TL

Thomas Lengauer

Max Planck Institute for Informatics

Affiliated withMax Planck Institute for Informatics

Research Area

Immunology and Infection

Biography

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JoVE Journal Publications

ArticleTotal : 1
Year
Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach
Publication title

Cited by 16

2011

Other Publications

Article
Year
Docking and scoring with alternative side-chain conformations.

Proteins| PubMed ID: 18704939

2009
Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype.

Proceedings of the National Academy of Sciences of the United States of America| PubMed ID: 12060770

2002
Confidence measures for protein fold recognition.

Bioinformatics (Oxford, England)| PubMed ID: 12075015

2002
Co-clustering of biological networks and gene expression data.

Bioinformatics (Oxford, England)| PubMed ID: 12169542

2002
Structural modeling of ataxin-3 reveals distant homology to adaptins.

Proteins| PubMed ID: 12486728

2003
ProML--the protein markup language for specification of protein sequences, structures and families.

In silico biology| PubMed ID: 12542416

2002
Improving fold recognition of protein threading by experimental distance constraints.

In silico biology| PubMed ID: 12542417

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

In silico biology| PubMed ID: 12542418

2002
Identification of mammalian orthologs associates PYPAF5 with distinct functional roles.

FEBS letters| PubMed ID: 12633874

2003
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes.

Nucleic acids research| PubMed ID: 12824435

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

Bioinformatics (Oxford, England)| PubMed ID: 12835264

2003
Methods for optimizing antiviral combination therapies.

Bioinformatics (Oxford, England)| PubMed ID: 12855433

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

Protein engineering| PubMed ID: 12915722

2003
Microarrays: how many do you need?

Journal of computational biology : a journal of computational molecular cell biology| PubMed ID: 12935350

2003
Tenofovir resistance and resensitization.

Antimicrobial agents and chemotherapy| PubMed ID: 14576105

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

FEBS letters| PubMed ID: 14623123

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

Bioinformatics (Oxford, England)| PubMed ID: 14630645

2003
Software tool for automated processing of 13C labeling data from mass spectrometric spectra.

BioTechniques| PubMed ID: 14682055

2003
Novel technologies for virtual screening.

Drug discovery today| PubMed ID: 14761803

2004
Survey on the PABC recognition motif PAM2.

Biochemical and biophysical research communications| PubMed ID: 15003521

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

Bioinformatics (Oxford, England)| PubMed ID: 15059818

2004
Genetic variation in DLG5 is associated with inflammatory bowel disease.

Nature genetics| PubMed ID: 15107852

2004
Protein function from sequence and structure data.

Applied bioinformatics| PubMed ID: 15130830

2003
Novel Sm-like proteins with long C-terminal tails and associated methyltransferases.

FEBS letters| PubMed ID: 15225602

2004
Structural and functional analysis of ataxin-2 and ataxin-3.

European journal of biochemistry / FEBS| PubMed ID: 15265035

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

Blood| PubMed ID: 15294858

2004
Automated clustering of ensembles of alternative models in protein structure databases.

Protein engineering, design & selection : PEDS| PubMed ID: 15319469

2004
Ensemble methods for classification in cheminformatics.

Journal of chemical information and computer sciences| PubMed ID: 15554666

2004
The HIN domain of IFI-200 proteins consists of two OB folds.

Biochemical and biophysical research communications| PubMed ID: 15649401

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

Bioinformatics (Oxford, England)| PubMed ID: 15657098

2005
An integrative approach to gain insights into the cellular function of human ataxin-2.

Journal of molecular biology| PubMed ID: 15663938

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

Bioinformatics (Oxford, England)| PubMed ID: 15705654

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

Nature genetics| PubMed ID: 15735647

2005
Synthesis and evaluation of (pyridylmethylene)tetrahydronaphthalenes/-indanes and structurally modified derivatives: potent and selective inhibitors of aldosterone synthase.

Journal of medicinal chemistry| PubMed ID: 15743198

2005
Synthesis and evaluation of imidazolylmethylenetetrahydronaphthalenes and imidazolylmethyleneindanes: potent inhibitors of aldosterone synthase.

Journal of medicinal chemistry| PubMed ID: 15771425

2005
A new CARD15 mutation in Blau syndrome.

European journal of human genetics : EJHG| PubMed ID: 15812565

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

The Journal of infectious diseases| PubMed ID: 15871130

2005
Confirmation of human protein interaction data by human expression data.

BMC bioinformatics| PubMed ID: 15877815

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

Human genetics| PubMed ID: 16028060

2005
ROCR: visualizing classifier performance in R.

Bioinformatics (Oxford, England)| PubMed ID: 16096348

2005
Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays.

PLoS medicine| PubMed ID: 16107186

2005
Learning multiple evolutionary pathways from cross-sectional data.

Journal of computational biology : a journal of computational molecular cell biology| PubMed ID: 16108705

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

Human molecular genetics| PubMed ID: 16115810

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

Bioinformatics (Oxford, England)| PubMed ID: 16141249

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

Bioinformatics (Oxford, England)| PubMed ID: 16144807

2005
Automatic generation of complementary descriptors with molecular graph networks.

Journal of chemical information and modeling| PubMed ID: 16180893

2005
POEM: Parameter Optimization using Ensemble Methods: application to target specific scoring functions.

Journal of chemical information and modeling| PubMed ID: 16180906

2005
Decomposing protein networks into domain-domain interactions.

Bioinformatics (Oxford, England)| PubMed ID: 16204107

2005
Multiple-ligand-based virtual screening: methods and applications of the MTree approach.

Journal of medicinal chemistry| PubMed ID: 16220974

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

The Journal of infectious diseases| PubMed ID: 16235168

2005
Patients with high-grade gliomas harboring deletions of chromosomes 9p and 10q benefit from temozolomide treatment.

Neoplasia (New York, N.Y.)| PubMed ID: 16242071

2005
Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family.

Proceedings of the National Academy of Sciences of the United States of America| PubMed ID: 16260744

2005
Local protein structure prediction using discriminative models.

BMC bioinformatics| PubMed ID: 16405736

2006
NOXclass: prediction of protein-protein interaction types.

BMC bioinformatics| PubMed ID: 16423290

2006
A fully computational model for predicting percutaneous drug absorption.

Journal of chemical information and modeling| PubMed ID: 16426076

2006
Recco: recombination analysis using cost optimization.

Bioinformatics (Oxford, England)| PubMed ID: 16488909

2006
Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation.

Plant physiology| PubMed ID: 16489136

2006
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure.

PLoS genetics| PubMed ID: 16520826

2006
Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies.

Journal of chemical information and modeling| PubMed ID: 16563022

2006
Computational recognition of potassium channel sequences.

Bioinformatics (Oxford, England)| PubMed ID: 16595554

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

Bioinformatics (Oxford, England)| PubMed ID: 16606683

2006
Calculating the statistical significance of changes in pathway activity from gene expression data.

Statistical applications in genetics and molecular biology| PubMed ID: 16646794

2004
A new measure for functional similarity of gene products based on Gene Ontology.

BMC bioinformatics| PubMed ID: 16776819

2006
Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors.

Journal of virology| PubMed ID: 16809324

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

Antiviral therapy| PubMed ID: 16856625

2006
Flexible docking of ligands into synthetic receptors using a two-sided incremental construction algorithm.

Journal of chemical information and modeling| PubMed ID: 16859301

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

BMC bioinformatics| PubMed ID: 16872519

2006
DynaPred: a structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations.

Bioinformatics (Oxford, England)| PubMed ID: 16873467

2006
Bioinformatics-assisted anti-HIV therapy.

Nature reviews. Microbiology| PubMed ID: 16980939

2006
Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART.

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology| PubMed ID: 17005445

2006
Model selection for mixtures of mutagenetic trees.

Statistical applications in genetics and molecular biology| PubMed ID: 17049028

2006
Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair.

Nucleic acids research| PubMed ID: 17135187

2006
A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1.

Nature genetics| PubMed ID: 17200669

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

Molecular cancer| PubMed ID: 17280610

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

Genome biology| PubMed ID: 17346342

2007
The implications of alternative splicing in the ENCODE protein complement.

Proceedings of the National Academy of Sciences of the United States of America| PubMed ID: 17372197

2007
Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage.

PLoS computational biology| PubMed ID: 17397254

2007
Functional evaluation of domain-domain interactions and human protein interaction networks.

Bioinformatics (Oxford, England)| PubMed ID: 17456608

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

Antiviral therapy| PubMed ID: 17503659

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

Journal of molecular graphics & modelling| PubMed ID: 17507273

2007
Expression pattern analysis of transcribed HERV sequences is complicated by ex vivo recombination.

Retrovirology| PubMed ID: 17550625

2007
Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas.

International journal of cancer. Journal international du cancer| PubMed ID: 17557299

2007
CpG island mapping by epigenome prediction.

PLoS computational biology| PubMed ID: 17559301

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

Protein science : a publication of the Protein Society| PubMed ID: 17567749

2007
Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening.

Chemistry (Weinheim an der Bergstrasse, Germany)| PubMed ID: 17610225

2007
Computational analysis of human protein interaction networks.

Proteomics| PubMed ID: 17647236

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

Journal of virology| PubMed ID: 17686836

2007
Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level.

Clinical and vaccine immunology : CVI| PubMed ID: 17715334

2007
Fifteen years of env C2V3C3 evolution in six individuals infected clonally with human immunodeficiency virus type 1.

Journal of medical virology| PubMed ID: 17854039

2007
Conformational analysis of alternative protein structures.

Bioinformatics (Oxford, England)| PubMed ID: 17933849

2007
Identification of PatL1, a human homolog to yeast P body component Pat1.

Biochimica et biophysica acta| PubMed ID: 17936923

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

Bioinformatics (Oxford, England)| PubMed ID: 17977888

2007
Computing topological parameters of biological networks.

Bioinformatics (Oxford, England)| PubMed ID: 18006545

2008
Predicting HIV coreceptor usage on the basis of genetic and clinical covariates.

Antiviral therapy| PubMed ID: 18018768

2007
Computational epigenetics.

Bioinformatics (Oxford, England)| PubMed ID: 18024971

2008
Bioinformatics prediction of HIV coreceptor usage.

Nature biotechnology| PubMed ID: 18066037

2007
Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus.

Genome biology| PubMed ID: 18215275

2008
Stability analysis of mixtures of mutagenetic trees.

BMC bioinformatics| PubMed ID: 18366778

2008
Alignment of non-covalent interactions at protein-protein interfaces.

PloS one| PubMed ID: 18382693

2008
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.

Nucleic acids research| PubMed ID: 18413340

2008
Selecting anti-HIV therapies based on a variety of genomic and clinical factors.

Bioinformatics (Oxford, England)| PubMed ID: 18586740

2008
Local function conservation in sequence and structure space.

PLoS computational biology| PubMed ID: 18604264

2008
An integrative approach for predicting interactions of protein regions.

Bioinformatics (Oxford, England)| PubMed ID: 18689837

2008
Integrating expression data with domain interaction networks.

Bioinformatics (Oxford, England)| PubMed ID: 18710874

2008
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores.

Bioinformatics (Oxford, England)| PubMed ID: 18718947

2008
Comparison of classifier fusion methods for predicting response to anti HIV-1 therapy.

PloS one| PubMed ID: 18941628

2008
Clinical relevance of the 2'-5'-oligoadenylate synthetase/RNase L system for treatment response in chronic hepatitis C.

Journal of hepatology| PubMed ID: 19022516

2009
Dynamics of NRTI resistance mutations during therapy interruption.

AIDS research and human retroviruses| PubMed ID: 19182921

2009
EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.

Genome biology| PubMed ID: 19208250

2009
Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database.

The Journal of infectious diseases| PubMed ID: 19239365

2009
DASMI: exchanging, annotating and assessing molecular interaction data.

Bioinformatics (Oxford, England)| PubMed ID: 19420069

2009
Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype.

Antiviral therapy| PubMed ID: 19430102

2009
[Resistance screening].

MMW Fortschritte der Medizin| PubMed ID: 19769083

2009
MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays.

Genome biology| PubMed ID: 19804638

2009
V3 loop sequence space analysis suggests different evolutionary patterns of CCR5- and CXCR4-tropic HIV.

PloS one| PubMed ID: 19816596

2009
Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks.

Journal of integrative bioinformatics| PubMed ID: 20134061

2008
Only slight impact of predicted replicative capacity for therapy response prediction.

PloS one| PubMed ID: 20140263

2010
Predicting MHC class I epitopes in large datasets.

BMC bioinformatics| PubMed ID: 20163709

2010
Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy.

Methods in molecular biology (Clifton, N.J.)| PubMed ID: 20238087

2010
Short communication: selection of thymidine analogue resistance mutational patterns in children infected from a common HIV type 1 subtype G source.

AIDS research and human retroviruses| PubMed ID: 20334563

2010
Permutation importance: a corrected feature importance measure.

Bioinformatics (Oxford, England)| PubMed ID: 20385727

2010
Dimerization of the hepatitis C virus nonstructural protein 4B depends on the integrity of an aminoterminal basic leucine zipper.

Protein science : a publication of the Protein Society| PubMed ID: 20506268

2010
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.

Nucleic acids research| PubMed ID: 20513647

2010
Positive selection of HIV host factors and the evolution of lentivirus genes.

BMC evolutionary biology| PubMed ID: 20565842

2010
Dealing with sparse data in predicting outcomes of HIV combination therapies.

Bioinformatics (Oxford, England)| PubMed ID: 20624779

2010
HLA class I allele associations with HCV genetic variants in patients with chronic HCV genotypes 1a or 1b infection.

Journal of hepatology| PubMed ID: 20800922

2010
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms.

Bioinformatics (Oxford, England)| PubMed ID: 20823322

2010
Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.

Medical microbiology and immunology| PubMed ID: 20853118

2011
Improved prediction of HIV‐1 coreceptor usage with sequence information from the second hypervariable loop of gp120.

The Journal of infectious diseases| PubMed ID: 20874088

2010
Reconstructing the ancestral germ line methylation state of young repeats.

Molecular biology and evolution| PubMed ID: 21212152

2011
Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment.

Cell host & microbe| PubMed ID: 21238945

2011
Learning from past treatments and their outcome improves prediction of in vivo response to anti-HIV therapy.

Statistical applications in genetics and molecular biology| PubMed ID: 21291416

2011
HIV prevalence and route of transmission in Turkish immigrants living in North-Rhine Westphalia, Germany.

Medical microbiology and immunology| PubMed ID: 21461764

2011
Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially.

Antiviral therapy| PubMed ID: 21555814

2011
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing.

Nucleic acids research| PubMed ID: 21565797

2011
Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.

BMC medical informatics and decision making| PubMed ID: 21569501

2011
APOBEC3G/F as one possible driving force for co-receptor switch of the human immunodeficiency virus-1.

Medical microbiology and immunology| PubMed ID: 21573951

2012
Classification with correlated features: unreliability of feature ranking and solutions.

Bioinformatics (Oxford, England)| PubMed ID: 21576180

2011
A DNA methylation fingerprint of 1628 human samples.

Genome research| PubMed ID: 21613409

2012
Preserving charge and oxidation state of Au(III) ions in an agent-functionalized nanocrystal model system.

ACS nano| PubMed ID: 21736315

2011
HIV-1 mutational pathways under multidrug therapy.

AIDS research and therapy| PubMed ID: 21794106

2011
Peptidomimetic Escape Mechanisms Arise via Genetic Diversity in the Ligand-Binding Site of the Hepatitis C Virus NS3/4A Serine Protease.

Gastroenterology| PubMed ID: 22155364

2011
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types.

PLoS genetics| PubMed ID: 22174693

2011
Endogenous or exogenous spreading of HIV-1 in Nordrhein-Westfalen, Germany, investigated by phylodynamic analysis of the RESINA Study cohort.

Medical microbiology and immunology| PubMed ID: 22262052

2012
Bioinformatical Assistance of Selecting Anti-HIV Therapies: Where Do We Stand?

Intervirology| PubMed ID: 22286878

2012
Geno2pheno[454]: A Web Server for the Prediction of HIV-1 Coreceptor Usage from Next-Generation Sequencing Data.

Intervirology| PubMed ID: 22286879

2012
Predicting Response to Antiretroviral Treatment by Machine Learning: The EuResist Project.

Intervirology| PubMed ID: 22286881

2012
Risk Factors Associated with Older Age in Treatment-Naive HIV-Positive Patients.

Intervirology| PubMed ID: 22286885

2012
Epidemiology of Transmitted Drug Resistance in Chronically HIV-Infected Patients in Germany: The RESINA Study 2001-2009.

Intervirology| PubMed ID: 22286886

2012
On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking.

Journal of chemical information and modeling| PubMed ID: 22320151

2012