Sahin, Özgür, Fröhlich, Holger, Löbke, Christian, Korf, Ulrike, Burmester, Sara, Majety, Meher, ...
Abstract Background In breast cancer, overexpression of the transmembrane tyrosine kinase ERBB2 is an adverse prognostic marker, and occurs in almost 30% of the patients. For therapeutic...
KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor (2009)
Zhang, Jitao David, Wiemann, Stefan
Motivation: KEGG PATHWAY is a service of Kyoto Encyclopedia of Genes and Genomes (KEGG), constructing manually curated pathway maps that represent current knowledge on biological networks in graph...
Taylor, Chris, Field, Dawn, Sansone, Susanna-Assunta, Apweiler, Rolf, Ashburner, Michael, Ball, Cathy, ...
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those...
Taylor, Chris F., Field, Dawn, Sansone, Susanna-Assunta, Aerts, Jan, Apweiler, Rolf, Asburner, Michael, ...
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project provides a resource for those exploring the range of extant minimum information checklists and fosters coordinated...
Integrating systems biology with clinical research (2008)
Pepperkok, Rainer, Wiemann, Stefan
A report on the conference 'Systems Genomics 2008', Heidelberg, Germany, 2-3 May 2008.
The First RSBI (ISA-TAB) Workshop: "Can a Simple Format Work for Complex Studies?" (2008)
Sansone, Susanna-Assunta, Rocca-Serra, Philippe, Brandizi, Marco, Brazma, Alvis, Field, Dawn, Fostel, Jennifer, ...
This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6–8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of...
Automated production of recombinant human proteins as resource for proteome research (2008)
Kohl, Thorsten, Schmidt, Christian, Wiemann, Stefan, Poustka, Annemarie, Korf, Ulrike
Abstract Background An arbitrary set of 96 human proteins was selected and tested to set-up a fully automated protein production strategy, covering all steps from DNA preparation to protein...
Extending pathways based on gene lists using InterPro domain signatures (2008)
Hahne, Florian, Mehrle, Alexander, Arlt, Dorit, Poustka, Annemarie, Wiemann, Stefan, Beissbarth, Tim
Abstract Background High-throughput technologies like functional screens and gene expression analysis produce extended lists of candidate genes. Gene-Set Enrichment Analysis is a commonly used and...
The full-ORF clone resource of the German cDNA Consortium (2007)
Bechtel, Stephanie, Rosenfelder, Heiko, Duda, Anny, Schmidt, Christian, Ernst, Ute, Wellenreuther, Ruth, ...
Abstract Background With the completion of the human genome sequence the functional analysis and characterization of the encoded proteins has become the next urging challenge in the post-genome era....
BMC Genomics Methodology article The full-ORF clone resource of the German cDNA Consortium (2007)
Stephanie Bechtel, Heiko Rosenfelder, Anny Duda, Christian Peter Schmidt, Ute Ernst, Ruth Wellenreuther, ...
© 2007 Bechtel et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
CAFTAN: a tool for fast mapping, and quality assessment of cDNAs (2006)
Del Val, Coral, Kuryshev, Vladimir, Glatting, Karl-Heinz, Ernst, Peter, Hotz-Wagenblatt, Agnes, Poustka, Annemarie, ...
Abstract Background The German cDNA Consortium has been cloning full length cDNAs and continued with their exploitation in protein localization experiments and cellular assays. However, the efficient...
Hahne, Florian, Arlt, Dorit, Sauermann, Mamatha, Majety, Meher, Poustka, Annemarie, Wiemann, Stefan, ...
Abstract Highthroughput cell-based assays with flow cytometric readout provide a powerful technique for identifying components of biologic pathways and their interactors. Interpretation of these...
Orchard, Sandra, Apweiler, Rolf, Barkovich, Robert, Field, Dawn, Garavelli, John S., Horn, David, ...
The theme of the third annual Spring workshop of the HUPO-PSI was proteomics and beyond and its underlying goal was to reach beyond the boundaries of the proteomics community to interact with groups...
The 3of5 web application for complex and comprehensive pattern matching in protein sequences (2006)
Seiler, Markus, Mehrle, Alexander, Poustka, Annemarie, Wiemann, Stefan
Abstract Background The identification of patterns in biological sequences is a key challenge in genome analysis and in proteomics. Frequently such patterns are complex and highly variable,...
The systematic functional characterisation of Xq28 genes prioritises candidate disease genes (2006)
Kolb-Kokocinski, Anja, Mehrle, Alexander, Bechtel, Stephanie, Simpson, Jeremy C, Kioschis, Petra, Wiemann, Stefan, ...
Abstract Background Well known for its gene density and the large number of mapped diseases, the human sub-chromosomal region Xq28 has long been a focus of genome research. Over 40 of approximately...
The LIFEdb database in 2006 (2006)
Er Mehrle, Heiko Rosenfelder, Coral Del Val, Dorit Arlt, Florian Hahne, Stephanie Bechtel, ...
LIFEdb
Bmc Bioinformatics, Coral Del Val, Vladimir Yurjevich Kuryshev, Karl-heinz Glatting, Peter Ernst, Agnes Hotz-wagenblatt, ...
Software CAFTAN: a tool for fast mapping, and quality assessment of cDNAs
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, ...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and...
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, ...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and...
The LIFEdb database in 2006 (2006)
Mehrle, Alexander, Rosenfelder, Heiko, Schupp, Ingo, Del Val, Coral, Arlt, Dorit, Hahne, Florian, ...
LIFEdb (http://www.LIFEdb.de) integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb...
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, ...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and...
Wiemann, Stefan, Kolb-Kokocinski, Anja, Poustka, Annemarie
Abstract Background Given the complexity of higher organisms, the number of genes encoded by their genomes is surprisingly small. Tissue specific regulation of expression and splicing are major...
gamma-BAR, a novel AP-1-interacting protein involved in post-Golgi trafficking (2005)
Neubrand,Veronika E., Will,Rainer D., Möbius,Wiebke, Poustka,Annemarie, Wiemann,Stefan, Schu,Peter, ...
gamma-BAR, a novel AP-1-interacting protein involved in post-Golgi trafficking (2005)
Neubrand, Veronika E., Will, Rainer D., Möbius, Wiebke, Poustka, Annemarie, Wiemann, Stefan, Schu, Peter, ...
Wellenreuther, Ruth, Schupp, Ingo, Poustka, Annemarie, Wiemann, Stefan
Abstract Background cDNA libraries are widely used to identify genes and splice variants, and as a physical resource for full-length clones. Conventionally-generated cDNA libraries contain a high...
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...
Starkuviene, Vytaute, Liebel, Urban, Simpson, Jeremy C., Erfle, Holger, Poustka, Annemarie, Wiemann, Stefan, ...
Here we describe the establishment of microscope-based functional screening assays in intact cells that allow us to systematically identify new proteins involved in secretory membrane traffic, and...
High-throughput protein analysis integrating bioinformatics and experimental assays (2004)
Del Val, Coral, Mehrle, Alexander, Falkenhahn, Mechthild, Seiler, Markus, Glatting, Karl-Heinz, Poustka, Annemarie, ...
The wealth of transcript information that has been made publicly available in recent years requires the development of high‐throughput functional genomics and proteomics approaches for its...
Bannasch, Detlev, Mehrle, Alexander, Glatting, Karl-Heinz, Pepperkok, Rainer, Poustka, Annemarie, Wiemann, Stefan
We have implemented LIFEdb (http://www.dkfz.de/LIFEdb) to link information regarding novel human full‐length cDNAs generated and sequenced by the German cDNA Consortium with functional...
From ORFeome to Biology: A Functional Genomics Pipeline (2004)
Wiemann, Stefan, Arlt, Dorit, Huber, Wolfgang, Wellenreuther, Ruth, Schleeger, Simone, Mehrle, Alexander, ...
As several model genomes have been sequenced, the elucidation of protein function is the next challenge toward the understanding of biological processes in health and disease. We have generated a...
Mollenhauer, Jan, Herbertz, Stephan, Helmke, Burkhard, Kollender, Gaby, Krebs, Inge, Madsen, Jens, ...
Deleted in Malignant Brain Tumors 1 (DMBT1) has been proposed as a candidate tumor suppressor gene for brain, lung, and digestive tract cancer. In particular, alterations of the gene and/or a loss of...
Being in the right location at the right time (2001)
Pepperkok, Rainer, Simpson, Jeremy C, Wiemann, Stefan
Abstract Taking each coding sequence from the human genome in turn and identifying the subcellular localization of the corresponding protein would be a significant contribution to understanding the...
Wiemann, Stefan, Weil, Bernd, Wellenreuther, Ruth, Gassenhuber, Johannes, Glassl, Sabine, Ansorge, Wilhelm, ...
Wiemann, Stefan, Weil, Bernd, Wellenreuther, Ruth, Gassenhuber, Johannes, Glassl, Sabine, Ansorge, Wilhelm, ...
Wiemann, Stefan, Weil, Bernd, Wellenreuther, Ruth, Gassenhuber, Johannes, Glassl, Sabine, Ansorge, Wilhelm, ...
Two dinucleotide repeat polymorphisms at 21q22.3 (D21S416 and D21S1235) (1993)
Bosch, Assumpció, Wiemann, Stefan, Jordi, Guimer{acute}, Ansorge, Wilhalm, Partterson, David, Estivill, Xavier
Separation of up to 1000 bases on a modified A.L.F. DNA sequencer (1993)
Grothues, Dietmar, Voss, Hartmut, Stegemann, Josef, Wiemann, Stefan, Sensen, Christoph, Zimmermann, Jürgen, ...
Isoformen der katalytischen Untereinheit der cAMP-abhängigen Proteinkinase. (1990)
Kaiserslautern, Univ., Diss., 1991 (Nicht für den Austausch).
Being in the right location at the right time
Pepperkok, Rainer, Simpson, Jeremy C, Wiemann, Stefan
Taking each coding sequence from the human genome in turn and identifying the subcellular localization of the corresponding protein would be a significant contribution to understanding the function...
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...
Bannasch, Detlev, Mehrle, Alexander, Glatting, Karl-Heinz, Pepperkok, Rainer, Poustka, Annemarie, Wiemann, Stefan
We have implemented LIFEdb (http://www.dkfz.de/LIFEdb) to link information regarding novel human full-length cDNAs generated and sequenced by the German cDNA Consortium with functional information on...
High-throughput protein analysis integrating bioinformatics and experimental assays
Del Val, Coral, Mehrle, Alexander, Falkenhahn, Mechthild, Seiler, Markus, Glatting, Karl-Heinz, Poustka, Annemarie, ...
The wealth of transcript information that has been made publicly available in recent years requires the development of high-throughput functional genomics and proteomics approaches for its analysis....
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...
Starkuviene, Vytaute, Liebel, Urban, Simpson, Jeremy C., Erfle, Holger, Poustka, Annemarie, Wiemann, Stefan, ...
Here we describe the establishment of microscope-based functional screening assays in intact cells that allow us to systematically identify new proteins involved in secretory membrane traffic, and...
From ORFeome to Biology: A Functional Genomics Pipeline
Wiemann, Stefan, Arlt, Dorit, Huber, Wolfgang, Wellenreuther, Ruth, Schleeger, Simone, Mehrle, Alexander, ...
As several model genomes have been sequenced, the elucidation of protein function is the next challenge toward the understanding of biological processes in health and disease. We have generated a...
γ-BAR, a novel AP-1-interacting protein involved in post-Golgi trafficking
Neubrand, Veronika E, Will, Rainer D, Möbius, Wiebke, Poustka, Annemarie, Wiemann, Stefan, Schu, Peter, ...
A novel peripheral membrane protein (2c18) that interacts directly with the gamma ‘ear' domain of the adaptor protein complex 1 (AP-1) in vitro and in vivo is described. Ultrastructural analysis...
Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing
Simpson, Jeremy C., Wellenreuther, Ruth, Poustka, Annemarie, Pepperkok, Rainer, Wiemann, Stefan
As a first step towards a more comprehensive functional characterization of cDNAs than bioinformatic analysis, which can only make functional predictions for about half of the cDNAs sequenced, we...
Alternative pre-mRNA processing regulates cell-type specific expression of the IL4l1 and NUP62 genes
Mehrle, Alexander, Rosenfelder, Heiko, Schupp, Ingo, Del Val, Coral, Arlt, Dorit, Hahne, Florian, ...
LIFEdb () integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb include (i) an...
The systematic functional characterisation of Xq28 genes prioritises candidate disease genes
Kolb-Kokocinski, Anja, Mehrle, Alexander, Bechtel, Stephanie, Simpson, Jeremy C, Kioschis, Petra, Wiemann, Stefan, ...
The 3of5 web application for complex and comprehensive pattern matching in protein sequences
Seiler, Markus, Mehrle, Alexander, Poustka, Annemarie, Wiemann, Stefan
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, ...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and...
CAFTAN: a tool for fast mapping, and quality assessment of cDNAs
Del Val, Coral, Kuryshev, Vladimir Yurjevich, Glatting, Karl-Heinz, Ernst, Peter, Hotz-Wagenblatt, Agnes, Poustka, Annemarie, ...
Being in the right location at the right time
Pepperkok, Rainer, Simpson, Jeremy C, Wiemann, Stefan
Taking each coding sequence from the human genome in turn and identifying the subcellular localization of the corresponding protein would be a significant contribution to understanding the function...
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...
Bannasch, Detlev, Mehrle, Alexander, Glatting, Karl-Heinz, Pepperkok, Rainer, Poustka, Annemarie, Wiemann, Stefan
We have implemented LIFEdb (http://www.dkfz.de/LIFEdb) to link information regarding novel human full-length cDNAs generated and sequenced by the German cDNA Consortium with functional information on...
High-throughput protein analysis integrating bioinformatics and experimental assays
Del Val, Coral, Mehrle, Alexander, Falkenhahn, Mechthild, Seiler, Markus, Glatting, Karl-Heinz, Poustka, Annemarie, ...
The wealth of transcript information that has been made publicly available in recent years requires the development of high-throughput functional genomics and proteomics approaches for its analysis....
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...
Starkuviene, Vytaute, Liebel, Urban, Simpson, Jeremy C., Erfle, Holger, Poustka, Annemarie, Wiemann, Stefan, ...
Here we describe the establishment of microscope-based functional screening assays in intact cells that allow us to systematically identify new proteins involved in secretory membrane traffic, and...
From ORFeome to Biology: A Functional Genomics Pipeline
Wiemann, Stefan, Arlt, Dorit, Huber, Wolfgang, Wellenreuther, Ruth, Schleeger, Simone, Mehrle, Alexander, ...
As several model genomes have been sequenced, the elucidation of protein function is the next challenge toward the understanding of biological processes in health and disease. We have generated a...
γ-BAR, a novel AP-1-interacting protein involved in post-Golgi trafficking
Neubrand, Veronika E, Will, Rainer D, Möbius, Wiebke, Poustka, Annemarie, Wiemann, Stefan, Schu, Peter, ...
A novel peripheral membrane protein (2c18) that interacts directly with the gamma ‘ear' domain of the adaptor protein complex 1 (AP-1) in vitro and in vivo is described. Ultrastructural analysis...
Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing
Simpson, Jeremy C., Wellenreuther, Ruth, Poustka, Annemarie, Pepperkok, Rainer, Wiemann, Stefan
As a first step towards a more comprehensive functional characterization of cDNAs than bioinformatic analysis, which can only make functional predictions for about half of the cDNAs sequenced, we...
Alternative pre-mRNA processing regulates cell-type specific expression of the IL4l1 and NUP62 genes
Mehrle, Alexander, Rosenfelder, Heiko, Schupp, Ingo, Del Val, Coral, Arlt, Dorit, Hahne, Florian, ...
LIFEdb () integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb include (i) an...
The systematic functional characterisation of Xq28 genes prioritises candidate disease genes
Kolb-Kokocinski, Anja, Mehrle, Alexander, Bechtel, Stephanie, Simpson, Jeremy C, Kioschis, Petra, Wiemann, Stefan, ...
The 3of5 web application for complex and comprehensive pattern matching in protein sequences
Seiler, Markus, Mehrle, Alexander, Poustka, Annemarie, Wiemann, Stefan
Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, ...
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and...
CAFTAN: a tool for fast mapping, and quality assessment of cDNAs
Del Val, Coral, Kuryshev, Vladimir Yurjevich, Glatting, Karl-Heinz, Ernst, Peter, Hotz-Wagenblatt, Agnes, Poustka, Annemarie, ...
Hahne, Florian, Arlt, Dorit, Sauermann, Mamatha, Majety, Meher, Poustka, Annemarie, Wiemann, Stefan, ...
A software tool for the analysis of high-throughput cell-based assays is presented.
High-Content Microscopy Identifies New Neurite Outgrowth Regulators
Laketa, Vibor, Simpson, Jeremy C., Bechtel, Stephanie, Wiemann, Stefan, Pepperkok, Rainer
Neurons, with their long axons and elaborate dendritic arbour, establish the complex circuitry that is essential for the proper functioning of the nervous system. Whereas a catalogue of structural,...
Combinatorial RNAi for quantitative protein network analysis
Sahin, Özgür, Löbke, Christian, Korf, Ulrike, Appelhans, Heribert, Sültmann, Holger, Poustka, Annemarie, ...
The elucidation of cross-talk events between intersecting signaling pathways is one main challenge in biological research. The complexity of protein networks, composed of different pathways, requires...
The full-ORF clone resource of the German cDNA Consortium
Bechtel, Stephanie, Rosenfelder, Heiko, Duda, Anny, Schmidt, Christian Peter, Ernst, Ute, Wellenreuther, Ruth, ...
Extending pathways based on gene lists using InterPro domain signatures
Hahne, Florian, Mehrle, Alexander, Arlt, Dorit, Poustka, Annemarie, Wiemann, Stefan, Beissbarth, Tim
Automated production of recombinant human proteins as resource for proteome research
Kohl, Thorsten, Schmidt, Christian, Wiemann, Stefan, Poustka, Annemarie, Korf, Ulrike
Integrating systems biology with clinical research
Pepperkok, Rainer, Wiemann, Stefan
A report on the conference 'Systems Genomics 2008', Heidelberg, Germany, 2-3 May 2008.
KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor
Zhang, Jitao David, Wiemann, Stefan
Motivation: KEGG PATHWAY is a service of Kyoto Encyclopedia of Genes and Genomes (KEGG), constructing manually curated pathway maps that represent current knowledge on biological networks in graph...