Quantitative phylogenetic assessment of microbial communities in diverse environments (2008)
Von Mering, C., Hugenholtz, P., Raes, J., Tringe, S.G., Doerks, T., Jensen, L.J., ...
networks on protein secondary structure. In: O Benhar, S (2008)
B Rost, B Rost, P Delgiudice, M Gr, Olfo (eds. Neural, ...
protein structure prediction? TIBS 18:120-123.
Summary: The Helmholtz Network for Bioinformatics (HNB) (2008)
T. Crass, I. Antes, R. Basekow, P. Bork, C. Buning, M. Christensen, ...
Prediction of effective genome size in metagenomic samples. (2007)
Raes, J, Korbel, J O, Lercher, M J, Von Mering, C, Bork, P
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) from short...
String 7-recent developments in the integration and prediction of protein interactions (2007)
Mering, C. Von, Jensen, L.J., Kuhn, M., Chaffron, S., Doerks, T., Kruger, B., ...
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...
Insights into social insects from the genome of the honeybee Apis mellifera (2006)
Weinstock, GM, Robinson, GE, Gibbs, RA, Worley, KC, Evans, JD, Maleszka, R, ...
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,...
Insights into social insects from the genome of the honeybee Apis mellifera (2006)
Weinstock, GM, Robinson, GE, Gibbs, RA, Worley, KC, Evans, JD, Maleszka, R, ...
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,...
Similar gene expression profiles do not imply similar tissue functions (2006)
Yanai, I., Korbel, J. O., Boue, S., McWeeney, S. K., Bork, P., Lercher, M. J.
Although similarities in gene expression among tissues are commonly inferred to reflect functional constraints, this has never been formally tested. Furthermore, it is unclear which evolutionary...
InterPro, progress and status in 2005 (2005)
Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., ...
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,...
doi:10.1093/nar/gki442 InterProScan: protein domains identifier (2005)
E. Quevillon, V. Silventoinen, S. Pillai, N. Harte, N. Mulder, R. Apweiler, ...
InterProScan [E. M. Zdobnov and R. Apweiler (2001) Bioinformatics, 17, 847–848] is a tool that combines different protein signature recognition methods from
Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., ...
The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single...
Crass, T., Antes, I., Basekow, W., Bork, P., Buning, C., Christensen, M., ...
The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single...
Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., ...
The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single...
Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., ...
Summary: The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a...
The InterPro Database, 2003 brings increased coverage and new features (2003)
Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Barrell, D., Bateman, A., ...
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...
Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., ...
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...
Fredman, D., Siegfried, M., Yuan, Y. P., Bork, P., Lehväslaiho, H., Brookes, A. J.
HGVbase (Human Genome Variation database; http://hgvbase.cgb.ki.se, formerly known as HGBASE) is an academic effort to provide a high quality and non-redundant database of available genomic...
Initial sequencing and analysis of the human genome (2001)
Lander, ES, Linton, LM, Birren, B, Nusbaum, C, Zody, MC, Baldwin, J, ...
The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and...
Gönczy, P., Echeverri, C., Oegema, K., Coulson, A., Jones, S. J., Copley, R. R., ...
Genome sequencing projects generate a wealth of information; however, the ultimate goal of such projects is to accelerate the identification of the biological function of genes. This creates a need...
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene (2000)
Snel, B., Lehmann, G., Bork, P., Huynen, M. A.
The repeated occurrence of genes in each other’s neighbourhood on genomes has been shown to indicate a functional association between the proteins they encode. Here we introduce STRING (search tool...
Stutz, F., Bachi, A., Doerks, T., Braun, I. C., Seraphin, B., Wilm, M., ...
Smalla, M, Schmieder, P, Kelly, M, Ter Laak, A, Krause, G, Ball, L, ...
A Novel Class of RanGTP Binding Proteins (1997)
Goerlich, D., Dabrowski, M., Bischoff, F. R., Kutay, U., Bork, P., Hartmann, E., ...
A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins (1997)
Bork, P., Hofmann, K., Bucher, P., Neuwald, A. F., Altschul, S. F., Koonin, E. V.
Computer analysis of a conserved domain, BRCT, first described at the carboxyl terminus of the breast cancer protein BRCA1, a p53 binding protein (53BP1), and the yeast cell cycle checkpoint protein...
Structural motifs of the PKD1 protein (1996)
Löhning, C., Pohlschmidt, M., Glücksmann-Kuis, M. A., Duyk, G., Bork, P., Schneider, M. O., ...
The complete sequence of the polycystic kidney disease gene (PKD1) and its transcript have been described. The predicted protein is not a member of a previously described gene family, but contains...
Downloaded From, C. Ouzounis, P. Bork, G. Casari, C. Sander, Christos Ouzounis, ...
Article cited in:
A fast, sensitive pattern-matching approach for protein sequences (1993)
Pattern-matching algorithms are a powerful tool for finding similarities and relationships among the steadily growing amount of known protein sequences. We present a fast, sensitive pattern-matching...
Bork, P, Sander, C, Valencia, A
The functionally diverse actin, hexokinase, and hsp70 protein families have in common an ATPase domain of known three-dimensional structure. Optimal superposition of the three structures and...
Proposed acquisition of an animal protein domain by bacteria.
A systematic screen of a protein sequence data base confirms that the fibronectin type III (Fn3) domain is widely distributed among animal proteins and occurs also in several bacterial...
Fredman, D., Siegfried, M., Yuan, Y. P., Bork, P., Lehväslaiho, H., Brookes, A. J.
HGVbase (Human Genome Variation database; http://hgvbase.cgb.ki.se, formerly known as HGBASE) is an academic effort to provide a high quality and non-redundant database of available genomic variation...
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene
Snel, B., Lehmann, G., Bork, P., Huynen, M. A.
The repeated occurrence of genes in each other’s neighbourhood on genomes has been shown to indicate a functional association between the proteins they encode. Here we introduce STRING (search tool...
SMART: identification and annotation of domains from signalling and extracellular protein sequences.
Ponting, C P, Schultz, J, Milpetz, F, Bork, P
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...
Koonin, E V, Bork, P, Sander, C
Using computer methods for database search, multiple alignment, protein sequence motif analysis and secondary structure prediction, a putative new RNA-binding motif was identified. The novel motif is...
Yeast chromosome III: new gene functions.
Koonin, E V, Bork, P, Sander, C
One year after the release of the sequence of yeast chromosome III, we have re-examined its open reading frames (ORFs) by computer methods. More than 61% of the 171 probable gene products have...
Pathway alignment: application to the comparative analysis of glycolytic enzymes.
Dandekar, T, Schuster, S, Snel, B, Huynen, M, Bork, P
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...
Stutz, F, Bachi, A, Doerks, T, Braun, I C, Séraphin, B, Wilm, M, ...
Vertebrate TAP and its yeast ortholog Mex67p are involved in the export of messenger RNAs from the nucleus. TAP has also been implicated in the export of simian type D viral RNAs bearing the...
Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III.
Bork, P., Ouzounis, C., Sander, C., Scharf, M., Schneider, R., Sonnhammer, E.
With the completion of the first phase of the European yeast genome sequencing project, the complete DNA sequence of chromosome III of Saccharomyces cerevisiae has become available (Oliver, S. G., et...
Bork, P., Sander, C., Valencia, A.
Kinases that catalyze phosphorylation of sugars, called here sugar kinases, can be divided into at least three distinct nonhomologous families. The first is the hexokinase family, which contains many...
Koonin, E. V., Mushegian, A. R., Tatusov, R. L., Altschul, S. F., Bryant, S. H., Bork, P., ...
Using computer methods for multiple alignment, sequence motif search, and tertiary structure modeling, we show that eukaryotic translation elongation factor 1 gamma (EF1 gamma) contains an N-terminal...
A new family of carbon-nitrogen hydrolases.
Using computer methods for database search and multiple alignment, statistically significant sequence similarities were identified between several nitrilases with distinct substrate specificity,...
New protein functions in yeast chromosome VIII.
Ouzounis, C., Bork, P., Casari, G., Sander, C.
The analysis of the 269 open reading frames of yeast chromosome VIII by computational methods has yielded 24 new significant sequence similarities to proteins of known function. The resulting...
Bork, P., Gellerich, J., Groth, H., Hooft, R., Martin, F.
Study of the most conserved region in many beta/alpha-barrels, the phosphate-binding site, revealed a sequence motif in a few beta/alpha-barrels with known tertiary structure, namely glycolate...
The SEA module: a new extracellular domain associated with O-glycosylation.
Using a variety of homology search methods and multiple alignments, a new extracellular module was identified in (1) agrin, (2) enterokinase, (3) a 63-kDa sea urchin sperm protein, (4) perlecan, (5)...
Self-organizing hierarchic networks for pattern recognition in protein sequence.
Hanke, J., Beckmann, G., Bork, P., Reich, J. G.
We present a method based on hierarchical self-organizing maps (SOMs) for recognizing patterns in protein sequences. The method is fully automatic, does not require prealigned sequences, is...
The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues.
Bork, P., Brown, N. P., Hegyi, H., Schultz, J.
A thorough sequence analysis of the various members of the eukaryotic protein serine/threonine phosphatase 2C (PP2C) family revealed the conservation of 11 motifs. These motifs could be identified in...
SAM as a protein interaction domain involved in developmental regulation.
Schultz, J., Ponting, C. P., Hofmann, K., Bork, P.
More than 60 previously undetected SAM domain-containing proteins have been identified using profile searching methods. Among these are over 40 EPH-related receptor tyrosine kinases (RPTK),...
Smalla, M., Schmieder, P., Kelly, M., Ter Laak, A., Krause, G., Ball, L., ...
The sterile alpha motif (SAM) is a protein interaction domain of around 70 amino acids present predominantly in the N- and C-termini of more than 60 diverse proteins that participate in signal...
Quantitative assessment of protein function prediction from metagenomics shotgun sequences
Harrington, E. D., Singh, A. H., Doerks, T., Letunic, I., Von Mering, C., Jensen, L. J., ...
To assess the potential of protein function prediction in environmental genomics data, we analyzed shotgun sequences from four diverse and complex habitats. Using homology searches as well as...