Thomas Lengauer

Correlation of amino acid variations within nonstructural 4B protein with initial viral kinetics during interferon-alpha-based therapy in HCV-1b-infected patients (2007)

Welker, Martin W., Hofmann, Wolf-Peter, Welsch, Christoph, Von Wagner, Michael, Herrmann, Eva, Lengauer, Thomas, ...

Functional evaluation of domain–domain interactions and human protein interaction networks (2007)

Schlicker, Andreas, Huthmacher, Carola, Ramírez, Fidel, Lengauer, Thomas, Albrecht, Mario

Motivation: Large amounts of protein and domain interaction data are being produced by experimental high-throughput techniques and computational approaches. To gain insight into the value of the...

Structural Descriptors of gp120 V3 Loop for the Prediction of {HIV-1} Coreceptor Usage (2007)

Sander, Oliver, Sing, Tobias, Sommer, Ingolf, Low, Andrew J., Cheung, Peter K., Harrigan, P. Richard, ...

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...

Computational analysis of human protein interaction networks (2007)

Ramírez, Fidel, Schlicker, Andreas, Assenov, Yassen, Lengauer, Thomas, Albrecht, Mario

Structural and functional comparison of the non-structural protein 4B in flaviviridae (2007)

Welsch, Christoph, Albrecht, Mario, Maydt, Jochen, Herrmann, Eva, Welker, Martin W., Sarrazin, Christoph, ...

Factor interaction analysis for chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer (2007)

Schulz, Wolfgang A., Alexa, Adrian, Jung, Volker, Hader, Christiane, Hoffmann, Michele J., Yamanaka, Masanori, ...

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 cases, they...

Lead Identification by Virtual Screening (2007)

Kämper, Andreas, Rognan, Didier, Lengauer, Thomas

Expression pattern analysis of transcribed HERV sequences is complicated by ex vitvo recombination (2007)

Flockerzi, Aline, Maydt, Jochen, Frank, Oliver, Ruggieri, Alessia, Maldener, Esther, Seifarth, Wolfgang, ...

Characterization and structural analysis of novel mutations in human immunodeficiency virus type 1 reverse transcriptase involved in the regulation of restistance to nonnucleoside inhibitors (2007)

Ceccherini-Silberstein, Francesca, Svicher, Valentina, Sing, Tobias, Artese, Anna, Santoro, Maria Mercedes, Forbici, Federica, ...

Resistance to antivirals is a complex and dynamic phenomenon that involves more mutations than are currently known. Here, we characterize 10 additional mutations (L74V, K101Q, I135M/T, V179I, H221Y,...

Bioinformatics - From Genomes to Therapies - Introduction (2007)

Bioinformatics - From Genomes to Therapies 3. The Holy Grail: Molecular Function (2007)

Inferring Protein Function from Protein Structure (2007)

Domingues, Francisco S., Lengauer, Thomas

Bioinformatics - From Genomes to Therapies 1. The Building Blocks: Molecular Sequences and Structures (2007)

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for {Crohn} disease in {ATG16L1} (2007)

Hampe, Jochen, Franke, Andre, Rosenstiel, Philip, Till, Andreas, Teuber, Markus, Huse, Klaus, ...

We performed a genome-wide association study of 19,779 nonsynonymous SNPs in 735 individuals with Crohn disease and 368 controls. A total of 7,159 of these SNPs were informative. We followed up on...

Analysis of Expression Data: Classification of genes (2007)

Rahnenführer, Jörg, Lengauer, Thomas

Genotypic coreceptor analysis (2007)

Sierra, Saleta, Kaiser, Rolf, Thielen, Alexander, Lengauer, Thomas

HIV infects target cells by binding of its envelope gp120 protein to CD4 and a coreceptor on the cell surface. In vivo, the different HIV-strains use either CCR5 or CXCR4 as coreceptor. CCR5-using...

CpG Island Mapping by Epigenome Prediction (2007)

Bock, Christoph, Walter, Jörn, Paulsen, Martina, Lengauer, Thomas

IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models. (2007)

Hartmann, Christoph, Antes, Iris, Lengauer, Thomas

We introduce a new algorithm, IRECS (Iterative REduction of Conformational Space), for identifying ensembles of most probable side-chain conformations for homology modeling. On the basis of a given...

Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance (2007)

Altmann, Andre, Beerenwinkel, Niko, Sing, Tobias, Savenkov, Igor, Däumer, Martin, Kaiser, Rolf, ...

Background: The outcome of antiretroviral combination therapy depends on many factors involving host, virus, and drugs. We investigate prediction of treatment response from the applied drug...

GOTax: investigating biological processes and biochemical activities along the taxonomic tree (2007)

Schlicker, Andreas, Rahnenführer, Jörg, Albrecht, Mario, Lengauer, Thomas, Domingues, Francisco S.

We describe GOTax (http://gotax.bioinf.mpi-inf.mpg.de/), a comparative genomics platform that integrates protein annotation with protein family classification and taxonomy. User-defined sets of...

The implications of alternative splicing in the ENCODE protein complement (2007)

Tress, Michael L., Martelli, Pier L., Frankish, Adam, Reeves, Gabrielle A., Wesselink, Jan J., Yeats, Corin, ...

Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential to alter the biological...

Bioinformatics - From Genomes to Therapies 2. Getting at the Inner Workings: Molecular Interactions (2007)

Conformational analysis of alternative protein structures (2007)

Domingues, Francisco S., Rahnenführer, Jörg, Lengauer, Thomas

Motivation: Alternative structural models determined experimentally are available for an increasing number of proteins. Structural and functional studies of these proteins need to take these models...

Moment invariants as shape recognition technique for comparing protein binding sites (2007)

Sommer, Ingolf, Müller, Oliver, Domingues, Francisco S., Sander, Oliver, Weickert, Joachim, Lengauer, Thomas

Motivation: An approach for identifying similarities of protein–protein binding sites is presented. The geometric shape of a binding site is described by computing a feature vector based on moment...

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, RahnenfÃ¼hrer, JÃ¶rg, 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, RahnenfÃ¼hrer, JÃ¶rg, 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, RahnenfÃ¼hrer, JÃ¶rg, 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, RahnenfÃ¼hrer, JÃ¶rg, 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...

CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure (2006)

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)

CpG island methylation in human lymphocytes is highly correlated with DNA sequence patterns, repeat frequencies and predicted DNA structure (2006)

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...

Computational recognition of potassium channel sequences (2006)

Burkhard Heil, Jost Ludwig, Hella Lichtenberg-fraté, Thomas Lengauer

doi:10.1093/bioinformatics/btl132

GCB2005 Thermodynamics of RNA-RNA Binding (2006)

Ulrike Mückstein A, Hakim Tafer A, Jörg Hackermüller B, ...

Background: Reliable predictions of RNA-RNA binding energies is crucial e.g. for the understanding on RNAi, microRNA-mRNA binding, and antisense interactions. The thermodynamics of such RNA-RNA...

Development and validation of a consistency based multiple structure alignment algorithm (2006)

Jessica Ebert, Douglas Brutlag, Thomas Lengauer

*To whom correspondence should be addressed Summary: We introduce an algorithm that uses the information gained from simultaneous consideration of an entire group of related proteins to create...

BMC Bioinformatics Methodology article Local protein structure prediction using discriminative models (2006)

Oliver S, Ingolf Sommer, Thomas Lengauer

Background: In recent years protein structure prediction methods using local structure information have shown promising improvements. The quality of new fold predictions has risen significantly and...

BIOINFORMATICS Family specific rates of protein evolution (2006)

Hannes Luz, Martin Vingron, Thomas Lengauer

Motivation: Amino acid changing mutations in proteins are contstrained by purifying selection and accumulate at different rates. We estimate evolutionary rates on multiple alignments of eukaryotic...

Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes (2006)

Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Hannu Maaheimo, Thomas Lengauer

Motivation: Flux estimation using isotopomer information of metabolites is currently the most reliable method to obtain quantitative estimates of the activity of metabolic pathways. However, the...

Geno2pheno[coreceptor]: a tool for predicting coreceptor usage from genotype and for monitoring coreceptor-associated sequence alterations (2006)

Sing, Tobias, Beerenwinkel, Niko, Kaiser, Rolf, Hoffmann, Daniel, Däumer, Martin, Lengauer, Thomas

Bioinformatisches Data Mining erschließt neue Strategien gegen Krebs (2006)

Bock, Christoph, Halachev, Konstantin, Lengauer, Thomas, Haasis, Klaus, Heinzl, Armin, Klumpp, Dieter

Development of Computational Methods for Analysis of Metabolic Profiling Data (2006)

Talwar, Priti, Lengauer, Thomas, Wittmann, Christoph, Velagapudi, VR, Heinzle, Elmar

Stable coreceptor usage of HIV in patients with ongoing treatment failure on {HAART} (2006)

Lehmann, Clara, Däumer, Martin, Bousaad, Ibrahim, Sing, Tobias, Beerenwinkel, Niko, Lengauer, Thomas, ...

Background Disease progression in HIV infection has been associated with switch of viral coreceptor usage from CCR5 to CXCR4. Objectives To investigate the relationship between HIV-coreceptor tropism...

Improving the quality of protein structure models by selecting from alignment alternatives (2006)

Sommer, Ingolf, Toppo, Stefano, Sander, Oliver, Lengauer, Thomas, Tosatto, Silvio

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 protein...

Involvement of novel HIV-1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors (2006)

Svicher, V., Sing, Tobias, Santoro, M. M., Forbici, F., Bertoli, A., ...

Computational recognition of potassium channel sequences (2006)

Heil, Burkhard, Ludwig, Jost, Lichtenberg-Fraté, Hella, Lengauer, Thomas

Motivation: Potassium channels are mainly known for their role in regulating and maintaining the membrane potential. Since this is one of the key mechanisms of signal transduction, malfunction of...

Mutations in the NB-ARC domain of {I-2} that impair {ATP} hydrolysis cause autoactivation (2006)

Tameling, Wladimir I., Vossen, Jack H., Albrecht, Mario, Lengauer, Thomas, Berden, Jan A., Haring, Michel A., ...

Resistance (R) proteins in plants confer specificity to the innate immune system. Most R proteins have a centrally located NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4)...

Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV (2006)

Roomp, Kirsten, Beerenwinkel, Niko, Sing, Tobias, Schülter, Eugen, Büch, Joachim, Sierra-Aragon, Saleta, ...

Despite the availability of antiretroviral combination therapies, success in drug treatment of HIV-infected patients is limited. One reason for therapy failure is the development of drug-resistant...

Flexible Docking of Ligands into Synthetic Receptors Using a Two-Sided Incremental Construction Algorithm (2006)

Steffen, Andreas, Kämper, Andreas, Lengauer, Thomas

We present a new algorithm for the fast and reliable structure prediction of synthetic receptor-ligand complexes. Our method is based on the protein-ligand docking program FlexX and extends our...

Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies (2006)

Kämper, Andreas, Apostolakis, Joannis, Rarey, Matthias, Marian, Christel M., Lengauer, Thomas

The prediction of the structure of host-guest complexes is one of the most challenging problems in supramolecular chemistry. Usual procedures for docking of ligands into receptors do not take full...

Metabolic high- content screening of Saccharomyces cerevisiae reveals superior performance of single gene deletion strains (2006)

Velagapudi, V.R., Wittmann, C., Lengauer, Thomas, Talwar, Priti, Heinzle, E.

A new measure for functional similarity of gene products based on Gene Ontology (2006)

Schlicker, Andreas, Domingues, Francisco S., Rahnenführer, Jörg, Lengauer, Thomas

\paragraph*{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...

Refinement of homology modeled protein structures for molecular docking (2006)

Antes, Iris, Lengauer, Thomas

Functional evaluation of domain-domain interactions and human protein interaction networks (2006)

Schlicker, Andreas, Huthmacher, Carola, Ramírez, Fidel, Lengauer, Thomas, Albrecht, Mario, Huson, Daniel, ...

Large amounts of protein and domain interaction data are being produced by experimental high-throughput techniques and computational approaches. To gain insight into the value of the provided data,...

Local protein structure prediction using discriminative models (2006)

Bioinformatics-assisted anti-HIV therapy (2006)

Background In recent years protein structure prediction methods using local structure information have shown promising improvements. The quality of new fold predictions has risen significantly and in...

Lengauer, Thomas, Sing, Tobias

Highly active antiretroviral therapy (HAART), in which three or more drugs are given in combination, has substantially improved the clinical management of HIV-1 infection. Still, the emergence of...

NOXclass: prediction of protein-protein interaction types (2006)

Zhu, Hongbo, Domingues, Francisco S., Sommer, Ingolf, Lengauer, Thomas

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 requires the...

A Fully Computational Model for Predicting Percutaneous Drug Absorption (2006)

Neumann, Dirk, Kohlbacher, Oliver, Merkwirth, Christian, Lengauer, Thomas

The prediction of transdermal absorption for arbitrary penetrant structures has several important applications in the pharmaceutical industry. We propose a new data-driven, predictive model for skin...

Virtual screening for guest molecules of a biosensor (2006)

Steffen, Andreas, Kämper, Andreas, Lengauer, Thomas, Turner, Anthony P. F.

CpG Island Methylation in Human Lymphocytes Is Highly Correlated with {DNA} Sequence, Repeats, and Predicted {DNA} Structure (2006)

Bock, Christoph, Paulsen, Martina, Tierling, Sascha, Mikeska, Thomas, Lengauer, Thomas, Walter, Jörn

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...

Recco: recombination analysis using cost optimization (2006)

Maydt, Jochen, Lengauer, Thomas

Motivation: Recombination plays an important role in the evolution of many pathogens, such as HIV or malaria. Despite substantial prior work, there is still a pressing need for efficient and...

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...

Mutations in the MutSalpha interaction interface of {MLH1} can abolish {DNA} mismatch repair (2006)

Plotz, Guido, Welsch, Christoph, Giron-Monzon, Luis, Friedhoff, Peter, Albrecht, Mario, Piiper, Albrecht, ...

MutL, a heterodimer of MLH1 and PMS2, plays a central role in human DNA mismatch repair. It interacts ATP-dependently with the mismatch detector MutS and assembles and controls further repair...

Amino acid variations in hepatitis C virus p7 and sensitivity to antiviral combination therapy with amantadine in chronic hepatitis C (2006)

Mihm, Ulrike, Grigorian, Natalia, Welsch, Christoph, Herrmann, Eva, Kronenberger, Bernd, Teuber, Gerlinde, ...

DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequence and conformations (2006)

Antes, Iris, Siu, Weng-In, Lengauer, Thomas

Motivation: The binding of endogenous antigenic peptides to MHC class I molecules is an important step during the immunologic response of a host against a pathogen. Thus, various sequence- and...

Improved Scoring of Functional Groups from Gene Expression Data by Decorrelating GO Graph Structure (2006)

Alexa, Adrian, Rahnenführer, Jörg, Lengauer, Thomas

\begin{abstract} \section{Motivation:} The result of a typical microarray experiment is a long list of genes with corresponding expression measurements. This list is only the starting point for a...

Improving the quality of protein structure models by selecting from alignment alternatives (2006)

Sommer, Ingolf, Toppo, Stefano, Sander, Olivier, Lengauer, Thomas, Tosatto, Silvio CE

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 protein...

Editorial (2006)

Torda, Andrew E., Lengauer, Thomas

Computational recognition of potassium channel sequences (2006)

Heil, Burkhard, Ludwig, Jost, Lichtenberg-Fraté, Hella, Lengauer, Thomas

Motivation: Potassium channels are mainly known for their role in regulating and maintaining the membrane potential. Since this is one of the key mechanisms of signal transduction, malfunction of...

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure (2006)

Alexa, Adrian, Rahnenführer, Jörg, Lengauer, Thomas

Motivation: The result of a typical microarray experiment is a long list of genes with corresponding expression measurements. This list is only the starting point for a meaningful biological...

Recco: recombination analysis using cost optimization (2006)

Maydt, Jochen, Lengauer, Thomas

Motivation: Recombination plays an important role in the evolution of many pathogens, such as HIV or malaria. Despite substantial prior work, there is still a pressing need for efficient and...

DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations (2006)

Antes, Iris, Siu, Shirley W. I., Lengauer, Thomas

Motivation: The binding of endogenous antigenic peptides to MHC class I molecules is an important step during the immunologic response of a host against a pathogen. Thus, various sequence- and...

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...

Development of a new tool for predicting the structure of host-guest complexes (2005)

Steffen, Andreas, Kämper, Andreas, Lengauer, Thomas

FlexR - Predicting the structure of host-guest complexes (2005)

Steffen, Andreas, Kämper, Andreas, Lengauer, Thomas

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...

Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways (2005)

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...

BIOINFORMATICS REVIEW (2005)

Niko Beerenwinkel, Tobias Sing, Thomas Lengauer, Jörg Rahnenführer, Kirsten Roomp, Igor Savenkov, ...

Data and text mining Vol. 21 no. 21 2005, pages 3943–3950 doi:10.1093/bioinformatics/bti654 Computational methods for the design of effective therapies against drug resistant HIV strains

Sequence analysis BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing (2005)

Christoph Bock, Sabine Reither, Thomas Mikeska, Martina Paulsen, Jörn Walter, Thomas Lengauer

Summary: Manual processing of DNA methylation data from bisulfite sequencing is a tedious and error-prone task. Here we present an interactivesoftwaretool that providesstart-to-endsupportfor...

Lengauer T: Recco: Recombination analysis using cost optimization (2005)

Jochen Maydt, Thomas Lengauer, Martin Bishop

Motivation: Recombination plays an important role in the evolution of many pathogens, such as HIV or malaria. Despite substantial prior work, there is still a pressing need for efficient and...

Lengauer T: Recco: Recombination analysis using cost optimization (2005)

Jochen Maydt, Thomas Lengauer

Motivation: Recombination plays an important role in the evolution of many pathogens, such as HIVor malaria. Despite substantial prior work, there is still a pressing need for efficient and effective...

Development of a new tool for predicting the structure of host-guest complexes (2005)

Steffen, Andreas, Kämper, Andreas, Lengauer, Thomas

FlexR - Predicting the structure of host-guest complexes (2005)

Steffen, Andreas, Kämper, Andreas, Lengauer, Thomas

Patients with high grade gliomas harboring delections of chromosomes 9p and 10q benefit from temozolomide treatment (2005)

Wemmert, Silke, Ketter, Ralf, Rahnenführer, Jörg, Beerenwinkel, Niko, Strowitzki, Martin, Feiden, Wolfgang, ...

A new CARD15 mutation in Blau syndrome (2005)

Van Duist, Marjan M., Albrecht, Mario, Podswiadek, Marta, Giachino, Daniela, Lengauer, Thomas, Punzi, Leonardo, ...

Sarcoidosis is associated with a truncating splice site mutation in BTNL2 (2005)

Valentonyte, Ruta, Hampe, Jochen, Huse, Klaus, Rosenstiel, Philip, Albrecht, Mario, Stenzel, Annette, ...

Synthesis and Evaluation of Imidazolylmethylenetetrahydronaphthalenes and Imidazolylmethyleneindanes: Potent Inhibitors of Aldosterone Synthase (2005)

Ulmschneider, Sarah, Mueller-Vieira, Ursula, Mitrenga, Markus, Hartmann, Rolf W., Oberwinkler-Marchais, S, Klein, Christian D., ...

Synthesis and Evaluation of Pyridylmethylene-tetrahydronaphthalenes and -indanes: Potent and Selective Inhibitors of Aldosterone Synthase (CYP11B2) (2005)

Ulmschneider, Sarah, Mueller-Vieira, Ursula, Klein, Christian D., Antes, Iris, Lengauer, Thomas, Hartmann, Rolf W.

FlexR - A new tool for predicting the structure of synthetic host-guest complexes (2005)

Steffen, Andreas, Kämper, Andreas, Lengauer, Thomas, Turner, A.P.F.

Clinical significance of in vitro replication-enhancing mutations of the hepatitis C virus (HCV) replicon in patients with chronic HCV infection (2005)

Sarrazin, Christoph, Mihm, Ulrike, Herrmann, Eva, Welsch, Christoph, Albrecht, Mario, Sarrazin, Ulrike, ...

Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways (2005)

Ralser, Markus, Nonhoff, Ute, Albrecht, Mario, Lengauer, Thomas, Wanker, Erich E., Lehrach, Hans, ...

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

Estimating cancer survival and clinical outcome based on genetic tumor progression scores (2005)

Rahnenführer, Jörg, Beerenwinkel, Niko, Schulz, Wolfgang A., Hartmann, Christian, Von Deimling, Andreas, Wullich, Bernd, ...

Informatics (Computational Biology) (2005)

Lengauer, Thomas, Meyers, Robert A.

Automatic Generation of complementary descriptors with molecular graph networks (2005)

Lengauer, Thomas, Merkwirth, Christian

Efficient conformational analysis of synthetic receptors with macrocyclic and fused ring systems (2005)

Kämper, Andreas, Kaspar, Melanie, Lengauer, Thomas

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing (2005)

Bock, Christoph, Lengauer, Thomas, Reither, Sabine, Mikeska, Thomas, Paulsen, Martina, Walter, Jörn

SUMMARY: Manual processing of DNA methylation data from bisulfite sequencing is a tedious and error-prone task. Here we present an interactive software tool that provides start-to-end support for...

Computational methods for the design of effective therapies against drug resistant HIV strains (2005)

Beerenwinkel, Niko, Sing, Tobias, Lengauer, Thomas, Rahnenführer, Jörg, Roomp, Kirsten, Savenkov, Igor, ...

Mtreemix: a software package for learning and using mixture models of mutagenetic trees (2005)

Beerenwinkel, Niko, Rahnenführer, Jörg, Kaiser, Rolf, Hoffmann, Daniel, Selbig, Joachim, Lengauer, Thomas

Learning multiple evolutionary pathways from cross-sectional data (2005)

Beerenwinkel, Niko, Rahnenführer, Jörg, Däumer, Martin, Hoffmann, Daniel, Kaiser, Rolf, Selbig, Joachim, ...

Estimating HIV evolutionary pathways and the genetic barrier to drug resistance (2005)

Beerenwinkel, Niko, Däumer, Martin, Sing, Tobias, Rahnenführer, Jörg, Lengauer, Thomas, Selbig, Joachim, ...

POEM: Parameter Optimization using Ensemble Methods: Application to target specific scoring functions (2005)

Antes, Iris, Merkwirth, Christian, Lengauer, Thomas

Decomposing protein networks into domain-domain interactions (2005)

Albrecht, Mario, Huthmacher, Carola, Tosatto, Silvio C.E., Lengauer, Thomas

The HIN domain of IFI-200 proteins consists of two OB folds (2005)

Albrecht, Mario, Choubey, Divaker, Lengauer, Thomas

Multiple-Ligand-Based Virtual Screening: Methods and Applications of the MTree Approach (2005)

Hessler, G., Zimmermann, M., Matter, H., Evers, A., Naumann, T., Lengauer, Thomas, ...

Confirmation of human protein interaction data by human expression data (2005)

Hahn, Andreas, Rahnenführer, Jörg, Talwar, Priti, Lengauer, Thomas

Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays identifies novel candidate disease genes (2005)

Costello, Christine M., Mah, Nancy, Häsler, Robert, Rosenstiel, Philip, Waetzig, Georg H., Hahn, Andreas, ...

Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family (2005)

Castellano, Sergi, Lobanov, Alexey V., Chapple, Charles, Novoselov, Sergey V., Albrecht, Mario, Hua, Deame, ...

Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiency (2005)

Bojunga, Jörg, Welsch, Christoph, Antes, Iris, Albrecht, Mario, Lengauer, Thomas, Zeuzem, Stefan

ROCR: visualizing classifier performance in R (2005)

Sing, Tobias, Sander, Oliver, Beerenwinkel, Niko, Lengauer, Thomas

Summary: ROCR is a package for evaluating and visualizing the performance of scoring classifiers in the statistical language R. It features over 25 performance measures that can be freely combined to...

Decomposing protein networks into domain-domain interactions (2005)

Albrecht, Mario, Huthmacher, Carola, Tosatto, Silvio C. E., Lengauer, Thomas

Summary: The application of novel experimental techniques has generated large networks of protein–protein interactions. Frequently, important information on the structure and cellular function of...

Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways (2005)

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...

Estimating cancer survival and clinical outcome based on genetic tumor progression scores (2005)

Rahnenführer, Jörg, Beerenwinkel, Niko, Schulz, Wolfgang A., Hartmann, Christian, Von Deimling, Andreas, Wullich, Bernd, ...

Motivation: In cancer research, prediction of time to death or relapse is important for a meaningful tumor classification and selecting appropriate therapies. Survival prognosis is typically based on...

Mtreemix: a software package for learning and using mixture models of mutagenetic trees (2005)

Beerenwinkel, Niko, Rahnenführer, Jörg, Kaiser, Rolf, Hoffmann, Daniel, Selbig, Joachim, Lengauer, Thomas

Summary: Mixture models of mutagenetic trees constitute a class of probabilistic models for describing evolutionary processes that are characterized by the accumulation of permanent genetic changes....

Mtreemix: a software package for learning and using mixture models of mutagenetic trees (2005)

Beerenwinke, Niko, Rahnenführer, Jörg, Kaiser, Rolf, Hoffmann, Daniel, Selbig, Joachim, Lengauer, Thomas

Summary: Mixture models of mutagenetic trees constitute a class of probabilistic models for describing evolutionary processes that are characterized by the accumulation of permanent genetic changes....

Mtreemix: a software package for learning and using mixture models of mutagenetic trees (2005)

Beerenwinkel, Niko, Rahnenführer, Jörg, Kaiser, Rolf, Hoffmann, Daniel, Selbig, Joachim, Lengauer, Thomas

Summary: Mixture models of mutagenetic trees constitute a class of probabilistic models for describing evolutionary processes that are characterized by the accumulation of permanent genetic changes....

Estimating cancer survival and clinical outcome based on genetic tumor progression scores (2005)

Rahnenführer, Jörg, Beerenwinkel, Niko, Schulz, Wolfgang A., Hartmann, Christian, Von Deimling, Andreas, Wullich, Bernd, ...

Motivation: In cancer research, prediction of time to death or relapse is important for a meaningful tumor classification and selecting appropriate therapies. Survival prognosis is typically based on...

Estimating cancer survival and clinical outcome based on genetic tumor progression scores (2005)

Rahnenführer, Jörg, Beerenwinkel, Niko, Schulz, Wolfgang A., Hartmann, Christian, Von Deimling, Andreas, Wullich, Bernd, ...

Motivation: In cancer research, prediction of time to death or relapse is important for a meaningful tumor classification and selecting appropriate therapies. Survival prognosis is typically based on...

ROCR: visualizing classifier performance in R (2005)

Sing, Tobias, Sander, Oliver, Beerenwinkel, Niko, Lengauer, Thomas

Summary: ROCR is a package for evaluating and visualizing the performance of scoring classifiers in the statistical language R. It features over 25 performance measures which can be freely combined...

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulphite sequencing (2005)

Bock, Christoph, Reither, Sabine, Mikeska, Thomas, Paulsen, Martina, Walter, Jörn, Lengauer, Thomas

Summary: Manual processing of DNA methylation data from bisulphite sequencing is a tedious and error-prone task. Here we present an interactive software tool that provides start-to-end support for...

Computational methods for the design of effective therapies against drug resistant HIV strains (2005)

Beerenwinkel, Niko, Sing, Tobias, Lengauer, Thomas, Rahnenführer, Jörg, Roomp, Kirsten, Savenkov, Igor, ...

Motivation: The development of drug resistance is a major obstacle to successful treatment of HIV infection. The extraordinary replication dynamics of HIV facilitates its escape from selective...

Computational methods for the design of effective therapies against drug resistant HIV strains (2005)

Beerenwinkel, Niko, Sing, Tobias, Lengauer, Thomas, Rahnenführer, Jörg, Roomp, Kirsten, Savenkov, Igor, ...

Summary: The development of drug resistance is a major obstacle to successful treatment of HIV infection. The extraordinary replication dynamics of HIV facilitates its escape from selective pressure...

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing (2005)

Bock, Christoph, Reither, Sabine, Mikeska, Thomas, Paulsen, Martina, Walter, Jörn, Lengauer, Thomas

Summary: Manual processing of DNA methylation data from bisulfite sequencing is a tedious and error-prone task. Here we present an interactive software tool that provides start-to-end support for...

Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data (2004)

RahnenfÃ¼hrer, JÃ¶rg, 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...

Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data (2004)

RahnenfÃ¼hrer, JÃ¶rg, 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...

Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data (2004)

RahnenfÃ¼hrer, JÃ¶rg, 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...

Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data (2004)

RahnenfÃ¼hrer, JÃ¶rg, 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...

Calculating the statistical significance of changes in pathway activity from gene expression data (2004)

Rahnenführer,Jörg, Domingues,Francisco S., Maydt,Jochen, Lengauer,Thomas

Association of HCV-related mixed cryoglobulinemia with specific mutational patterns of the HCV E2 protein and CD81 expression on peripheral B lymphocytes (2004)

Hofmann,W.P., Herrmann,E., Kronenberger,B., Merkwirth,Christian, Welsch,Christian, Lengauer,Thomas, ...

Learning mixtures of localized rules by maximizing the area under the ROC curve (2004)

Sing,Tobias, Beerenwinkel,Niko, Lengauer,Thomas

Predicting Protein Structure Classes from Function Predictions (2004)

Sommer,Ingolf, Rahnenführer,Jörg, Domingues,Francisco S., De Lichtenberg,Ulrik, Lengauer,Thomas

Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures (2004)

Öhsen Von,Niklas, Sommer,Ingolf, Zimmer,Ralf, Lengauer,Thomas

Ensemble methods for classification in cheminformatics (2004)

Merkwirth,Christian, Mauser,H., Schulz-Gasch,T., Roche,O., Stahl,M., Lengauer,Thomas

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

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources (2004)

Crass,T., Antes,Iris, Basekow,R., Bork,P., Buning,Christian, Christensen,M., ...

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

Novel Sm-like proteins with long C-terminal tails and associated methyltransferases (2004)

Albrecht,Mario, Lengauer,Thomas

Survey on the PABC recognition motif PAM2 (2004)

Albrecht,Mario, Lengauer,Thomas

Docking into the homology models of CYP11B1 and CYP11B2 (2004)

Antes, Iris, Lengauer, Thomas

Virtual Screening for novel Urease Inhibitors (2004)

Kämper, Andreas, Lengauer, Thomas

Calculating the statistical significance of changes in pathway activity from gene expression data (2004)

Rahnenführer, Jörg, Domingues, Francisco S., Maydt, Jochen, Lengauer, Thomas

Association of HCV-related mixed cryoglobulinemia with specific mutational patterns of the HCV E2 protein and CD81 expression on peripheral B lymphocytes (2004)

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

Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures (2004)

Öhsen Von, Niklas, Sommer, Ingolf, Zimmer, Ralf, Lengauer, Thomas

Ensemble methods for classification in cheminformatics (2004)

Merkwirth, Christian, Mauser, H., Schulz-Gasch, T., Roche, O., Stahl, M., Lengauer, Thomas

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

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources (2004)

Crass, T., Antes, Iris, Basekow, R., Bork, P., Buning, Christian, Christensen, M., ...

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

Novel Sm-like proteins with long C-terminal tails and associated methyltransferases (2004)

Survey on the PABC recognition motif PAM2 (2004)

Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computional Biology 2004 (ISMB/ECCB 2004) (2004)

Thornton, J., Bourne, P., Gilbert, D., Goble, C., Goldman, N., Gribskov, M., ...

Learning mixtures of localized rules by maximizing the area under the ROC curve (2004)

Tobias Sing, Niko Beerenwinkel, Thomas Lengauer

Abstract. We introduce a model class for statistical learning which is based on mixtures of propositional rules. In our mixture model, the weight of a rule is not uniform over the entire instance...

Structural and functional analysis of ataxin-2 and ataxin-3 (2004)

Thomas Lengauer, Thomas Lengauer, Christian Lemmen, Christian Lemmen, Matthias Rarey, Matthias Rarey, ...

There are several methods for virtual screening of databases of small organic compounds to find tight binders to a given protein target. Recent reviews in Drug Discovery Today have concentrated on...

Albrecht, Mario, Golatta, Michael, Wüllner, Ullrich, Lengauer, Thomas

Novel Sm-like proteins with long {C-terminal} tails and associated methyltransferases (2004)

Survey on the PABC recognition motif {PAM2} (2004)

Learning multiple evolutionary pathways from cross-sectional data (2004)

Beerenwinkel, Niko, Rahnenführer, Jörg, Däumer, Martin, Hoffmann, Daniel, Kaiser, Rolf, Selbig, Joachim, ...

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources (2004)

Crass, T., Antes, Iris, Basekow, R., Bork, P., Buning, Christian, Christensen, M., ...

Protein Structure Prediction and Databases (2004)

Domingues, Francisco S., Lengauer, Thomas, Sommer, Ingolf, Cooper, David

Automated clustering of ensembles of alternative models in protein structure databases (2004)

Domingues, Francisco S., Rahnenführer, Jörg, Lengauer, Thomas

Modelling amorphous Si3B3N7: Structure and elastic properties (2004)

Hannemann, A., Schön, J.C., Jansen, M., Putz, H., Lengauer, Thomas

Association of HCV-related mixed cryoglobulinemia with specific mutational patterns of the HCV E2 protein and CD81 expression on peripheral B lymphocytes (2004)

Hofmann, W.P., Herrmann, E., Kronenberger, B., Merkwirth, Christian, Welsch, Christian, Lengauer, Thomas, ...

Lengauer, Thomas, Lemmen, Christian, Rarey, Matthias, Zimmermann, M.

Ensemble methods for classification in cheminformatics (2004)

Merkwirth, Christian, Mauser, H., Schulz-Gasch, T., Roche, O., Stahl, M., Lengauer, Thomas

Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures (2004)

Öhsen Von, Niklas, Sommer, Ingolf, Zimmer, Ralf, Lengauer, Thomas

Learning mixtures of localized rules by maximizing the area under the ROC curve (2004)

Sing, Tobias, Beerenwinkel, Niko, Lengauer, Thomas, Hern{\'a}ndez-Orallo, Jos{\'e}, Ferri, C{\'e}sar, Lachiche, Nicolas, ...

Predicting Protein Structure Classes from Function Predictions (2004)

Sommer, Ingolf, Rahnenführer, Jörg, Domingues, Francisco S., De Lichtenberg, Ulrik, Lengauer, Thomas

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, ...

Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computional Biology 2004 (ISMB/ECCB 2004) (2004)

Thornton, J., Bourne, P., Gilbert, D., Goble, C., Goldman, N., Gribskov, M., ...

Calculating the statistical significance of changes in pathway activity from gene expression data (2004)

Rahnenführer, Jörg, Domingues, Francisco S., Maydt, Jochen, Lengauer, Thomas

Arby: automatic protein structure prediction using profile-profile alignment and confidence measures (2004)

Von Öhsen, Niklas, Sommer, Ingolf, Zimmer, Ralf, Lengauer, Thomas

Motivation: Arby is a new server for protein structure prediction that combines several homology-based methods for predicting the three-dimensional structure of a protein, given its sequence. The...

Automated clustering of ensembles of alternative models in protein structure databases (2004)

Domingues, Francisco S., Rahnenführer, Jörg, Lengauer, Thomas

Experimentally determined protein structures have been classified in different public databases according to their structural and evolutionary relationships. Frequently, alternative structural...

Automated clustering of ensembles of alternative models in protein structure databases (2004)

Domingues, Francisco S., Rahnenführer, Jörg, Lengauer, Thomas

Experimentally determined protein structures have been classified in different public databases according to their structural and evolutionary relationships. Frequently, alternative structural...

Arby: automatic protein structure prediction using profile-profile alignment and confidence measures (2004)

Von Öhsen, Niklas, Sommer, Ingolf, Zimmer, Ralf, Lengauer, Thomas

Motivation: Arby is a new server for protein structure prediction that combines several homology-based methods for predicting the three-dimensional structure of a protein, given its sequence. The...

Arby: automatic protein structure prediction using profile-profile alignment and confidence measures (2004)

Von Öhsen, Niklas, Sommer, Ingolf, Zimmer, Ralf, Lengauer, Thomas

Motivation: Arby is a new server for protein structure prediction that combines several homology-based methods for predicting the three-dimensional structure of a protein, given its sequence. The...

Automated clustering of ensembles of alternative models in protein structure databases (2004)

Domingues, Francisco S., Rahnenführer, Jörg, Lengauer, Thomas

Experimentally determined protein structures have been classified in different public databases according to their structural and evolutionary relationships. Frequently, alternative structural...

Tenofovir resistance and resensitization (2003)

Walter, Hauke, Beerenwinkel, Niko, Keulen, Wilco, Kaiser, Rolf, Hoffmann, Daniel, ...

Human immunodeficiency viruses in 321 samples from tenofovir-naïve patients were retrospectively evaluated for resistance to this nucleotide analogue. All virus strains with insertions between amino...

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

Estimating effective drug combinations against drug-resistant mutants from genotypes (2003)

Beerenwinkel,Niko, Däumer,Martin, Kaiser,Rolf, Walter,Hauke, Korn,Klaus, Hoffmann,Daniel, ...

Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes (2003)

Beerenwinkel,Niko, Däumer,Martin, Oette,Mark, Korn,Klaus, Hoffmann,Daniel, Kaiser,Rolf, ...

Combinatorial Optimization Techniques for Three-Dimensional Arrangement Problems (2003)

Lengauer,Thomas, Schäfer,M.

Parallel "go with the winners algorithms" in Distributed Memory Models (2003)

Peinado,M., Lengauer,Thomas

Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence (2003)

Albrecht,Mario, Lengauer,Thomas, Schreiber,Stefan

Software tool for automated processing of 13C labeling data from mass spectrometry data (2003)

Talwar,Priti, Wittmann,Christoph, Lengauer,Thomas, Heinzle,Elmar

Microarrays: How many do you need? (2003)

Zien,Alexander, Fluck,Juliane, Zimmer,Ralf, Lengauer,Thomas

Protein Function from Sequence and Structure Data (2003)

Domingues,Francisco S., Lengauer,Thomas

Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2 (2003)

Albrecht,Mario, Domingues,Francisco S., Schreiber,Stefan, Lengauer,Thomas

Simple consensus procedures are effective and sufficient in secondary structure prediction (2003)

Albrecht,Mario, Tosatto,Silvio C.E., Lengauer,Thomas, Valle,Giorgio

Identification of mammalian orthologs associates PYPAF5 with distinct functional roles (2003)

Albrecht,Mario, Domingues,Francisco S., Schreiber,Stefan, Lengauer,Thomas

Pyranose oxidase identified as a member of the GMC oxidoreductase family (2003)

Albrecht,Mario, Lengauer,Thomas

New inhibitors of human cathepsin G identified by surface display library screening and peptide-protein docking (2003)

Jose,Joachim, Betschieder,Dirk, Ray,Somak, Lengauer,Thomas, Zangen,D

Methods for optimizing antiviral combination therapies (2003)

Beerenwinkel,Niko, Lengauer,Thomas, Däumer,Martin, Kaiser,Rolf, Walter,Hauke, Korn,Klaus, ...

Structural modeling of ataxin-3 reveals distant homology to adaptins (2003)

Albrecht,Mario, Hoffmann,Daniel, Evert,Bernd O., Schmitt,Ina, Wüllner,Ullrich, Lengauer,Thomas

Tree models for the evolution of drug resistance (2003)

Beerenwinkel,Niko, Kaiser,Rolf, Rahnenführer,Jörg, Däumer,Martin, Hoffmann,Daniel, Selbig,Joachim, ...

Tenofovir resistance and resensitization (2003)

Wolf,Katharina, Walter,Hauke, Beerenwinkel,Niko, Keulen,Wilco, Kaiser,Rolf, Hoffmann,Daniel, ...

ECLIPPSE: Environment for Chemical Library Inspection, Pre- and Postprocessing, and Screening Evaluation. User Guide (2003)

Kämper,Andreas, 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

Estimating effective drug combinations against drug-resistant mutants from genotypes (2003)

Beerenwinkel, Niko, Däumer, Martin, Kaiser, Rolf, Walter, Hauke, Korn, Klaus, Hoffmann, Daniel, ...

Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes (2003)

Beerenwinkel, Niko, Däumer, Martin, Oette, Mark, Korn, Klaus, Hoffmann, Daniel, Kaiser, Rolf, ...

Combinatorial Optimization Techniques for Three-Dimensional Arrangement Problems (2003)

Lengauer, Thomas, Schäfer, M., Jäger, Willi, Krebs, Hans-Joachim

Parallel "go with the winners algorithms" in Distributed Memory Models (2003)

Peinado, M., Lengauer, Thomas

Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence (2003)

Albrecht, Mario, Lengauer, Thomas, Schreiber, Stefan

Software tool for automated processing of 13C labeling data from mass spectrometry data (2003)

Talwar, Priti, Wittmann, Christoph, Lengauer, Thomas, Heinzle, Elmar

Microarrays: How many do you need? (2003)

Zien, Alexander, Fluck, Juliane, Zimmer, Ralf, Lengauer, Thomas

Protein Function from Sequence and Structure Data (2003)

Domingues, Francisco S., Lengauer, Thomas

Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2 (2003)

Albrecht, Mario, Domingues, Francisco S., Schreiber, Stefan, Lengauer, Thomas

Simple consensus procedures are effective and sufficient in secondary structure prediction (2003)

Albrecht, Mario, Tosatto, Silvio C.E., Lengauer, Thomas, Valle, Giorgio

Identification of mammalian orthologs associates PYPAF5 with distinct functional roles (2003)

Albrecht, Mario, Domingues, Francisco S., Schreiber, Stefan, Lengauer, Thomas

Pyranose oxidase identified as a member of the GMC oxidoreductase family (2003)

New inhibitors of human cathepsin G identified by surface display library screening and peptide-protein docking (2003)

Jose, Joachim, Betschieder, Dirk, Ray, Somak, Lengauer, Thomas, Zangen, D

Methods for optimizing antiviral combination therapies (2003)

Beerenwinkel, Niko, Lengauer, Thomas, Däumer, Martin, Kaiser, Rolf, Walter, Hauke, Korn, Klaus, ...

Structural modeling of ataxin-3 reveals distant homology to adaptins (2003)

Albrecht, Mario, Hoffmann, Daniel, Evert, Bernd O., Schmitt, Ina, Wüllner, Ullrich, Lengauer, Thomas

Analyzing resistance phenomena in HIV with bioinformatics methods (2003)

Tree models for the evolution of drug resistance (2003)

Beerenwinkel, Niko, Kaiser, Rolf, Rahnenführer, Jörg, Däumer, Martin, Hoffmann, Daniel, Selbig, Joachim, ...

Tenofovir resistance and resensitization (2003)

Wolf, Katharina, Walter, Hauke, Beerenwinkel, Niko, Keulen, Wilco, Kaiser, Rolf, Hoffmann, Daniel, ...

ECLIPPSE: Environment for Chemical Library Inspection, Pre- and Postprocessing, and Screening Evaluation. User Guide (2003)

Kämper, Andreas, Lengauer, Thomas

DOI: 10.1093/bioinformatics/btg1001 (2003)

Niko Beerenwinkel, Thomas Lengauer, Martin Däumer, Hauke Walter, Klaus Korn, Daniel Hoffmann, ...

Vol. 19 Suppl. 1 2003, pages i16–i25

Microarrays: how many do you need (2003)

Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer

We estimate the number of microarrays that is required in order to gain reliable results from a common type of study: the pairwise comparison of different classes of samples. We show that current...

Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes (2003)

Beerenwinkel, Niko, Däumer, Martin, Oette, Mark, Korn, Klaus, Hoffmann, Daniel, Kaiser, Rolf, ...

Therapeutic success of anti-HIV therapies is limited by the development of drug resistant viruses. These genetic variants display complex mutational patterns in their pol gene, which codes for...

Simple consensus procedures are effective and sufficient in secondary structure prediction (2003)

Albrecht, Mario, Tosatto, Silvio C.E., Lengauer, Thomas, Valle, Giorgio

We have analyzed the performance of majority voting on minimal combination sets of three state‐of‐the‐art secondary structure prediction methods in order to obtain a consensus...

Pyranose oxidase identified as a member of the GMC oxidoreductase family (2003)

Analyzing resistance phenomena in HIV with bioinformatics methods (2003)

Fungal pyranose oxidase is a flavoenzyme whose preferred substrate among several monosaccharides is d-glucose. After a comprehensive analysis of conserved features in a structure-based multiple...

Methods for optimizing antiviral combination therapies (2003)

We report on research that is targeted towards understanding the resistance phenomena that HIV undergoes in the presence of selective pressure presented by combination drug therapies. The ultimate...

Beerenwinkel, Niko, Lengauer, Thomas, Däumer, Martin, Kaiser, Rolf, Walter, Hauke, Korn, Klaus, ...

Motivation: Despite some progress with antiretroviral combination therapies, therapeutic success in the management of HIV-infected patients is limited. The evolution of drug-resistant genetic...

Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence (2003)

Albrecht, Mario, Lengauer, Thomas, Schreiber, Stefan

Sequence variations in the gene products PYPAF1/CIAS1 and NOD2/CARD15 have been associated with several autoinflammatory diseases that, although clinically different, share a similar inflammatory...

Improving fold recognition of protein threading by experimental distance constraints (2002)

Albrecht,Mario, Hanisch,Daniel, Zimmer,Ralf, Lengauer,Thomas

Microarrays: How Many Do You Need? (2002)

Zien,Alexander, Fluck,Juliane, Zimmer,Ralf, Lengauer,Thomas

Confidence measures for protein fold recognition (2002)

Sommer,Ingolf, Zien,Alexander, Öhsen Von,Niklas, Zimmer,Ralf, Lengauer,Thomas

Geno2pheno is predictive of short-term virological response (2002)

Beerenwinkel,Niko, Lengauer,Thomas, Däumer,Martin, Sierra,S., Schmidt,Barbara, Walter,Hauke, ...

Quantitative phenotype prediction by support vector machines (2002)

Beerenwinkel,Niko, Lengauer,Thomas, Schmidt,Barbara, Walter,Hauke, Kaiser,Rolf, Hoffmann,Daniel, ...

Co-clustering of biological networks and gene expression data (2002)

Hanisch,Daniel, Zien,Alexander, Zimmer,Ralf, Lengauer,Thomas

A hypergraph-based method for unification of existing protein structure- and sequence-families (2002)

Freudenberg,Jan, Zimmer,Ralf, Hanisch,Daniel, Lengauer,Thomas

Diversity and complexity of HIV-1drug resistance: A bioinformatics approach to predicting phenotype from genotype (2002)

Beerenwinkel,Niko, Schmidt,Barbara, Walter,Hauke, Kaiser,Rolf, Lengauer,Thomas, Hoffmann,Daniel, ...

Flexible docking under pharmacophore type constraints (2002)

Hindle,Sally A., Rarey,Matthias, Buning,Christian, Lengauer,Thomas

ProML - the Protein Markup Language for specification of protein sequences, structures and families (2002)

Hanisch,Daniel, Zimmer,Ralf, Lengauer,Thomas

A Fast Algorithm for finding Dominators in a Flow Graph, (2002)

Lengauer,Thomas, Tarjan,Robert Endre

This paper presents a fast algorithm for finding dominators in a flow graph. The algorithm uses depth-first search and an efficient method of computing functions defined on paths in trees. A simple...

Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics (2002)

Althaus, Ernst, Caprara, Alberto, Lenhof, Hans-Peter, Reinert, Knut, Lengauer, Thomas

Multiple sequence alignment is one of the dominant problems in computational molecular biology. Numerous scoring functions and methods have been proposed, most of which result in NP-hard problems. In...

Improving fold recognition of protein threading by experimental distance constraints (2002)

Albrecht, Mario, Hanisch, Daniel, Zimmer, Ralf, Lengauer, Thomas

Microarrays: How Many Do You Need? (2002)

Zien, Alexander, Fluck, Juliane, Zimmer, Ralf, Lengauer, Thomas, Myers, Gene, Hannenhalli, Sridhar, ...

Confidence measures for protein fold recognition (2002)

Sommer, Ingolf, Zien, Alexander, Öhsen Von, Niklas, Zimmer, Ralf, Lengauer, Thomas

Geno2pheno is predictive of short-term virological response (2002)

Beerenwinkel, Niko, Lengauer, Thomas, Däumer, Martin, Sierra, S., Schmidt, Barbara, Walter, Hauke, ...

Quantitative phenotype prediction by support vector machines (2002)

Beerenwinkel, Niko, Lengauer, Thomas, Schmidt, Barbara, Walter, Hauke, Kaiser, Rolf, Hoffmann, Daniel, ...

Co-clustering of biological networks and gene expression data (2002)

Hanisch, Daniel, Zien, Alexander, Zimmer, Ralf, Lengauer, Thomas

A hypergraph-based method for unification of existing protein structure- and sequence-families (2002)

Freudenberg, Jan, Zimmer, Ralf, Hanisch, Daniel, Lengauer, Thomas

Diversity and complexity of HIV-1drug resistance: A bioinformatics approach to predicting phenotype from genotype (2002)

Beerenwinkel, Niko, Schmidt, Barbara, Walter, Hauke, Kaiser, Rolf, Lengauer, Thomas, Hoffmann, Daniel, ...

Preface: Special RECOMB 2001 Issue (2002)

Ausbildung im Bereich Bioinformatik (2002)

Flexible docking under pharmacophore type constraints (2002)

Hindle, Sally A., Rarey, Matthias, Buning, Christian, Lengauer, Thomas

ProML - the Protein Markup Language for specification of protein sequences, structures and families (2002)

Hanisch, Daniel, Zimmer, Ralf, Lengauer, Thomas

Proceedings of the European Conference on Computational Biology (ECCB 2002) (2002)

Lengauer, Thomas, Lenhof, Hans-Peter

Confidence measures for protein fold recognition (2002)

Sommer, Ingolf, Zien, Alexander, Von Öhsen, Niklas, Zimmer, Ralf, Lengauer, Thomas

Motivation: We present an extensive evaluation of different methods and criteria to detect remote homologs of a given protein sequence. We investigate two associated problems: first, to develop a...

Editorial (2002)

Co-clustering of biological networks and gene expression data (2002)

Hanisch, Daniel, Zien, Alexander, Zimmer, Ralf, Lengauer, Thomas

Motivation: Large scale gene expression data are often analysed by clustering genes based on gene expression data alone, though a priori knowledge in the form of biological networks is available. The...

Centralization: a new method for the normalization of gene expression data (2001)

Zien, Alexander, Aigner, Thomas, Zimmer, Ralf, Lengauer, Thomas

Microarrays measure values that are approximately proportional to the numbers of copies of different mRNA molecules in samples. Due to technical difficulties, the constant of proportionality between...

Analysis of gene expression data with pathway scores (2000)

Er Zien, Robert Ku Ner, Ralf Zimmer, Thomas Lengauer

We present a new approach for the evaluation of gene expression data. The basic idea is to generate biologically possible pathways and to score them with respect to gene expression measurements. We...

Analysis of gene expression data with pathway scores (2000)

Er Zien, Robert Kuffner, Ralf Zimmer, Thomas Lengauer

We present a new approach for the evaluation of gene expression data. The basic idea is to generate biologically possible pathways and to score them with respect to gene expression measurements. We...

Analysis of Gene Expression Data with Pathway Scores (2000)

Alexander Zien, Robert Küffner, Er Zien, Robert Ku Ner, Ralf Zimmer, Thomas Lengauer

Wepresent a new approachfortheevaluation of gene expression data. The basic idea is to generate biologically possible pathways and to score them with respect to gene expression measurements. We...

Protein structure prediction methods for drug design (2000)

Lengauer, Thomas, Zimmer, Ralf

Along the long path from genomic data to a new drug, the knowledge of three-dimensional protein structure can be of significant help in several places. This paper points out such places, discusses...

Pathway analysis in metabolic databases via differential metabolic display (DMD) (2000)

Küffner, Robert, Zimmer, Ralf, Lengauer, Thomas

Motivation: A number of metabolic databases are available electronically, some with features for querying and visualizing metabolic pathways and regulatory networks. We present a unifying, systematic...

Decision tree-based formation of consensus protein secondary structure prediction (1999)

Selbig, Joachim, Mevissen, Theo, Lengauer, Thomas

Motivation: Prediction of protein secondary structure provides information that is useful for other prediction methods like fold recognition and ab initio 3D prediction. A consensus prediction...

Lengauer T.; Parallel “go with the winners algorithms” in the LogP Model (1997)

Marcus Peinado, Thomas Lengauer

We parallelize the ‘Go with the winners ’ algorithm of Aldous and Vazirani [1] and analyze the resulting parallel algorithm in the LogP-model [4]. The main issues in the analysis are load...

Lengauer T.; Parallel “go with the winners algorithms” in the LogP Model (1997)

Marcus Peinado, Thomas Lengauer

We parallelize the `Go with the winners ' algorithm of Aldous and Vazirani [1] and analyze the resulting parallel algorithm in the LogP-model [4]. The main issues in the analysis are load...

A Fast Flexible Docking Method using an Incremental Construction Algorithm (1996)

Matthias Rarey, Bernd Kramer, Thomas Lengauer, Gerhard Klebe

We present an automatic method for docking organic ligands into protein Center for Information binding sites. The method can be used in the design process of specific Technology (GMD), Institute...

On the selection of candidates for point and line correspondences (1995)

Stefan Lanser, Thomas Lengauer

This paper addresses the selection of possible candidates for point or line correspondences between model and image features in the context of pose estimation or navigation tasks. The selection...

Recursive Dynamic Programming for Adaptive Sequence and Structure Alignment (1995)

Ralf Thiele, Ralf Zimmer, Thomas Lengauer

We propose a new alignment procedure that is capable of aligning protein sequences and structures in a unified manner. Recursive dynamic programming (RDP) is a hierarchical method which, on each...

On the Construction of Abstract Voronoi Diagrams (1990)

Mehlhorn, Kurt, Meiser, Stefan, Ó'Dúnlaing, Colm, Choffrut, Christian, Lengauer, Thomas

VLSI complexity, efficient VLSI algorithms and the HILL design system (1986)

Lengauer, Thomas, Mehlhorn, Kurt, Trullemans, C

Four results on the complexity of VLSI computation (1984)

The HILL system: A design environment for the hierarchical spezification, compaction, and simulation of integrated circuit layouts (1984)

Lengauer, Thomas, Mehlhorn, Kurt, Penfield, Paul

The HILL System: A Design Environment for the Hierarchical Specification, Compaction, and Simulation of Integrated Circuit Layouts (1983)

Four results on the complexity of VLSI computations (1983)

VLSI Complexity, Efficient VLSI Algorithms and the HILL Design System (1983)

On the Complexity of VLSI-Computations (1981)

Upper and lower bounds on time-space tradeoffs in a pebble game / (1979)

Lengauer, Thomas.

Thesis--Stanford University.

Upper and lower bounds on time-space tradeoffs in a pebble game /--Thomas Lengauer. (1979)

A fast algorithm for finding dominators in a flowgraph (1979)

Microfiche (negative). -- 1 sheet ; 11 x 15 cm.

Thomas Lengauer, Robert Endre, Tar Jan

A fast algoritbm for finding dominators in a flowgraph is presented. The algorithm uses depth-first search and an efficient method of computing functions defined on paths in trees. A simple...

Strukturelle Aspekte der Nebenläufigkeit / (1976)

Lengauer, Thomas.

Zugl.: Berlin, Freie Univ., Fachbereich 19 - Mathematik, Diss., 1975.

Docking into the homology models of CYP11B1 and CYP11B2

Antes,Iris, Lengauer,Thomas

Virtual Screening for novel Urease Inhibitors

Kämper,Andreas, Lengauer,Thomas

Development of a new tool for predicting the structure of host-guest complexes

Steffen,Andreas, Kämper,Andreas, Lengauer,Thomas

FlexR - Predicting the structure of host-guest complexes

Steffen,Andreas, Kämper,Andreas, Lengauer,Thomas

Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype

Beerenwinkel, Niko, Schmidt, Barbara, Walter, Hauke, Kaiser, Rolf, Lengauer, Thomas, Hoffmann, Daniel, ...

Drug resistance testing has been shown to be beneficial for clinical management of HIV type 1 infected patients. Whereas phenotypic assays directly measure drug resistance, the commonly used...

Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes

Beerenwinkel, Niko, Däumer, Martin, Oette, Mark, Korn, Klaus, Hoffmann, Daniel, Kaiser, Rolf, ...

Therapeutic success of anti-HIV therapies is limited by the development of drug resistant viruses. These genetic variants display complex mutational patterns in their pol gene, which codes for...

Tenofovir Resistance and Resensitization

Wolf, Katharina, Walter, Hauke, Beerenwinkel, Niko, Keulen, Wilco, Kaiser, Rolf, Hoffmann, Daniel, ...

Human immunodeficiency viruses in 321 samples from tenofovir-naïve patients were retrospectively evaluated for resistance to this nucleotide analogue. All virus strains with insertions between amino...

Confirmation of human protein interaction data by human expression data

Hahn, Andreas, Rahnenführer, Jörg, Talwar, Priti, Lengauer, Thomas

Dissection of the Inflammatory Bowel Disease Transcriptome Using Genome-Wide cDNA Microarrays

Costello, Christine M, Mah, Nancy, Häsler, Robert, Rosenstiel, Philip, Waetzig, Georg H, Hahn, Andreas, ...

cDNA analysis of colonic samples from patients with Crohn disease and ulcerative colitis suggests substantial differences in pathophysiology between the two diseases.

Local protein structure prediction using discriminative models

NOXclass: prediction of protein-protein interaction types

Zhu, Hongbo, Domingues, Francisco S, Sommer, Lngolf, Lengauer, Thomas

CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure

Bock, Christoph, Paulsen, Martina, Tierling, Sascha, Mikeska, Thomas, Lengauer, Thomas, Walter, Jörn

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...

Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family

Castellano, Sergi, Lobanov, Alexey V., Chapple, Charles, Novoselov, Sergey V., Albrecht, Mario, Hua, Deame, ...

Selenoproteins are a diverse group of proteins that contain selenocysteine (Sec), the 21st amino acid. In the genetic code, UGA serves as a termination signal and a Sec codon. This dual role has...

Mutations in the NB-ARC Domain of I-2 That Impair ATP Hydrolysis Cause Autoactivation1[OA]

Tameling, Wladimir I.L., Vossen, Jack H., Albrecht, Mario, Lengauer, Thomas, Berden, Jan A., Haring, Michel A., ...

Resistance (R) proteins in plants confer specificity to the innate immune system. Most R proteins have a centrally located NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4)...

A new measure for functional similarity of gene products based on Gene Ontology

Schlicker, Andreas, Domingues, Francisco S, Rahnenführer, Jörg, Lengauer, Thomas

Improving the quality of protein structure models by selecting from alignment alternatives

Sommer, Ingolf, Toppo, Stefano, Sander, Oliver, Lengauer, Thomas, Tosatto, Silvio CE

Involvement of Novel Human Immunodeficiency Virus Type 1 Reverse Transcriptase Mutations in the Regulation of Resistance to Nucleoside Inhibitors

Svicher, Valentina, Sing, Tobias, Santoro, Maria Mercedes, Forbici, Federica, Rodríguez-Barrios, Fátima, Bertoli, Ada, ...

We characterized 16 additional mutations in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) whose role in drug resistance is still unknown by analyzing 1,906 plasma-derived...

Patients with High-Grade Gliomas Harboring Deletions of Chromosomes 9p and 10q Benefit from Temozolomide Treatment1

Wemmert, Silke, Ketter, Ralf, Rahnenführer, Jörg, Beerenwinkel, Niko, Strowitzki, Martin, Feiden, Wolfgang, ...

Surgical cure of glioblastomas is virtually impossible and their clinical course is mainly determined by the biologic behavior of the tumor cells and their response to radiation and chemotherapy. We...

Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype

Beerenwinkel, Niko, Schmidt, Barbara, Walter, Hauke, Kaiser, Rolf, Lengauer, Thomas, Hoffmann, Daniel, ...

Drug resistance testing has been shown to be beneficial for clinical management of HIV type 1 infected patients. Whereas phenotypic assays directly measure drug resistance, the commonly used...

Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes

Beerenwinkel, Niko, Däumer, Martin, Oette, Mark, Korn, Klaus, Hoffmann, Daniel, Kaiser, Rolf, ...

Therapeutic success of anti-HIV therapies is limited by the development of drug resistant viruses. These genetic variants display complex mutational patterns in their pol gene, which codes for...

Tenofovir Resistance and Resensitization

Wolf, Katharina, Walter, Hauke, Beerenwinkel, Niko, Keulen, Wilco, Kaiser, Rolf, Hoffmann, Daniel, ...

Human immunodeficiency viruses in 321 samples from tenofovir-naïve patients were retrospectively evaluated for resistance to this nucleotide analogue. All virus strains with insertions between amino...

Confirmation of human protein interaction data by human expression data

Hahn, Andreas, Rahnenführer, Jörg, Talwar, Priti, Lengauer, Thomas

Dissection of the Inflammatory Bowel Disease Transcriptome Using Genome-Wide cDNA Microarrays

Costello, Christine M, Mah, Nancy, Häsler, Robert, Rosenstiel, Philip, Waetzig, Georg H, Hahn, Andreas, ...

cDNA analysis of colonic samples from patients with Crohn disease and ulcerative colitis suggests substantial differences in pathophysiology between the two diseases.

Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family

Castellano, Sergi, Lobanov, Alexey V., Chapple, Charles, Novoselov, Sergey V., Albrecht, Mario, Hua, Deame, ...

Selenoproteins are a diverse group of proteins that contain selenocysteine (Sec), the 21st amino acid. In the genetic code, UGA serves as a termination signal and a Sec codon. This dual role has...

Local protein structure prediction using discriminative models