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Docking and scoring with alternative side-chain conformations.
Proteins Feb, 2009 | Pubmed ID: 18704939
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 Jun, 2002 | Pubmed ID: 12060770
Confidence measures for protein fold recognition.
Bioinformatics (Oxford, England) Jun, 2002 | Pubmed ID: 12075015
Co-clustering of biological networks and gene expression data.
Bioinformatics (Oxford, England) , 2002 | Pubmed ID: 12169542
Structural modeling of ataxin-3 reveals distant homology to adaptins.
Proteins Feb, 2003 | Pubmed ID: 12486728
ProML--the protein markup language for specification of protein sequences, structures and families.
In silico biology , 2002 | Pubmed ID: 12542416
Improving fold recognition of protein threading by experimental distance constraints.
In silico biology , 2002 | Pubmed ID: 12542417
A hypergraph-based method for unification of existing protein structure- and sequence-families.
In silico biology , 2002 | Pubmed ID: 12542418
Identification of mammalian orthologs associates PYPAF5 with distinct functional roles.
FEBS letters Mar, 2003 | Pubmed ID: 12633874
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes.
Nucleic acids research Jul, 2003 | Pubmed ID: 12824435
Pyranose oxidase identified as a member of the GMC oxidoreductase family.
Bioinformatics (Oxford, England) Jul, 2003 | Pubmed ID: 12835264
Methods for optimizing antiviral combination therapies.
Bioinformatics (Oxford, England) , 2003 | Pubmed ID: 12855433
Simple consensus procedures are effective and sufficient in secondary structure prediction.
Protein engineering Jul, 2003 | Pubmed ID: 12915722
Microarrays: how many do you need?
Journal of computational biology : a journal of computational molecular cell biology , 2003 | Pubmed ID: 12935350
Tenofovir resistance and resensitization.
Antimicrobial agents and chemotherapy Nov, 2003 | Pubmed ID: 14576105
Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2.
FEBS letters Nov, 2003 | Pubmed ID: 14623123
Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence.
Bioinformatics (Oxford, England) Nov, 2003 | Pubmed ID: 14630645
Software tool for automated processing of 13C labeling data from mass spectrometric spectra.
BioTechniques Dec, 2003 | Pubmed ID: 14682055
Novel technologies for virtual screening.
Drug discovery today Jan, 2004 | Pubmed ID: 14761803
Survey on the PABC recognition motif PAM2.
Biochemical and biophysical research communications Mar, 2004 | Pubmed ID: 15003521
Arby: automatic protein structure prediction using profile-profile alignment and confidence measures.
Bioinformatics (Oxford, England) Sep, 2004 | Pubmed ID: 15059818
Genetic variation in DLG5 is associated with inflammatory bowel disease.
Nature genetics May, 2004 | Pubmed ID: 15107852
Protein function from sequence and structure data.
Applied bioinformatics , 2003 | Pubmed ID: 15130830
Novel Sm-like proteins with long C-terminal tails and associated methyltransferases.
FEBS letters Jul, 2004 | Pubmed ID: 15225602
Structural and functional analysis of ataxin-2 and ataxin-3.
European journal of biochemistry / FEBS Aug, 2004 | Pubmed ID: 15265035
Association of HCV-related mixed cryoglobulinemia with specific mutational pattern of the HCV E2 protein and CD81 expression on peripheral B lymphocytes.
Blood Aug, 2004 | Pubmed ID: 15294858
Automated clustering of ensembles of alternative models in protein structure databases.
Protein engineering, design & selection : PEDS Jun, 2004 | Pubmed ID: 15319469
Ensemble methods for classification in cheminformatics.
Journal of chemical information and computer sciences Nov-Dec, 2004 | Pubmed ID: 15554666
The HIN domain of IFI-200 proteins consists of two OB folds.
Biochemical and biophysical research communications Feb, 2005 | Pubmed ID: 15649401
Mtreemix: a software package for learning and using mixture models of mutagenetic trees.
Bioinformatics (Oxford, England) May, 2005 | Pubmed ID: 15657098
An integrative approach to gain insights into the cellular function of human ataxin-2.
Journal of molecular biology Feb, 2005 | Pubmed ID: 15663938
Estimating cancer survival and clinical outcome based on genetic tumor progression scores.
Bioinformatics (Oxford, England) May, 2005 | Pubmed ID: 15705654
Sarcoidosis is associated with a truncating splice site mutation in BTNL2.
Nature genetics Apr, 2005 | Pubmed ID: 15735647
Synthesis and evaluation of (pyridylmethylene)tetrahydronaphthalenes/-indanes and structurally modified derivatives: potent and selective inhibitors of aldosterone synthase.
Journal of medicinal chemistry Mar, 2005 | Pubmed ID: 15743198
Synthesis and evaluation of imidazolylmethylenetetrahydronaphthalenes and imidazolylmethyleneindanes: potent inhibitors of aldosterone synthase.
Journal of medicinal chemistry Mar, 2005 | Pubmed ID: 15771425
A new CARD15 mutation in Blau syndrome.
European journal of human genetics : EJHG Jun, 2005 | Pubmed ID: 15812565
Estimating HIV evolutionary pathways and the genetic barrier to drug resistance.
The Journal of infectious diseases Jun, 2005 | Pubmed ID: 15871130
Confirmation of human protein interaction data by human expression data.
BMC bioinformatics , 2005 | Pubmed ID: 15877815
Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiency.
Human genetics Oct, 2005 | Pubmed ID: 16028060
ROCR: visualizing classifier performance in R.
Bioinformatics (Oxford, England) Oct, 2005 | Pubmed ID: 16096348
Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays.
PLoS medicine Aug, 2005 | Pubmed ID: 16107186
Learning multiple evolutionary pathways from cross-sectional data.
Journal of computational biology : a journal of computational molecular cell biology Jul-Aug, 2005 | Pubmed ID: 16108705
Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways.
Human molecular genetics Oct, 2005 | Pubmed ID: 16115810
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.
Bioinformatics (Oxford, England) Nov, 2005 | Pubmed ID: 16141249
Computational methods for the design of effective therapies against drug resistant HIV strains.
Bioinformatics (Oxford, England) Nov, 2005 | Pubmed ID: 16144807
Automatic generation of complementary descriptors with molecular graph networks.
Journal of chemical information and modeling Sep-Oct, 2005 | Pubmed ID: 16180893
POEM: Parameter Optimization using Ensemble Methods: application to target specific scoring functions.
Journal of chemical information and modeling Sep-Oct, 2005 | Pubmed ID: 16180906
Decomposing protein networks into domain-domain interactions.
Bioinformatics (Oxford, England) Sep, 2005 | Pubmed ID: 16204107
Multiple-ligand-based virtual screening: methods and applications of the MTree approach.
Journal of medicinal chemistry Oct, 2005 | Pubmed ID: 16220974
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 Nov, 2005 | Pubmed ID: 16235168
Patients with high-grade gliomas harboring deletions of chromosomes 9p and 10q benefit from temozolomide treatment.
Neoplasia (New York, N.Y.) Oct, 2005 | Pubmed ID: 16242071
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 Nov, 2005 | Pubmed ID: 16260744
Local protein structure prediction using discriminative models.
BMC bioinformatics , 2006 | Pubmed ID: 16405736
NOXclass: prediction of protein-protein interaction types.
BMC bioinformatics , 2006 | Pubmed ID: 16423290
A fully computational model for predicting percutaneous drug absorption.
Journal of chemical information and modeling Jan-Feb, 2006 | Pubmed ID: 16426076
Recco: recombination analysis using cost optimization.
Bioinformatics (Oxford, England) May, 2006 | Pubmed ID: 16488909
Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation.
Plant physiology Apr, 2006 | Pubmed ID: 16489136
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure.
PLoS genetics Mar, 2006 | Pubmed ID: 16520826
Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies.
Journal of chemical information and modeling Mar-Apr, 2006 | Pubmed ID: 16563022
Computational recognition of potassium channel sequences.
Bioinformatics (Oxford, England) Jul, 2006 | Pubmed ID: 16595554
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure.
Bioinformatics (Oxford, England) Jul, 2006 | Pubmed ID: 16606683
Calculating the statistical significance of changes in pathway activity from gene expression data.
Statistical applications in genetics and molecular biology , 2004 | Pubmed ID: 16646794
A new measure for functional similarity of gene products based on Gene Ontology.
BMC bioinformatics , 2006 | Pubmed ID: 16776819
Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors.
Journal of virology Jul, 2006 | Pubmed ID: 16809324
Amino acid variations in hepatitis C virus p7 and sensitivity to antiviral combination therapy with amantadine in chronic hepatitis C.
Antiviral therapy , 2006 | Pubmed ID: 16856625
Flexible docking of ligands into synthetic receptors using a two-sided incremental construction algorithm.
Journal of chemical information and modeling Jul-Aug, 2006 | Pubmed ID: 16859301
Improving the quality of protein structure models by selecting from alignment alternatives.
BMC bioinformatics , 2006 | Pubmed ID: 16872519
DynaPred: a structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations.
Bioinformatics (Oxford, England) Jul, 2006 | Pubmed ID: 16873467
Bioinformatics-assisted anti-HIV therapy.
Nature reviews. Microbiology Oct, 2006 | Pubmed ID: 16980939
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 Dec, 2006 | Pubmed ID: 17005445
Model selection for mixtures of mutagenetic trees.
Statistical applications in genetics and molecular biology , 2006 | Pubmed ID: 17049028
Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair.
Nucleic acids research , 2006 | Pubmed ID: 17135187
A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1.
Nature genetics Feb, 2007 | Pubmed ID: 17200669
Factor interaction analysis for chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer.
Molecular cancer , 2007 | Pubmed ID: 17280610
GOTax: investigating biological processes and biochemical activities along the taxonomic tree.
Genome biology , 2007 | Pubmed ID: 17346342
The implications of alternative splicing in the ENCODE protein complement.
Proceedings of the National Academy of Sciences of the United States of America Mar, 2007 | Pubmed ID: 17372197
Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage.
PLoS computational biology Mar, 2007 | Pubmed ID: 17397254
Functional evaluation of domain-domain interactions and human protein interaction networks.
Bioinformatics (Oxford, England) Apr, 2007 | Pubmed ID: 17456608
Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance.
Antiviral therapy , 2007 | Pubmed ID: 17503659
Structural and functional comparison of the non-structural protein 4B in flaviviridae.
Journal of molecular graphics & modelling Sep, 2007 | Pubmed ID: 17507273
Expression pattern analysis of transcribed HERV sequences is complicated by ex vivo recombination.
Retrovirology , 2007 | Pubmed ID: 17550625
Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas.
International journal of cancer. Journal international du cancer Oct, 2007 | Pubmed ID: 17557299
CpG island mapping by epigenome prediction.
PLoS computational biology Jun, 2007 | Pubmed ID: 17559301
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 Jul, 2007 | Pubmed ID: 17567749
Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening.
Chemistry (Weinheim an der Bergstrasse, Germany) , 2007 | Pubmed ID: 17610225
Computational analysis of human protein interaction networks.
Proteomics Aug, 2007 | Pubmed ID: 17647236
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 Oct, 2007 | Pubmed ID: 17686836
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 Oct, 2007 | Pubmed ID: 17715334
Fifteen years of env C2V3C3 evolution in six individuals infected clonally with human immunodeficiency virus type 1.
Journal of medical virology Nov, 2007 | Pubmed ID: 17854039
Conformational analysis of alternative protein structures.
Bioinformatics (Oxford, England) Dec, 2007 | Pubmed ID: 17933849
Identification of PatL1, a human homolog to yeast P body component Pat1.
Biochimica et biophysica acta Dec, 2007 | Pubmed ID: 17936923
Moment invariants as shape recognition technique for comparing protein binding sites.
Bioinformatics (Oxford, England) Dec, 2007 | Pubmed ID: 17977888
Computing topological parameters of biological networks.
Bioinformatics (Oxford, England) Jan, 2008 | Pubmed ID: 18006545
Predicting HIV coreceptor usage on the basis of genetic and clinical covariates.
Antiviral therapy , 2007 | Pubmed ID: 18018768
Computational epigenetics.
Bioinformatics (Oxford, England) Jan, 2008 | Pubmed ID: 18024971
Bioinformatics prediction of HIV coreceptor usage.
Nature biotechnology Dec, 2007 | Pubmed ID: 18066037
Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus.
Genome biology , 2008 | Pubmed ID: 18215275
Stability analysis of mixtures of mutagenetic trees.
BMC bioinformatics , 2008 | Pubmed ID: 18366778
Alignment of non-covalent interactions at protein-protein interfaces.
PloS one , 2008 | Pubmed ID: 18382693
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.
Nucleic acids research Jun, 2008 | Pubmed ID: 18413340
Selecting anti-HIV therapies based on a variety of genomic and clinical factors.
Bioinformatics (Oxford, England) Jul, 2008 | Pubmed ID: 18586740
Local function conservation in sequence and structure space.
PLoS computational biology , 2008 | Pubmed ID: 18604264
An integrative approach for predicting interactions of protein regions.
Bioinformatics (Oxford, England) Aug, 2008 | Pubmed ID: 18689837
Integrating expression data with domain interaction networks.
Bioinformatics (Oxford, England) Nov, 2008 | Pubmed ID: 18710874
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores.
Bioinformatics (Oxford, England) Oct, 2008 | Pubmed ID: 18718947
Comparison of classifier fusion methods for predicting response to anti HIV-1 therapy.
PloS one , 2008 | Pubmed ID: 18941628
Clinical relevance of the 2'-5'-oligoadenylate synthetase/RNase L system for treatment response in chronic hepatitis C.
Journal of hepatology Jan, 2009 | Pubmed ID: 19022516
Dynamics of NRTI resistance mutations during therapy interruption.
AIDS research and human retroviruses Jan, 2009 | Pubmed ID: 19182921
EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.
Genome biology , 2009 | Pubmed ID: 19208250
Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database.
The Journal of infectious diseases Apr, 2009 | Pubmed ID: 19239365
DASMI: exchanging, annotating and assessing molecular interaction data.
Bioinformatics (Oxford, England) May, 2009 | Pubmed ID: 19420069
Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype.
Antiviral therapy , 2009 | Pubmed ID: 19430102
[Resistance screening].
MMW Fortschritte der Medizin Apr, 2009 | Pubmed ID: 19769083
MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays.
Genome biology , 2009 | Pubmed ID: 19804638
V3 loop sequence space analysis suggests different evolutionary patterns of CCR5- and CXCR4-tropic HIV.
PloS one , 2009 | Pubmed ID: 19816596
Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks.
Journal of integrative bioinformatics , 2008 | Pubmed ID: 20134061
Only slight impact of predicted replicative capacity for therapy response prediction.
PloS one , 2010 | Pubmed ID: 20140263
Predicting MHC class I epitopes in large datasets.
BMC bioinformatics , 2010 | Pubmed ID: 20163709
Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy.
Methods in molecular biology (Clifton, N.J.) , 2010 | Pubmed ID: 20238087
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 Mar, 2010 | Pubmed ID: 20334563
Permutation importance: a corrected feature importance measure.
Bioinformatics (Oxford, England) May, 2010 | Pubmed ID: 20385727
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 Jul, 2010 | Pubmed ID: 20506268
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.
Nucleic acids research Jul, 2010 | Pubmed ID: 20513647
Positive selection of HIV host factors and the evolution of lentivirus genes.
BMC evolutionary biology , 2010 | Pubmed ID: 20565842
Dealing with sparse data in predicting outcomes of HIV combination therapies.
Bioinformatics (Oxford, England) Sep, 2010 | Pubmed ID: 20624779
HLA class I allele associations with HCV genetic variants in patients with chronic HCV genotypes 1a or 1b infection.
Journal of hepatology Dec, 2010 | Pubmed ID: 20800922
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms.
Bioinformatics (Oxford, England) Sep, 2010 | Pubmed ID: 20823322
Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.
Medical microbiology and immunology Feb, 2011 | Pubmed ID: 20853118
Improved prediction of HIVâ€1 coreceptor usage with sequence information from the second hypervariable loop of gp120.
The Journal of infectious diseases Nov, 2010 | Pubmed ID: 20874088
Reconstructing the ancestral germ line methylation state of young repeats.
Molecular biology and evolution Jun, 2011 | Pubmed ID: 21212152
Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment.
Cell host & microbe Jan, 2011 | Pubmed ID: 21238945
Learning from past treatments and their outcome improves prediction of in vivo response to anti-HIV therapy.
Statistical applications in genetics and molecular biology , 2011 | Pubmed ID: 21291416
HIV prevalence and route of transmission in Turkish immigrants living in North-Rhine Westphalia, Germany.
Medical microbiology and immunology Nov, 2011 | Pubmed ID: 21461764
Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially.
Antiviral therapy , 2011 | Pubmed ID: 21555814
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing.
Nucleic acids research Jul, 2011 | Pubmed ID: 21565797
Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.
BMC medical informatics and decision making , 2011 | Pubmed ID: 21569501
APOBEC3G/F as one possible driving force for co-receptor switch of the human immunodeficiency virus-1.
Medical microbiology and immunology Feb, 2012 | Pubmed ID: 21573951
Classification with correlated features: unreliability of feature ranking and solutions.
Bioinformatics (Oxford, England) Jul, 2011 | Pubmed ID: 21576180
A DNA methylation fingerprint of 1628 human samples.
Genome research Feb, 2012 | Pubmed ID: 21613409
Preserving charge and oxidation state of Au(III) ions in an agent-functionalized nanocrystal model system.
ACS nano Aug, 2011 | Pubmed ID: 21736315
HIV-1 mutational pathways under multidrug therapy.
AIDS research and therapy , 2011 | Pubmed ID: 21794106
Peptidomimetic Escape Mechanisms Arise via Genetic Diversity in the Ligand-Binding Site of the Hepatitis C Virus NS3/4A Serine Protease.
Gastroenterology Dec, 2011 | Pubmed ID: 22155364
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types.
PLoS genetics Dec, 2011 | Pubmed ID: 22174693
Endogenous or exogenous spreading of HIV-1 in Nordrhein-Westfalen, Germany, investigated by phylodynamic analysis of the RESINA Study cohort.
Medical microbiology and immunology Jan, 2012 | Pubmed ID: 22262052
Bioinformatical Assistance of Selecting Anti-HIV Therapies: Where Do We Stand?
Intervirology , 2012 | Pubmed ID: 22286878
Geno2pheno[454]: A Web Server for the Prediction of HIV-1 Coreceptor Usage from Next-Generation Sequencing Data.
Intervirology , 2012 | Pubmed ID: 22286879
Predicting Response to Antiretroviral Treatment by Machine Learning: The EuResist Project.
Intervirology , 2012 | Pubmed ID: 22286881
Risk Factors Associated with Older Age in Treatment-Naive HIV-Positive Patients.
Intervirology , 2012 | Pubmed ID: 22286885
Epidemiology of Transmitted Drug Resistance in Chronically HIV-Infected Patients in Germany: The RESINA Study 2001-2009.
Intervirology , 2012 | Pubmed ID: 22286886
On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking.
Journal of chemical information and modeling Feb, 2012 | Pubmed ID: 22320151
Saleta Sierra1,
Rolf Kaiser1,
Nadine Lübke1,
Alexander Thielen2,
Eugen Schuelter1,
Eva Heger1,
Martin Däumer3,
Stefan Reuter4,
Stefan Esser5,
Gerd Fätkenheuer6,
Herbert Pfister1,
Mark Oette7,
Thomas Lengauer2
1Institute of Virology, University of Cologne,
2, Max Planck Institute for Informatics,
3, Institute for Immune genetics,
4Department of Gastroenterology, Hepatology and Infectiology, University of Duesseldorf,
5Department of Dermatology, University of Essen,
6Department of Internal Medicine, University of Cologne,
7, Augustinerinnen Hospital
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