Thomas Lengauer

Docking and scoring with alternative side-chain conformations.

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

Confidence measures for protein fold recognition.

Co-clustering of biological networks and gene expression data.

Structural modeling of ataxin-3 reveals distant homology to adaptins.

ProML--the protein markup language for specification of protein sequences, structures and families.

Improving fold recognition of protein threading by experimental distance constraints.

A hypergraph-based method for unification of existing protein structure- and sequence-families.

Identification of mammalian orthologs associates PYPAF5 with distinct functional roles.

Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes.

Pyranose oxidase identified as a member of the GMC oxidoreductase family.

Methods for optimizing antiviral combination therapies.

Simple consensus procedures are effective and sufficient in secondary structure prediction.

Microarrays: how many do you need?

Tenofovir resistance and resensitization.

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

Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence.

Software tool for automated processing of 13C labeling data from mass spectrometric spectra.

Novel technologies for virtual screening.

Survey on the PABC recognition motif PAM2.

Arby: automatic protein structure prediction using profile-profile alignment and confidence measures.

Genetic variation in DLG5 is associated with inflammatory bowel disease.

Protein function from sequence and structure data.

Novel Sm-like proteins with long C-terminal tails and associated methyltransferases.

Structural and functional analysis of ataxin-2 and ataxin-3.

Association of HCV-related mixed cryoglobulinemia with specific mutational pattern of the HCV E2 protein and CD81 expression on peripheral B lymphocytes.

Automated clustering of ensembles of alternative models in protein structure databases.

Ensemble methods for classification in cheminformatics.

The HIN domain of IFI-200 proteins consists of two OB folds.

Mtreemix: a software package for learning and using mixture models of mutagenetic trees.

An integrative approach to gain insights into the cellular function of human ataxin-2.

Estimating cancer survival and clinical outcome based on genetic tumor progression scores.

Sarcoidosis is associated with a truncating splice site mutation in BTNL2.

Synthesis and evaluation of (pyridylmethylene)tetrahydronaphthalenes/-indanes and structurally modified derivatives: potent and selective inhibitors of aldosterone synthase.

Synthesis and evaluation of imidazolylmethylenetetrahydronaphthalenes and imidazolylmethyleneindanes: potent inhibitors of aldosterone synthase.

A new CARD15 mutation in Blau syndrome.

Estimating HIV evolutionary pathways and the genetic barrier to drug resistance.

Confirmation of human protein interaction data by human expression data.

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

ROCR: visualizing classifier performance in R.

Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays.

Learning multiple evolutionary pathways from cross-sectional data.

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

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.

Computational methods for the design of effective therapies against drug resistant HIV strains.

Automatic generation of complementary descriptors with molecular graph networks.

POEM: Parameter Optimization using Ensemble Methods: application to target specific scoring functions.

Decomposing protein networks into domain-domain interactions.

Multiple-ligand-based virtual screening: methods and applications of the MTree approach.

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

Patients with high-grade gliomas harboring deletions of chromosomes 9p and 10q benefit from temozolomide treatment.

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

Local protein structure prediction using discriminative models.

NOXclass: prediction of protein-protein interaction types.

A fully computational model for predicting percutaneous drug absorption.

Recco: recombination analysis using cost optimization.

Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation.

CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure.

Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies.

Computational recognition of potassium channel sequences.

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure.

Calculating the statistical significance of changes in pathway activity from gene expression data.

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

Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors.

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

Flexible docking of ligands into synthetic receptors using a two-sided incremental construction algorithm.

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

DynaPred: a structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations.

Bioinformatics-assisted anti-HIV therapy.

Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART.

Model selection for mixtures of mutagenetic trees.

Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair.

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1.

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

GOTax: investigating biological processes and biochemical activities along the taxonomic tree.

The implications of alternative splicing in the ENCODE protein complement.

Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage.

Functional evaluation of domain-domain interactions and human protein interaction networks.

Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance.

Structural and functional comparison of the non-structural protein 4B in flaviviridae.

Expression pattern analysis of transcribed HERV sequences is complicated by ex vivo recombination.

Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas.

CpG island mapping by epigenome prediction.

IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.

Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening.

Computational analysis of human protein interaction networks.

Characterization and structural analysis of novel mutations in human immunodeficiency virus type 1 reverse transcriptase involved in the regulation of resistance to nonnucleoside inhibitors.

Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level.

Fifteen years of env C2V3C3 evolution in six individuals infected clonally with human immunodeficiency virus type 1.

Conformational analysis of alternative protein structures.

Identification of PatL1, a human homolog to yeast P body component Pat1.

Moment invariants as shape recognition technique for comparing protein binding sites.

Computing topological parameters of biological networks.

Predicting HIV coreceptor usage on the basis of genetic and clinical covariates.

Computational epigenetics.

Bioinformatics prediction of HIV coreceptor usage.

Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus.

Stability analysis of mixtures of mutagenetic trees.

Alignment of non-covalent interactions at protein-protein interfaces.

Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.

Selecting anti-HIV therapies based on a variety of genomic and clinical factors.

Local function conservation in sequence and structure space.

An integrative approach for predicting interactions of protein regions.

Integrating expression data with domain interaction networks.

Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores.

Comparison of classifier fusion methods for predicting response to anti HIV-1 therapy.

Clinical relevance of the 2'-5'-oligoadenylate synthetase/RNase L system for treatment response in chronic hepatitis C.

Dynamics of NRTI resistance mutations during therapy interruption.

EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.

Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database.

DASMI: exchanging, annotating and assessing molecular interaction data.

Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype.

[Resistance screening].

MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays.

V3 loop sequence space analysis suggests different evolutionary patterns of CCR5- and CXCR4-tropic HIV.

Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks.

Only slight impact of predicted replicative capacity for therapy response prediction.

Predicting MHC class I epitopes in large datasets.

Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy.

Short communication: selection of thymidine analogue resistance mutational patterns in children infected from a common HIV type 1 subtype G source.

Permutation importance: a corrected feature importance measure.

Dimerization of the hepatitis C virus nonstructural protein 4B depends on the integrity of an aminoterminal basic leucine zipper.

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.

Positive selection of HIV host factors and the evolution of lentivirus genes.

Dealing with sparse data in predicting outcomes of HIV combination therapies.

HLA class I allele associations with HCV genetic variants in patients with chronic HCV genotypes 1a or 1b infection.

Improving disease gene prioritization using the semantic similarity of Gene Ontology terms.

Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.

Improved prediction of HIV‐1 coreceptor usage with sequence information from the second hypervariable loop of gp120.

Reconstructing the ancestral germ line methylation state of young repeats.

Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment.

Learning from past treatments and their outcome improves prediction of in vivo response to anti-HIV therapy.

HIV prevalence and route of transmission in Turkish immigrants living in North-Rhine Westphalia, Germany.

Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially.

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing.

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.

APOBEC3G/F as one possible driving force for co-receptor switch of the human immunodeficiency virus-1.

Classification with correlated features: unreliability of feature ranking and solutions.

A DNA methylation fingerprint of 1628 human samples.

Preserving charge and oxidation state of Au(III) ions in an agent-functionalized nanocrystal model system.

HIV-1 mutational pathways under multidrug therapy.

Peptidomimetic Escape Mechanisms Arise via Genetic Diversity in the Ligand-Binding Site of the Hepatitis C Virus NS3/4A Serine Protease.

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types.

Endogenous or exogenous spreading of HIV-1 in Nordrhein-Westfalen, Germany, investigated by phylodynamic analysis of the RESINA Study cohort.

Bioinformatical Assistance of Selecting Anti-HIV Therapies: Where Do We Stand?

Geno2pheno[454]: A Web Server for the Prediction of HIV-1 Coreceptor Usage from Next-Generation Sequencing Data.

Predicting Response to Antiretroviral Treatment by Machine Learning: The EuResist Project.

Risk Factors Associated with Older Age in Treatment-Naive HIV-Positive Patients.

Epidemiology of Transmitted Drug Resistance in Chronically HIV-Infected Patients in Germany: The RESINA Study 2001-2009.

On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking.