Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes (2009)
Kastenmüller, Gabi, Schenk, Maria, Gasteiger, Johann, Mewes, Hans-Werner
Abstract Identifying the biochemical basis of microbial phenotypes is a main objective of comparative genomics. Here we present a novel method using multivariate machine learning techniques for...
The DICS repository: module-assisted analysis of disease-related gene lists (2009)
Dietmann, Sabine, Georgii, Elisabeth, Antonov, Alexey, Tsuda, Koji, Mewes, Hans-Werner
Summary: The DICS database is a dynamic web repository of computationally predicted functional modules from the human protein-protein interaction network. It provides references to the CORUM,...
PEDANT covers all complete RefSeq genomes (2009)
Walter, Mathias C., Rattei, Thomas, Arnold, Roland, Güldener, Ulrich, Münsterkötter, Martin, Nenova, Karamfilka, ...
The PEDANT genome database provides exhaustive annotation of nearly 3000 publicly available eukaryotic, eubacterial, archaeal and viral genomes with more than 4.5 million proteins by a broad set of...
The DICS repository: module-assisted analysis of disease-related gene lists (2009)
Dietmann, Sabine, Georgii, Elisabeth, Antonov, Alexey, Tsuda, Koji, Mewes, Hans-Werner
Summary: The DICS database is a dynamic web repository of computationally predicted functional modules from the human protein–protein interaction network. It provides references to the CORUM,...
Apweiler, Rolf, Aslanidis, Charalampos, Deufel, Thomas, Gerstner, Andreas, Hansen, Jens, Hochstrasser, Dennis, ...
The field of clinical proteomics offers opportunities to identify new disease biomarkers in body fluids, cells and tissues. These biomarkers can be used in clinical applications for diagnosis,...
Can We Estimate the Accuracy of ADMET Predictions? (2008)
Igor V. Tetko, Pierre Bruneau, Hans-werner Mewes, Douglas C. Rohrer, Gennadiy I. Poda
property-based similarity Teaser: Is there a distinct relationship between the accuracy of prediction and molecular similarity? Can we estimate the accuracy of property prediction for new compounds?...
resource of functional annotation of proteins (2007)
Cathy H. Wu, Hongzhan Huang, Leslie Arminski, Jorge Castro-alvear, Yongxing Chen, Zhang-zhi Hu, ...
The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in...
Winona C. Barker, John S. Garavelli, Peter B. Mcgarvey, Christopher R. Marzec, Bruce C. Orcutt, Geetha Y. Srinivasarao, ...
The Protein Information Resource (PIR;
Winona C. Barker, John S. Garavelli, Zhenglin Hou, Hongzhan Huang, Robert S. Ledley, Peter B. Mcgarvey, ...
Winona C. Barker, John S. Garavelli, Hongzhan Huang, Peter B. Mcgarvey, Bruce C. Orcutt, Geetha Y. Srinivasarao, ...
The Protein Information Resource (PIR) produces the largest, most comprehensive, annotated protein sequence database in the public domain, the PIRInternational Protein Sequence Database, in...
Dmitrij Frishman, Jean Hani, Agnes Metanomski, Alfred Zollner, Hans-werner Mewes
Motivation: Enormous demand for fast and accurate analysis of biological sequences is fuelled by the pace of genome analysis efforts. There is also an acute need in reliable up-to-date genomic...
PEDANT genome database: 10 years online (2007)
M. Louise Riley, Thorsten Schmidt, Irena I. Artamonova, Christian Wagner, Andreas Volz, Klaus Heumann, ...
The PEDANT genome database provides exhaustive annotation of 468 genomes by a broad set of bioinformatics algorithms. We describe recent developments of the PEDANT Web server. The all-new Graphical...
PEDANT genome database: 10 years online (2007)
Riley, M. Louise, Schmidt, Thorsten, Artamonova, Irena I., Wagner, Christian, Volz, Andreas, Heumann, Klaus, ...
The PEDANT genome database provides exhaustive annotation of 468 genomes by a broad set of bioinformatics algorithms. We describe recent developments of the PEDANT Web server. The all-new Graphical...
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis (2006)
Kahmann, Regine, Bölker, Michael, Ma, Li-Jun, Brefort, Thomas, Saville, Barry J, ...
Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence...
Igor V. Tetko, Georg Haberer, Stephen Rudd, Blake Meyers, Hans-Werner Mewes
Scaffold/matrix attachment regions (S/MARs) are essential for structural organization of the chromatin within the nucleus and serve as anchors of chromatin loop domains. A significant fraction of...
PEDANT genome database: 10 years online (2006)
Riley, M. Louise, Schmidt, Thorsten, Artamonova, Irena I., Wagner, Christian, Volz, Andreas, Heumann, Klaus, ...
The PEDANT genome database provides exhaustive annotation of 468 genomes by a broad set of bioinformatics algorithms. We describe recent developments of the PEDANT Web server. The all-new Graphical...
MPact: the MIPS protein interaction resource on yeast (2006)
Güldener, Ulrich, Münsterkötter, Martin, Oesterheld, Matthias, Pagel, Philipp, Ruepp, Andreas, Mewes, Hans-Werner, ...
In recent years, the Munich Information Center for Protein Sequences (MIPS) yeast protein–protein interaction (PPI) dataset has been used in numerous analyses of protein networks and has been...
FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum (2006)
Güldener, Ulrich, Mannhaupt, Gertrud, Münsterkötter, Martin, Haase, Dirk, Oesterheld, Matthias, Stümpflen, Volker, ...
The MIPS Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat and barley. FGDB provides information on two...
PEDANT genome database: 10 years online (2006)
Riley, M. Louise, Schmidt, Thorsten, Artamonova, Irena I., Wagner, Christian, Volz, Andreas, Heumann, Klaus, ...
The PEDANT genome database provides exhaustive annotation of 468 genomes by a broad set of bioinformatics algorithms. We describe recent developments of the PEDANT Web server. The all-new Graphical...
Super paramagnetic clustering of protein sequences (2005)
Tetko, Igor V, Facius, Axel, Ruepp, Andreas, Mewes, Hans-Werner
Abstract Background Detection of sequence homologues represents a challenging task that is important for the discovery of protein families and the reliable application of automatic annotation...
doi:10.1093/nar/gkj003 MPact: the MIPS protein interaction resource on yeast (2005)
Ulrich Güldener, Martin Münsterkötter, Matthias Oesterheld, Hans-werner Mewes, Volker Stümpflen, J. D. Han, ...
In recent years, the Munich Information Center for Protein Sequences (MIPS) yeast protein–protein interaction (PPI) dataset has been used in numerous analyses of protein networks and has been...
Igor V Tetko, Axel Facius, Hans-werner Mewes
Background: Detection of sequence homologues represents a challenging task that is important for the discovery of protein families and the reliable application of automatic annotation methods. The...
Ulrich Güldener, Gertrud Mannhaupt, Martin Münsterkötter, Dirk Haase, Matthias Oesterheld, Volker Stümpflen, ...
FGDB: a comprehensive fungal genome resource
The PEDANT genome database in 2005 (2005)
Riley, M. Louise, Schmidt, Thorsten, Wagner, Christian, Mewes, Hans-Werner, Frishman, Dmitrij
The PEDANT genome database (http://pedant.gsf.de) contains pre-computed bioinformatics analyses of publicly available genomes. Its main mission is to provide robust automatic annotation of the vast...
The MIPS mammalian protein-protein interaction database (2005)
Pagel, Philipp, Kovac, Stefan, Oesterheld, Matthias, Brauner, Barbara, Dunger-Kaltenbach, Irmtraud, Frishman, Goar, ...
Summary: The MIPS mammalian protein–protein interaction database (MPPI) is a new resource of high-quality experimental protein interaction data in mammals. The content is based on published...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
An international team has systematically validated and annotated just over 21,000 human genes using full-length cDNA, thereby providing a valuable new resource for the human genetics community.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
doi:10.1093/nar/gki019 The PEDANT genome database in 2005 (2004)
M. Louise Riley, Thorsten Schmidt, Christian Wagner, Hans-werner Mewes, Dmitrij Frishman
The PEDANT genome database
The MIPS mammalian protein-protein interaction database (2004)
Pagel, Philipp, Kovac, Stefan, Oesterheld, Matthias, Brauner, Barbara, Dunger-Kaltenbach, Irmtraud, Frishman, Goar, ...
Summary: The MIPS mammalian protein-protein interaction database (MPPI) is a new resource of high-quality experimental protein interaction data in mammals. The content is based on published...
Schoof, Heiko, Ernst, Rebecca, Nazarov, Vladimir, Pfeifer, Lukas, Mewes, Hans-Werner, Mayer, Klaus F. X.
Arabidopsis thaliana is the most widely studied model plant. Functional genomics is intensively underway in many laboratories worldwide. Beyond the basic annotation of the primary sequence data, the...
The MIPS mammalian protein-protein interaction database (2004)
Pagel, Philipp, Kovac, Stefan, Oesterheld, Matthias, Brauner, Barbara, Dunger-Kaltenbach, Irmtraud, Frishman, Goar, ...
Summary: The MIPS mammalian protein-protein interaction database (MPPI) is a new resource of high-quality experimental protein interaction data in mammals. The content is based on published...
Sputnik: a database platform for comparative plant genomics (2003)
Stephen Rudd, Hans-werner Mewes
Two million plant ESTs, from 20 different plant species, and totalling more than one 1000 Mbp of DNA sequence, represents a formidable transcriptomic resource. Sputnik uses the potential of this...
Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns (2003)
Bon, Elisabeth, Casaregola, Serge, Blandin, Gaëlle, Llorente, Bertrand, Neuvéglise, Cécile, Munsterkotter, Martin, ...
As part of the exploratory sequencing program Génolevures, visual scrutinisation and bioinformatic tools were used to detect spliceosomal introns in seven hemiascomycetous yeast species. A total of...
Sputnik: a database platform for comparative plant genomics (2003)
Rudd, Stephen, Mewes, Hans-Werner, Mayer, Klaus F.X.
Two million plant ESTs, from 20 different plant species, and totalling more than one 1000 Mbp of DNA sequence, represents a formidable transcriptomic resource. Sputnik uses the potential of...
The PEDANT genome database (2003)
Frishman, Dmitrij, Mokrejs, Martin, Kosykh, Denis, Kastenmüller, Gabi, Kolesov, Grigory, Zubrzycki, Igor, ...
The PEDANT genome database (http://pedant.gsf.de) provides exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools through a comprehensive Web-based...
Heiko Schoof, Rebecca Ernst, Vladimir Nazarov, Lukas Pfeifer, Hans-werner Mewes
integrated biological knowledge resource for plant genomics
DOI: 10.1093/nar/gkg005 The PEDANT genome database (2002)
Dmitrij Frishman, Martin Mokrejs, Denis Kosykh, Gabi Kastenmüller, Grigory Kolesov, Igor Zubrzycki, ...
The PEDANT genome database
Exon discovery by genomic sequence alignment (2002)
Morgenstern, Burkhard, Rinner, Oliver, Abdeddaïm, Saïd, Haase, Dirk, Mayer, Klaus F. X., Dress, Andreas W. M., ...
Motivation: During evolution, functional regions in genomic sequences tend to be more highly conserved than randomly mutating ‘junk DNA’ so local sequence similarity often indicates biological...
Wu, Cathy H., Huang, Hongzhan, Arminski, Leslie, Castro-Alvear, Jorge, Chen, Yongxing, Hu, Zhang-Zhi, ...
The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in...
SNAPper: gene order predicts gene function (2002)
Kolesov, Grigory, Mewes, Hans-Werner, Frishman, Dmitrij
Summary: SNAPper is a network service for predicting gene function based on the conservation of gene order. Availability: The SNAPper server is available at http://pedant.gsf.de/snapper....
Protein Information Resource: a community resource for expert annotation of protein data (2001)
Barker, Winona C., Garavelli, John S., Hou, Zhenglin, Huang, Hongzhan, Ledley, Robert S., McGarvey, Peter B., ...
The Protein Information Resource, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most...
Wiemann, Stefan, Weil, Bernd, Wellenreuther, Ruth, Gassenhuber, Johannes, Glassl, Sabine, Ansorge, Wilhelm, ...
Wiemann, Stefan, Weil, Bernd, Wellenreuther, Ruth, Gassenhuber, Johannes, Glassl, Sabine, Ansorge, Wilhelm, ...
Functional and structural genomics using PEDANT (2001)
Frishman, Dmitrij, Albermann, Kaj, Hani, Jean, Heumann, Klaus, Metanomski, Agnes, Zollner, Alfred, ...
Motivation: Enormous demand for fast and accurate analysis of biological sequences is fuelled by the pace of genome analysis efforts. There is also an acute need in reliable up-to-date genomic...
The HIB database of annotated UniGene clusters (2001)
Geier, Birgitta, Kastenmüller, Gabi, Fellenberg, Matthias, Mewes, Hans-Werner, Morgenstern, Burkhard
Summary: The HumanInfoBase (HIB) is a database of putative human gene transcripts. UniGene clusters are assembled, and the resulting consensus sequences are submitted to the PEDANT software system...
Wiemann, Stefan, Weil, Bernd, Wellenreuther, Ruth, Gassenhuber, Johannes, Glassl, Sabine, Ansorge, Wilhelm, ...
Pages 571–572 The HIB database of annotated UniGene clusters (2000)
Birgitta Geier, Gabi Kastenmüller, Matthias Fellenberg, Hans-werner Mewes, Burkhard Morgenstern
Summary: The HumanInfoBase (HIB) is a database of putative human gene transcripts. UniGene clusters are assembled, and the resulting consensus sequences are submitted to the PEDANT software system...
The Protein Information Resource (PIR) (2000)
Barker, Winona C., Garavelli, John S., Huang, Hongzhan, McGarvey, Peter B., Orcutt, Bruce C., Srinivasarao, Geetha Y., ...
The Protein Information Resource (PIR) produces the largest, most comprehensive, annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database, in...
The PIR-International Protein Sequence Database (1998)
Winona C. Barker, John S. Garavelli, Daniel H. Haft, Lois T. Hunt, Christopher R. Marzec, Bruce C. Orcutt, ...
From its origin the Protein Information Resource (http://www-nbrf.georgetown.edu/pir/ ) has supported research on evolution and computational biology by designing and compiling a comprehensive,...
Combining diverse evidence for gene recognition in completely sequenced bacterial genomes (1998)
Dmitrij Frishman, Andrey Mironov, Hans-werner Mewes, Mikhail Gelf
Analysis of a newly sequenced bacterial genome starts with identification of protein-coding genes. Functional assignment of proteins requires the exact knowledge of protein N-termini. We present a...
The PIR-International protein sequence database (1996)
David G. George, Winona C. Barker, Hans-werner Mewes, Friedhelm Pfeiffer, Akira Tsugita
From its origin the Protein Sequence Database has been designed to support research and has focused on comprehensive coverage, quality control and organization of the data in accordance with...
The PIR-International protein sequence database (1996)
Winona C. Barker, John S. Garavelli, Daniel H. Haft, Lois T. Hunt, Christopher R. Marzec, Bruce C. Orcutt, ...
From its origin the Protein Information Resource
The PIR-International Protein Sequence Database (1992)
Barker, Winona C., George, David G., Mewes, Hans-Werner, Tsugita, Akira
Protein Information Resource: a community resource for expert annotation of protein data
Barker, Winona C., Garavelli, John S., Hou, Zhenglin, Huang, Hongzhan, Ledley, Robert S., McGarvey, Peter B., ...
The Protein Information Resource, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most...
The Protein Information Resource: an integrated public resource of functional annotation of proteins
Wu, Cathy H., Huang, Hongzhan, Arminski, Leslie, Castro-Alvear, Jorge, Chen, Yongxing, Hu, Zhang-Zhi, ...
The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in...
The Protein Information Resource (PIR)
Barker, Winona C., Garavelli, John S., Huang, Hongzhan, McGarvey, Peter B., Orcutt, Bruce C., Srinivasarao, Geetha Y., ...
The Protein Information Resource (PIR) produces the largest, most comprehensive, annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database, in...
Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns
Bon, Elisabeth, Casaregola, Serge, Blandin, Gaëlle, Llorente, Bertrand, Neuvéglise, Cécile, Munsterkotter, Martin, ...
As part of the exploratory sequencing program Génolevures, visual scrutinisation and bioinformatic tools were used to detect spliceosomal introns in seven hemiascomycetous yeast species. A total of...
Frishman, Dmitrij, Mokrejs, Martin, Kosykh, Denis, Kastenmüller, Gabi, Kolesov, Grigory, Zubrzycki, Igor, ...
The PEDANT genome database (http://pedant.gsf.de) provides exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools through a comprehensive Web-based...
Sputnik: a database platform for comparative plant genomics
Rudd, Stephen, Mewes, Hans-Werner, Mayer, Klaus F.X.
Two million plant ESTs, from 20 different plant species, and totalling more than one 1000 Mbp of DNA sequence, represents a formidable transcriptomic resource. Sputnik uses the potential of this...
Schoof, Heiko, Ernst, Rebecca, Nazarov, Vladimir, Pfeifer, Lukas, Mewes, Hans-Werner, Mayer, Klaus F. X.
Arabidopsis thaliana is the most widely studied model plant. Functional genomics is intensively underway in many laboratories worldwide. Beyond the basic annotation of the primary sequence data, the...
Wiemann, Stefan, Weil, Bernd, Wellenreuther, Ruth, Gassenhuber, Johannes, Glassl, Sabine, Ansorge, Wilhelm, ...
With the complete human genomic sequence being unraveled, the focus will shift to gene identification and to the functional analysis of gene products. The generation of a set of cDNAs, both sequences...
Mayer, Klaus, Murphy, George, Tarchini, Renato, Wambutt, Rolf, Volckaert, Guido, Pohl, Thomas, ...
The nucleotide sequence was determined for a 340-kb segment of rice chromosome 2, revealing 56 putative protein-coding genes. This represents a density of one gene per 6.1 kb, which is higher than...
The PIR-International Protein Sequence Database
Barker, Winona C., George, David G., Mewes, Hans-Werner, Tsugita, Akira
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
The PEDANT genome database in 2005
Riley, M. Louise, Schmidt, Thorsten, Wagner, Christian, Mewes, Hans-Werner, Frishman, Dmitrij
The PEDANT genome database (http://pedant.gsf.de) contains pre-computed bioinformatics analyses of publicly available genomes. Its main mission is to provide robust automatic annotation of the vast...
Super paramagnetic clustering of protein sequences
Tetko, Igor V, Facius, Axel, Ruepp, Andreas, Mewes, Hans-Werner
MPact: the MIPS protein interaction resource on yeast
Güldener, Ulrich, Münsterkötter, Martin, Oesterheld, Matthias, Pagel, Philipp, Ruepp, Andreas, Mewes, Hans-Werner, ...
In recent years, the Munich Information Center for Protein Sequences (MIPS) yeast protein–protein interaction (PPI) dataset has been used in numerous analyses of protein networks and has been...
FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum
Güldener, Ulrich, Mannhaupt, Gertrud, Münsterkötter, Martin, Haase, Dirk, Oesterheld, Matthias, Stümpflen, Volker, ...
The MIPS Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat and barley. FGDB provides information on two...
Tetko, Igor V, Haberer, Georg, Rudd, Stephen, Meyers, Blake, Mewes, Hans-Werner, Mayer, Klaus F. X
Scaffold/matrix attachment regions (S/MARs) are essential for structural organization of the chromatin within the nucleus and serve as anchors of chromatin loop domains. A significant fraction of...
Tetko, Igor V, Haberer, Georg, Rudd, Stephen, Meyers, Blake C, Mewes, Hans-Werner, Mayer, Klaus F. X
Protein Information Resource: a community resource for expert annotation of protein data
Barker, Winona C., Garavelli, John S., Hou, Zhenglin, Huang, Hongzhan, Ledley, Robert S., McGarvey, Peter B., ...
The Protein Information Resource, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most...
The Protein Information Resource: an integrated public resource of functional annotation of proteins
Wu, Cathy H., Huang, Hongzhan, Arminski, Leslie, Castro-Alvear, Jorge, Chen, Yongxing, Hu, Zhang-Zhi, ...
The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in...
The Protein Information Resource (PIR)
Barker, Winona C., Garavelli, John S., Huang, Hongzhan, McGarvey, Peter B., Orcutt, Bruce C., Srinivasarao, Geetha Y., ...
The Protein Information Resource (PIR) produces the largest, most comprehensive, annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database, in...
Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns
Bon, Elisabeth, Casaregola, Serge, Blandin, Gaëlle, Llorente, Bertrand, Neuvéglise, Cécile, Munsterkotter, Martin, ...
As part of the exploratory sequencing program Génolevures, visual scrutinisation and bioinformatic tools were used to detect spliceosomal introns in seven hemiascomycetous yeast species. A total of...
Frishman, Dmitrij, Mokrejs, Martin, Kosykh, Denis, Kastenmüller, Gabi, Kolesov, Grigory, Zubrzycki, Igor, ...
The PEDANT genome database (http://pedant.gsf.de) provides exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools through a comprehensive Web-based...
Sputnik: a database platform for comparative plant genomics
Rudd, Stephen, Mewes, Hans-Werner, Mayer, Klaus F.X.
Two million plant ESTs, from 20 different plant species, and totalling more than one 1000 Mbp of DNA sequence, represents a formidable transcriptomic resource. Sputnik uses the potential of this...
Schoof, Heiko, Ernst, Rebecca, Nazarov, Vladimir, Pfeifer, Lukas, Mewes, Hans-Werner, Mayer, Klaus F. X.
Arabidopsis thaliana is the most widely studied model plant. Functional genomics is intensively underway in many laboratories worldwide. Beyond the basic annotation of the primary sequence data, the...
Wiemann, Stefan, Weil, Bernd, Wellenreuther, Ruth, Gassenhuber, Johannes, Glassl, Sabine, Ansorge, Wilhelm, ...
With the complete human genomic sequence being unraveled, the focus will shift to gene identification and to the functional analysis of gene products. The generation of a set of cDNAs, both sequences...
Mayer, Klaus, Murphy, George, Tarchini, Renato, Wambutt, Rolf, Volckaert, Guido, Pohl, Thomas, ...
The nucleotide sequence was determined for a 340-kb segment of rice chromosome 2, revealing 56 putative protein-coding genes. This represents a density of one gene per 6.1 kb, which is higher than...
The PIR-International Protein Sequence Database
Barker, Winona C., George, David G., Mewes, Hans-Werner, Tsugita, Akira
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
The PEDANT genome database in 2005
Riley, M. Louise, Schmidt, Thorsten, Wagner, Christian, Mewes, Hans-Werner, Frishman, Dmitrij
The PEDANT genome database (http://pedant.gsf.de) contains pre-computed bioinformatics analyses of publicly available genomes. Its main mission is to provide robust automatic annotation of the vast...
Super paramagnetic clustering of protein sequences
Tetko, Igor V, Facius, Axel, Ruepp, Andreas, Mewes, Hans-Werner
MPact: the MIPS protein interaction resource on yeast
Güldener, Ulrich, Münsterkötter, Martin, Oesterheld, Matthias, Pagel, Philipp, Ruepp, Andreas, Mewes, Hans-Werner, ...
In recent years, the Munich Information Center for Protein Sequences (MIPS) yeast protein–protein interaction (PPI) dataset has been used in numerous analyses of protein networks and has been...
FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum
Güldener, Ulrich, Mannhaupt, Gertrud, Münsterkötter, Martin, Haase, Dirk, Oesterheld, Matthias, Stümpflen, Volker, ...
The MIPS Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat and barley. FGDB provides information on two...
Tetko, Igor V, Haberer, Georg, Rudd, Stephen, Meyers, Blake, Mewes, Hans-Werner, Mayer, Klaus F. X
Scaffold/matrix attachment regions (S/MARs) are essential for structural organization of the chromatin within the nucleus and serve as anchors of chromatin loop domains. A significant fraction of...
Tetko, Igor V, Haberer, Georg, Rudd, Stephen, Meyers, Blake C, Mewes, Hans-Werner, Mayer, Klaus F. X
PEDANT genome database: 10 years online
Riley, M. Louise, Schmidt, Thorsten, Artamonova, Irena I., Wagner, Christian, Volz, Andreas, Heumann, Klaus, ...
The PEDANT genome database provides exhaustive annotation of 468 genomes by a broad set of bioinformatics algorithms. We describe recent developments of the PEDANT Web server. The all-new Graphical...
Genetics Meets Metabolomics: A Genome-Wide Association Study of Metabolite Profiles in Human Serum
Gieger, Christian, Geistlinger, Ludwig, Altmaier, Elisabeth, Hrabé De Angelis, Martin, Kronenberg, Florian, Meitinger, Thomas, ...
The rapidly evolving field of metabolomics aims at a comprehensive measurement of ideally all endogenous metabolites in a cell or body fluid. It thereby provides a functional readout of the...
Sequence-Based Prediction of Type III Secreted Proteins
Arnold, Roland, Brandmaier, Stefan, Kleine, Frederick, Tischler, Patrick, Heinz, Eva, Behrens, Sebastian, ...
The type III secretion system (TTSS) is a key mechanism for host cell interaction used by a variety of bacterial pathogens and symbionts of plants and animals including humans. The TTSS represents a...
PEDANT covers all complete RefSeq genomes
Walter, Mathias C., Rattei, Thomas, Arnold, Roland, Güldener, Ulrich, Münsterkötter, Martin, Nenova, Karamfilka, ...
The PEDANT genome database provides exhaustive annotation of nearly 3000 publicly available eukaryotic, eubacterial, archaeal and viral genomes with more than 4.5 million proteins by a broad set of...
Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes
Kastenmüller, Gabi, Schenk, Maria Elisabeth, Gasteiger, Johann, Mewes, Hans-Werner
A new machine learning-based method is presented here for the identification of metabolic pathways related to specific phenotypes in multiple microbial genomes.
Correction: Sequence-Based Prediction of Type III Secreted Proteins
Arnold, Roland, Brandmaier, Stefan, Kleine, Frederick, Tischler, Patrick, Heinz, Eva, Behrens, Sebastian, ...
Barnickel, Thorsten, Weston, Jason, Collobert, Ronan, Mewes, Hans-Werner, Stümpflen, Volker
To reduce the increasing amount of time spent on literature search in the life sciences, several methods for automated knowledge extraction have been developed. Co-occurrence based approaches can...
A Novel Putative miRNA Target Enhancer Signal
Schmidt, Thorsten, Mewes, Hans-Werner, Stümpflen, Volker
It is known that miRNA target sites are very short and the effect of miRNA-target site interaction alone appears as being unspecific. Recent experiments suggest further context signals involved in...