Stability analysis of mixtures of mutagenetic trees (2008)
Bogojeska, Jasmina, Lengauer, Thomas, Rahnenführer, Jörg
Abstract Background Mixture models of mutagenetic trees are evolutionary models that capture several pathways of ordered accumulation of genetic events observed in different subsets of patients. They...
Welsch, Christoph, Domingues, Francisco S, Susser, Simone, Antes, Iris, Hartmann, Christoph, Mayr, Gabriele, ...
Abstract Background The inhibitor telaprevir (VX-950) of the hepatitis C virus (HCV) protease NS3-4A has been tested in a recent phase 1b clinical trial in patients infected with HCV genotype 1. This...
Emig, Dorothea, Cline, Melissa S., Klein, Karsten, Kunert, Anne, Mutzel, Petra, Lengauer, Thomas, ...
Proteins and their interactions are essential for the functioning of all organisms and for understanding biological processes. Alternative splicing is an important molecular mechanism for increasing...
Flockerzi, Aline, Maydt, Jochen, Frank, Oliver, Ruggieri, Alessia, Maldener, Esther, Seifarth, Wolfgang, ...
Abstract Background The human genome comprises numerous human endogenous retroviruses (HERVs) that formed millions of years ago in ancestral species. A number of loci of the HERV-K(HML-2) family are...
CpG Island Mapping by Epigenome Prediction (2007)
Christoph Bock, Jörn Walter, Martina Paulsen, Thomas Lengauer
CpG islands were originally identified by epigenetic and functional properties, namely, absence of DNA methylation and frequent promoter association. However, this concept was quickly replaced by...
CpG island mapping by epigenome prediction (2007)
Christoph Bock, Jorn E Walter, Martina Paulsen, Thomas Lengauer
CpG islands were originally identified by epigenetic and functional properties, namely absence of DNA methylation and frequent promoter association. However, this concept was quickly replaced by...
GOTax: investigating biological processes and biochemical activities along the taxonomic tree (2007)
Schlicker, Andreas, Rahnenführer, Jörg, Albrecht, Mario, Lengauer, Thomas, Domingues, Francisco S
Abstract We describe GOTax, a comparative genomics platform that integrates protein annotation with protein family classification and taxonomy. User-defined sets of proteins, protein families,...
GOTax: investigating biological processes and biochemical activities along the taxonomic tree (2007)
Schlicker, Andreas, Rahnenführer, Jörg, Albrecht, Mario, Lengauer, Thomas, Domingues, Francisco S
Abstract We describe GOTax, a comparative genomics platform that integrates protein annotation with protein family classification and taxonomy. User-defined sets of proteins, protein families,...
Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage (2007)
Oliver Sander, Tobias Sing, Ingolf Sommer, Andrew J. Low, Peter K. Cheung, P. Richard Harrigan, ...
HIV-1 cell entry commonly uses, in addition to CD4, one of the chemokine receptors CCR5 or CXCR4 as coreceptor. Knowledge of coreceptor usage is critical for monitoring disease progression as well as...
Schulz, Wolfgang A, Alexa, Adrian, Jung, Volker, Hader, Christiane, Hoffmann, Michèle J, Yamanaka, Masanori, ...
Abstract Background Alterations of chromosome 8 and hypomethylation of LINE-1 retrotransposons are common alterations in advanced prostate carcinoma. In a former study including many metastatic...
Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage (2007)
Oliver Sander, Tobias Sing, Ingolf Sommer, Andrew J Low, Peter K Cheung, P Richard Harrigan, ...
HIV-1 cell entry commonly uses, in addition to CD4, one of the chemokine receptors CCR5 or CXCR4 as coreceptor. Knowledge of coreceptor usage is critical for monitoring disease progression as well as...
Improving the quality of protein structure models by selecting from alignment alternatives (2006)
Sommer, Ingolf, Toppo, Stefano, Sander, Oliver, Lengauer, Thomas, Tosatto, Silvio CE
Abstract Background In the area of protein structure prediction, recently a lot of effort has gone into the development of Model Quality Assessment Programs (MQAPs). MQAPs distinguish high quality...
Model Selection for Mixtures of Mutagenetic Trees (2006)
Yin, Junming, Beerenwinkel, Niko, Rahnenführer, Jörg, Lengauer, Thomas
The evolution of drug resistance in HIV is characterized by the accumulation of resistance-associated mutations in the HIV genome. Mutagenetic trees, a family of restricted Bayesian tree models, have...
Model Selection for Mixtures of Mutagenetic Trees (2006)
Yin, Junming, Beerenwinkel, Niko, Rahnenführer, Jörg, Lengauer, Thomas
The evolution of drug resistance in HIV is characterized by the accumulation of resistance-associated mutations in the HIV genome. Mutagenetic trees, a family of restricted Bayesian tree models, have...
Model Selection for Mixtures of Mutagenetic Trees (2006)
Yin, Junming, Beerenwinkel, Niko, Rahnenführer, Jörg, Lengauer, Thomas
The evolution of drug resistance in HIV is characterized by the accumulation of resistance-associated mutations in the HIV genome. Mutagenetic trees, a family of restricted Bayesian tree models, have...
Model Selection for Mixtures of Mutagenetic Trees (2006)
Yin, Junming, Beerenwinkel, Niko, Rahnenführer, Jörg, Lengauer, Thomas
The evolution of drug resistance in HIV is characterized by the accumulation of resistance-associated mutations in the HIV genome. Mutagenetic trees, a family of restricted Bayesian tree models, have...
A new measure for functional similarity of gene products based on Gene Ontology (2006)
Schlicker, Andreas, Domingues, Francisco S, Rahnenführer, Jörg, Lengauer, Thomas
Abstract Background Gene Ontology (GO) is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare...
Christoph Bock, Martina Paulsen, Sascha Tierling, Thomas Mikeska, Thomas Lengauer, Jörn Walter
CpG island methylation plays an important role in epigenetic gene control during mammalian development and is frequently altered in disease situations such as cancer. The majority of CpG islands is...
NOXclass: prediction of protein-protein interaction types (2006)
Zhu, Hongbo, Domingues, Francisco S, Sommer, Lngolf, Lengauer, Thomas
Abstract Background Structural models determined by X-ray crystallography play a central role in understanding protein-protein interactions at the molecular level. Interpretation of these models...
Local protein structure prediction using discriminative models (2006)
Sander, Oliver, Sommer, Ingolf, Lengauer, Thomas
Abstract Background In recent years protein structure prediction methods using local structure information have shown promising improvements. The quality of new fold predictions has risen...
Christoph Bock, Martina Paulsen, Sascha Tierling, Thomas Mikeska, Thomas Lengauer, Jorn E Walter
CpG island methylation plays an important role in epigenetic gene control during mammalian development and is frequently altered in disease situations such as cancer. The majority of CpG islands is...
Dissection of the Inflammatory Bowel Disease Transcriptome Using Genome-Wide cDNA Microarrays (2005)
Christine M. Costello, Nancy Mah, Robert Häsler, Philip Rosenstiel, Georg H. Waetzig, Andreas Hahn, ...
cDNA analysis of colonic samples from patients with Crohn disease and ulcerative colitis suggests substantial differences in pathophysiology between the two diseases.
Dissection of the Inflammatory Bowel Disease Transcriptome Using Genome-Wide cDNA Microarrays (2005)
Christine M. Costello, Nancy Mah, Robert Häsler, Philip Rosenstiel, Georg H. Waetzig, Andreas Hahn, ...
Background The differential pathophysiologic mechanisms that trigger and maintain the two forms of inflammatory bowel disease (IBD), Crohn disease (CD), and ulcerative colitis (UC) are only partially...
Confirmation of human protein interaction data by human expression data (2005)
Hahn, Andreas, Rahnenführer, Jörg, Talwar, Priti, Lengauer, Thomas
Abstract Background With microarray technology the expression of thousands of genes can be measured simultaneously. It is well known that the expression levels of genes of interacting proteins are...
Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays (2005)
Costello, Christine M., Mah, Nancy, Häsler, Robert, Rosenstiel, Philip, Waetzig, Georg H., Hahn, Andreas, ...
Background The differential pathophysiologic mechanisms that trigger and maintain the two forms of inflammatory bowel disease (IBD), Crohn disease (CD), and ulcerative colitis (UC) are only partially...
An integrative approach to gain insights into the cellular function of human ataxin-2 (2005)
Ralser, Markus, Albrecht, Mario, Nonhoff, Ute, Lengauer, Thomas, Lehrach, Hans, Krobitsch, Sylvia
Spinocerebellar ataxia type 2 (SCA2) is a hereditary neurodegenerative disorder caused by a trinucleotide expansion in the SCA2 gene, encoding a polyglutamine stretch in the gene product ataxin-2...
Ralser, Markus, Nonhoff, Ute, Albrecht, Mario, Lengauer, Thomas, Wanker, Erich E., Lehrach, Hans, ...
Spinocerebellar ataxia type 2 is an inherited neurodegenerative disorder that is caused by an expanded trinucleotide repeat in the SCA2 gene, encoding a polyglutamine stretch in the gene product...
Rahnenführer, Jörg, Domingues, Francisco S, Maydt, Jochen, Lengauer, Thomas
We present a statistical approach to scoring changes in activity of metabolic pathways from gene expression data. The method identifies the biologically relevant pathways with corresponding...
Rahnenführer, Jörg, Domingues, Francisco S, Maydt, Jochen, Lengauer, Thomas
We present a statistical approach to scoring changes in activity of metabolic pathways from gene expression data. The method identifies the biologically relevant pathways with corresponding...
Rahnenführer, Jörg, Domingues, Francisco S, Maydt, Jochen, Lengauer, Thomas
We present a statistical approach to scoring changes in activity of metabolic pathways from gene expression data. The method identifies the biologically relevant pathways with corresponding...
Rahnenführer, Jörg, Domingues, Francisco S, Maydt, Jochen, Lengauer, Thomas
We present a statistical approach to scoring changes in activity of metabolic pathways from gene expression data. The method identifies the biologically relevant pathways with corresponding...
Hofmann,W.P., Herrmann,E., Kronenberger,B., Merkwirth,Christian, Welsch,Christian, Lengauer,Thomas, ...
Predicting Protein Structure Classes from Function Predictions (2004)
Sommer,Ingolf, Rahnenführer,Jörg, Domingues,Francisco S., De Lichtenberg,Ulrik, Lengauer,Thomas
Ensemble methods for classification in cheminformatics (2004)
Merkwirth,Christian, Mauser,H., Schulz-Gasch,T., Roche,O., Stahl,M., Lengauer,Thomas
Novel technologies for virtual screening (2004)
Lengauer,Thomas, Lemmen,Christian, Rarey,Matthias, Zimmermann,M.
Modelling amorphous Si3B3N7: Structure and elastic properties (2004)
Hannemann,A., Schön,J.C., Jansen,M., Putz,H., Lengauer,Thomas
Learning multiple evolutionary pathways from cross-sectional data (2004)
Beerenwinkel,Niko, Rahnenführer,Jörg, Däumer,Martin, Hoffmann,Daniel, Kaiser,Rolf, Selbig,Joachim, ...
Genetic variation in DLG5 is associated with inflammatory bowel disease (2004)
Stoll,Monika, Corneliussen,Brit, Costello,Christine M., Waetzig,Georg H., Mellgard,Bjorn, Koch,W. Andreas, ...
Structural and functional analysis of ataxin-2 and ataxin-3 (2004)
Albrecht,Mario, Golatta,Michael, Wüllner,Ullrich, Lengauer,Thomas
Hofmann, W.P., Herrmann, E., Kronenberger, B., Merkwirth, Christian, Welsch, Christoph, Lengauer, Thomas, ...
Learning mixtures of localized rules by maximizing the area under the ROC curve (2004)
Sing, Tobias, Beerenwinkel, Niko, Lengauer, Thomas, Hernández-Orallo, José, Ferri, César, Lachiche, Nicolas, ...
Predicting Protein Structure Classes from Function Predictions (2004)
Sommer, Ingolf, Rahnenführer, Jörg, Domingues, Francisco S., De Lichtenberg, Ulrik, Lengauer, Thomas
Ensemble methods for classification in cheminformatics (2004)
Merkwirth, Christian, Mauser, H., Schulz-Gasch, T., Roche, O., Stahl, M., Lengauer, Thomas
Novel technologies for virtual screening (2004)
Lengauer, Thomas, Lemmen, Christian, Rarey, Matthias, Zimmermann, M.
Modelling amorphous Si3B3N7: Structure and elastic properties (2004)
Hannemann, A., Schön, J.C., Jansen, M., Putz, H., Lengauer, Thomas
Automated clustering of ensembles of alternative models in protein structure databases (2004)
Domingues, Francisco S., Rahnenführer, Jörg, Lengauer, Thomas
Protein Structure Prediction and Databases (2004)
Domingues, Francisco S., Lengauer, Thomas, Sommer, Ingolf, Cooper, David
Learning multiple evolutionary pathways from cross-sectional data (2004)
Beerenwinkel, Niko, Rahnenführer, Jörg, Däumer, Martin, Hoffmann, Daniel, Kaiser, Rolf, Selbig, Joachim, ...
Genetic variation in DLG5 is associated with inflammatory bowel disease (2004)
Stoll, Monika, Corneliussen, Brit, Costello, Christine M., Waetzig, Georg H., Mellgard, Bjorn, Koch, W. Andreas, ...
Structural and functional analysis of ataxin-2 and ataxin-3 (2004)
Albrecht, Mario, Golatta, Michael, Wüllner, Ullrich, Lengauer, Thomas
Towards cellular function through metabolite screening (2003)
Talwar,Priti, Lengauer,Thomas, Wittmann,Christoph, Mangadu,Vidya, Heinzle,Elmar
Bioinformatikmethoden für die Optimierung antiviraler Kombinationstherapien (2003)
Beerenwinkel,Niko, Däumer,Martin, Hoffmann,Daniel, Kaiser,Rolf, Selbig,Joachim, Lengauer,Thomas