Wingender, Edgar

[["dc.bibliographiccitation.journal","European Journal of Cell Biology"],["dc.bibliographiccitation.volume","84"],["dc.contributor.author","Choi, C."],["dc.contributor.author","Kel-Margoulis, Olga V."],["dc.contributor.author","Kel, Alexander E."],["dc.contributor.author","Krull, M."],["dc.contributor.author","Pistor, S."],["dc.contributor.author","Voss, Nico"],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2018-11-07T11:19:06Z"],["dc.date.available","2018-11-07T11:19:06Z"],["dc.date.issued","2005"],["dc.format.extent","23"],["dc.identifier.isi","000228527700027"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/55192"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Urban & Fischer Verlag"],["dc.publisher.place","Jena"],["dc.relation.conference","Annual Meeting of the Deutsche-Gesellschaft-fur-Zellbiologie"],["dc.relation.eventlocation","Heidelberg, GERMANY"],["dc.relation.issn","0171-9335"],["dc.title","The TRANSPATH((R)) database: Identifying candidate pathways regulating the ubiquitin ligase parkin, a marker of Parkinson disease"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","481"],["dc.bibliographiccitation.issue","5-6"],["dc.bibliographiccitation.journal","SAR and QSAR in Environmental Research"],["dc.bibliographiccitation.lastpage","494"],["dc.bibliographiccitation.volume","19"],["dc.contributor.author","Kel, Alexander E."],["dc.contributor.author","Voss, Nico"],["dc.contributor.author","Valeev, T."],["dc.contributor.author","Stegmaier, Philip"],["dc.contributor.author","Kel-Margoulis, Olga V."],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2018-11-07T11:20:44Z"],["dc.date.available","2018-11-07T11:20:44Z"],["dc.date.issued","2008"],["dc.description.abstract","Different signal transduction pathways leading to the activation of transcription factors (TFs) converge at key molecules that master the regulation of many cellular processes. Such crossroads of signalling networks often appear as Achilles Heels causing a disease when not functioning properly. Novel computational tools are needed for analysis of the gene expression data in the context of signal transduction and gene regulatory pathways and for identification of the key nodes in the networks. An integrated computational system, ExPlain (TM) (www.biobase.de) was developed for causal interpretation of gene expression data and identification of key signalling molecules. The system utilizes data from two databases (TRANSFAC (R) and TRANSPATH (R)) and integrates two programs: (1) Composite Module Analyst (CMA) analyses 5'-upstream regions of co-expressed genes and applies a genetic algorithm to reveal composite modules (CMs) consisting of co-occurring single TF binding sites and composite elements; (2) ArrayAnalyzer (TM) is a fast network search engine that analyses signal transduction networks controlling the activities of the corresponding TFs and seeks key molecules responsible for the observed concerted gene activation. ExPlain (TM) system was applied to microarray data on inflammatory bowel diseases (IBD). The results obtained suggest a number of highly interesting biological hypotheses about molecular mechanisms of pathological genetic disregulation."],["dc.identifier.doi","10.1080/10629360802083806"],["dc.identifier.isi","000259995500004"],["dc.identifier.pmid","18853298"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/55611"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Taylor & Francis Ltd"],["dc.relation.issn","1062-936X"],["dc.title","ExPlain (TM): finding upstream drug targets in disease gene regulatory networks"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","European Journal of Cell Biology"],["dc.bibliographiccitation.volume","83"],["dc.contributor.author","Pistor, S."],["dc.contributor.author","Choi, C."],["dc.contributor.author","Krull, M."],["dc.contributor.author","Voss, Nico"],["dc.contributor.author","Potapov, Anatolij P."],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2018-11-07T10:50:35Z"],["dc.date.available","2018-11-07T10:50:35Z"],["dc.date.issued","2004"],["dc.format.extent","33"],["dc.identifier.isi","000220823900046"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/48689"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Urban & Fischer Verlag"],["dc.publisher.place","Jena"],["dc.relation.conference","Annual Meeting of the Deutschen-Gesellschaft-fur-Zellbiologie"],["dc.relation.eventlocation","Berlin, Germany"],["dc.relation.issn","0171-9335"],["dc.title","Analysis of the regulatory network of APP, amyloid beta protein precursor, with the signal transcluction database TRANSPATH (R) Professional"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1512"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.bibliographiccitation.lastpage","1516"],["dc.bibliographiccitation.volume","20"],["dc.contributor.author","Kel, Alexander E."],["dc.contributor.author","Tikunov, Y."],["dc.contributor.author","Voss, Nico"],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2018-11-07T10:47:29Z"],["dc.date.available","2018-11-07T10:47:29Z"],["dc.date.issued","2004"],["dc.description.abstract","Motivation: Transcription factor binding sites often differ significantly in their primary sequence and can hardly be aligned. Often one set of sites can contain several subsets of sequences that follow not just one but several different patterns. There is a need for sensitive methods to reveal multiple patterns in unaligned sets of sequences. Results: We developed a novel method for analysis of unaligned sets of sequences based on kernel estimation. The method is able to reveal 'multiple local patterns'-a set of weight matrices. Every weight matrix characterizes a pattern that can be found in a significant subset of sequences under analysis. The method developed has been compared with several other methods of pattern discovery such as Gibbs sampling, MEME, CONSENSUS, MULTIPROFILER and PROJECTION. The kernel method showed the best performance in terms of how close the revealed weight matrices are to the original ones. We applied the kernel method to analyze three samples of promoters (cell-cycle, T-cells and muscle-specific). We compared the multiple patterns revealed with the TRANSFAC library of weight matrices and found a strong similarity to several weight matrices for transcription factors known to be involved in the mentioned specific gene regulation."],["dc.identifier.doi","10.1093/bioinformatics/bth111"],["dc.identifier.isi","000222402400008"],["dc.identifier.pmid","15231544"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/47975"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.publisher.place","Oxford"],["dc.relation.conference","18th German Conference on Bioinformatics"],["dc.relation.eventlocation","Tech Univ Munchen, Garching, GERMANY"],["dc.relation.issn","1367-4803"],["dc.title","Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods"],["dc.type","conference_paper"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","D546"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","D551"],["dc.bibliographiccitation.volume","34"],["dc.contributor.author","Krull, Mathias"],["dc.contributor.author","Pistor, Susanne"],["dc.contributor.author","Voss, Nico"],["dc.contributor.author","Kel, Alexander E."],["dc.contributor.author","Reuter, Ingmar"],["dc.contributor.author","Kronenberg, Deborah"],["dc.contributor.author","Michael, Holger"],["dc.contributor.author","Schwarzer, Knut"],["dc.contributor.author","Potapov, Anatolij P."],["dc.contributor.author","Choi, Claudia"],["dc.contributor.author","Kel-Margoulis, Olga"],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2018-11-07T10:39:39Z"],["dc.date.available","2018-11-07T10:39:39Z"],["dc.date.issued","2006"],["dc.description.abstract","TRANSPATH (R) is a database about signal transduction events. It provides information about signaling molecules, their reactions and the pathways these reactions constitute. The representation of signaling molecules is organized in a number of orthogonal hierarchies reflecting the classification of the molecules, their species-specific or generic features, and their post-translational modifications. Reactions are similarly hierarchically organized in a three-layer architecture, differentiating between reactions that are evidenced by individual publications, generalizations of these reactions to construct species-independent 'reference pathways' and the 'semantic projections' of these pathways. A number of search and browse options allow easy access to the database contents, which can be visualized with the tool PathwayBuilder (TM). The module PathoSign adds data about pathologically relevant mutations in signaling components, including their genotypes and phenotypes. TRANSPATH (R) and PathoSign can be used as encyclopaedia, in the educational process, for vizualization and modeling of signal transduction networks and for the analysis of gene expression data. TRANSPATH (R) Public 6.0 is freely accessible for users from non-profit organizations under http://www.gene-regulation.com/pub/databases.html."],["dc.identifier.doi","10.1093/nar/gkj107"],["dc.identifier.isi","000239307700118"],["dc.identifier.pmid","16381929"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/46101"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","1362-4962"],["dc.relation.issn","0305-1048"],["dc.title","TRANSPATH (R): an information resource for storing and visualizing signaling pathways and their pathological aberrations"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","518"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Briefings in Bioinformatics"],["dc.bibliographiccitation.lastpage","531"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Michael, Holger"],["dc.contributor.author","Hogan, Jennifer D."],["dc.contributor.author","Kel, Alexander E."],["dc.contributor.author","Kel-Margoulis, Olga"],["dc.contributor.author","Schacherer, Frank"],["dc.contributor.author","Voss, Nico"],["dc.contributor.author","Wingender, Edgar"],["dc.date.accessioned","2018-11-07T11:09:20Z"],["dc.date.available","2018-11-07T11:09:20Z"],["dc.date.issued","2008"],["dc.description.abstract","Translating the exponentially growing amount of omics data into knowledge usable for a personalized medicine approach poses a formidable challenge. In this articletaking diabetes as a use casewe present strategies for developing data repositories into computer-accessible knowledge sources that can be used for a systemic view on the molecular causes of diseases, thus laying the foundation for systems pathology."],["dc.identifier.doi","10.1093/bib/bbn038"],["dc.identifier.isi","000261996300007"],["dc.identifier.pmid","19073714"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/52985"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","1467-5463"],["dc.title","Building a knowledge base for systems pathology"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]