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...
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...
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,...
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...
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...
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.
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...
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...
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...
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...
Birgit Eisenhaber, Peer Bork, Frank Eisenhaber
this paper, we present an analysis of the available sequence data aimed at a more complete description of this sequence signal in terms of physical properties of amino acid residues that are probably...
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 )....
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...
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...