Enno, ...
The importin-α/β complex and the GTPase Ran mediate nuclear import of proteins with a classical nuclear localization signal. Although Ran has been implicated also in a variety of other processes,...
Splicing factors stimulate polyadenylation via USEs at non-canonical 3′ end formation signals
Danckwardt, Sven, Kaufmann, Isabelle, Gentzel, Marc, Foerstner, Konrad U, Gantzert, Anne-Susan, Gehring, Niels H, ...
The prothrombin (F2) 3′ end formation signal is highly susceptible to thrombophilia-associated gain-of-function mutations. In its unusual architecture, the F2 3′ UTR contains an upstream sequence...
A Molecular Study of Microbe Transfer between Distant Environments
Hooper, Sean D., Raes, Jeroen, Foerstner, Konrad U., Harrington, Eoghan D., Dalevi, Daniel, Bork, Peer
KEGG Atlas mapping for global analysis of metabolic pathways
Okuda, Shujiro, Yamada, Takuji, Hamajima, Masami, Itoh, Masumi, Katayama, Toshiaki, Bork, Peer, ...
KEGG Atlas is a new graphical interface to the KEGG suite of databases, especially to the systems information in the PATHWAY and BRITE databases. It currently consists of a single global map and an...
Circular reasoning rather than cyclic expression
Jensen, Lars Juhl, De Lichtenberg, Ulrik, Jensen, Thomas Skøt, Brunak, Søren, Bork, Peer
A response to Combined analysis reveals a core set of cycling genes by Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden and Z Bar-Joseph. Genome Biol 2007, 8:R146.
Kunin, Victor, Raes, Jeroen, Harris, J Kirk, Spear, John R, Walker, Jeffrey J, Ivanova, Natalia, ...
To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from...
A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data
Foerstner, Konrad U., Doerks, Tobias, Creevey, Christopher J., Doerks, Anja, Bork, Peer
Korff, Sebastian, Woerner, Stefan M, Yuan, Yan P, Bork, Peer, Von Knebel Doeberitz, Magnus, Gebert, Johannes
A Nitrile Hydratase in the Eukaryote Monosiga brevicollis
Foerstner, Konrad U., Doerks, Tobias, Muller, Jean, Raes, Jeroen, Bork, Peer
Bacterial nitrile hydratase (NHases) are important industrial catalysts and waste water remediation tools. In a global computational screening of conventional and metagenomic sequence data for...
Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages
Pincus, David, Letunic, Ivica, Bork, Peer, Lim, Wendell A.
Multicellular animals use a three-part molecular toolkit to mediate phospho-tyrosine signaling: Tyrosine kinases (TyrK), protein tyrosine phosphatases (PTP), and Src Homology 2 (SH2) domains...
Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution
Quijano, Carlos, Tomancak, Pavel, Lopez-Marti, Jesus, Suyama, Mikita, Bork, Peer, Milan, Marco, ...
Genes occurring in conserved, tandemly-arrayed clusters in Drosophila melanogaster are co-expressed to a much higher extent than other duplicated genes.
Perotti, Christian, Liu, Ruixuan, Parusel, Christine T, Böcher, Nadine, Schultz, Jörg, Bork, Peer, ...
STRING 8—a global view on proteins and their functional interactions in 630 organisms
Jensen, Lars J., Kuhn, Michael, Stark, Manuel, Chaffron, Samuel, Creevey, Chris, Muller, Jean, ...
Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data...
SMART 6: recent updates and new developments
Letunic, Ivica, Doerks, Tobias, Bork, Peer
Simple modular architecture research tool (SMART) is an online tool (http://smart.embl.de/) for the identification and annotation of protein domains. It provides a user-friendly platform for the...
InterPro: the integrative protein signature database
Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse...
Sequence-based feature prediction and annotation of proteins
Juncker, Agnieszka S, Jensen, Lars J, Pierleoni, Andrea, Bernsel, Andreas, Tress, Michael L, Bork, Peer, ...
The combination of prediction tools in complex workflows and pipelines facilitates prediction of protein features from sequence.
Quantifying environmental adaptation of metabolic pathways in metagenomics
Gianoulis, Tara A., Raes, Jeroen, Patel, Prianka V., Bjornson, Robert, Korbel, Jan O., Letunic, Ivica, ...
Recently, approaches have been developed to sample the genetic content of heterogeneous environments (metagenomics). However, by what means these sequences link distinct environmental conditions with...
Discovering Functional Novelty in Metagenomes: Examples from Light-Mediated Processes▿
Singh, Amoolya H., Doerks, Tobias, Letunic, Ivica, Raes, Jeroen, Bork, Peer
The emerging coverage of diverse habitats by metagenomic shotgun data opens new avenues of discovering functional novelty using computational tools. Here, we apply three different concepts for...