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MPI-INF D3 Publications

MPI-INF D3 Publications

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1
Hide details for Adams, Altucci, Antonarakis, Ballesteros, Beck, Bird, Bock, Boehm, Campo, Caricasole, Dahl, Dermitzakis, EnverAdams, Altucci, Antonarakis, Ballesteros, Beck, Bird, Bock, Boehm, Campo, Caricasole, Dahl, Dermitzakis, Enver, Esteller, Estivill, Ferguson-Smith, Fitzgibbon, Flicek, Giehl, Graf, Grosveld, Guigó, Gut, Helin, Jarvius, Küppers, Lehrach, Lengauer, Lernmark, Leslie, Loeffler, Macintyre, Mai, Martens, Minucci, Ouwehand, Pelicci, Pendeville, Porse, Rakyan, Reik, Schrappe, Schübeler, Seifert, Siebert, Simmons, Soranzo, Spicuglia, Stratton, Stunnenberg, Tanay, Torrents, Valencia, Vellenga, Vingron, Walter, Willcocks
2012BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226
Journal Article
1
Hide details for Adams, McHardy, Lundegaard, LengauerAdams, McHardy, Lundegaard, Lengauer
2009Viral Bioinformatics
In: Modern Genome Annotation - The BioSapiens Network, 429-452
Part of a Book
1
Hide details for Ahlenstiel, Roomp, Däumer, Nattermann, Vogel, Rockstroh, Beerenwinkel, Kaiser, Nischalke, Sauerbruch, LengauerAhlenstiel, Roomp, Däumer, Nattermann, Vogel, Rockstroh, Beerenwinkel, Kaiser, Nischalke, Sauerbruch, Lengauer, Spengler
2007Attachment IconSelective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level
In: Clinical and Vaccine Immunology [14], 1266-1273
Journal Article
3
Hide details for AlbrechtAlbrecht
2010Color blindness
In: Nature Methods [7], 775
Journal Article
2006Combining protein structure prediction with experiments and functional information
Universität des Saarlandes
Thesis - PhD thesis
2005LRRK2 mutations and parkinsonism
In: The Lancet [365], 1230
Journal Article
1
Hide details for Albrecht, Choubey, LengauerAlbrecht, Choubey, Lengauer
2005The HIN domain of IFI-200 proteins consists of two OB folds
In: Biochemical and Biophysical Research Communications [327], 679-687
Journal Article
2
Hide details for Albrecht, Domingues, Schreiber, LengauerAlbrecht, Domingues, Schreiber, Lengauer
2003Identification of mammalian orthologs associates PYPAF5 with distinct functional roles
In: FEBS Letters [538], 173-177
Journal Article
2003Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2
In: FEBS Letters [554], 520-528
Journal Article
1
Hide details for Albrecht, Golatta, Wüllner, LengauerAlbrecht, Golatta, Wüllner, Lengauer
2004Structural and functional analysis of ataxin-2 and ataxin-3
In: European Journal of Biochemistry [271], 3155-3170
Journal Article
1
Hide details for Albrecht, Hanisch, Zimmer, LengauerAlbrecht, Hanisch, Zimmer, Lengauer
2002Attachment IconImproving fold recognition of protein threading by experimental distance constraints
In: In Silico Biology [2], 325-337
Journal Article
1
Hide details for Albrecht, Hoffmann, Evert, Schmitt, Wüllner, LengauerAlbrecht, Hoffmann, Evert, Schmitt, Wüllner, Lengauer
2003Structural modeling of ataxin-3 reveals distant homology to adaptins
In: Proteins: Structure, Function, and Genetics [50], 355-370
Journal Article
1
Hide details for Albrecht, Huthmacher, Tosatto, LengauerAlbrecht, Huthmacher, Tosatto, Lengauer
2005Decomposing protein networks into domain-domain interactions
In: Bioinformatics [21], ii220-ii221
Journal Article
1
Hide details for Albrecht, Kerren, Klein, Kohlbacher, Mutzel, Paul, Schreiber, WybrowAlbrecht, Kerren, Klein, Kohlbacher, Mutzel, Paul, Schreiber, Wybrow
2010On open problems in biological network visualization
In: Graph Drawing : 17th International Symposium, GD 2009, 256-267
Proceedings Article
3
Hide details for Albrecht, LengauerAlbrecht, Lengauer
2004Novel Sm-like proteins with long C-terminal tails and associated methyltransferases
In: FEBS Letters [569], 18-26
Journal Article
2004Survey on the PABC recognition motif PAM2
In: Biochemical and Biophysical Research Communications [316], 129-138
Journal Article
2003Pyranose oxidase identified as a member of the GMC oxidoreductase family
In: Bioinformatics [19], 1216-1220
Journal Article
1
Hide details for Albrecht, Lengauer, SchreiberAlbrecht, Lengauer, Schreiber
2003Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence
In: Bioinformatics [19], 2171-2175
Journal Article
1
Hide details for Albrecht, TakkenAlbrecht, Takken
2006Update on the domain architectures of NLRs and R proteins
In: Biochemical and Biophysical Research Communications [339], 459-462
Journal Article
1
Hide details for Albrecht, Tosatto, Lengauer, ValleAlbrecht, Tosatto, Lengauer, Valle
2003Simple consensus procedures are effective and sufficient in secondary structure prediction
In: Protein Engineering [16], 459-462
Journal Article
1
Hide details for Alcaraz, Kucuk, Weile, Wipat, BaumbachAlcaraz, Kucuk, Weile, Wipat, Baumbach
2012KeyPathwayMiner - Detecting case-specific biological pathways by using expression data
In: Internet Mathematics [7], 299-313
Journal Article
1
Hide details for Alcaro, Alteri, Artese, Ceccherini-Silberstein, Costa, Ortuso, Forbici, Santoro, Parrotta, Flandre, Descamps, Alcaro, Alteri, Artese, Ceccherini-Silberstein, Costa, Ortuso, Forbici, Santoro, Parrotta, Flandre, Descamps, Calvez, Marcelin, Perno, Sing, Svicher
2011Docking Analysis and Resistance Evaluation of Clinically Relevant Mutations Associated with the HIV-1 Nonnucleoside Reverse Transcriptase Inhibitors Nevirapine, Efavirenz and Etravirine
In: ChemMedChem [6], 2203-2213
Journal Article
1
Hide details for Alcaro, Artese, Ceccherini-Silberstein, Ortuso, Perno, Sing, SvicherAlcaro, Artese, Ceccherini-Silberstein, Ortuso, Perno, Sing, Svicher
2009Molecular Dynamics and Free Energy Studies on the Wild-Type and Mutated HIV-1
Protease Complexed with Four Approved Drugs: Mechanism of Binding and
In: Journal of Chemical Information and Modeling [49], 1751-1761
Journal Article
1
Hide details for AlexaAlexa
2005Integrating the GO graph structure in scoring the
significance of Gene Ontology terms
Universität des Saarlandes
Thesis - Masters thesis
1
Hide details for Alexa, Rahnenführer, LengauerAlexa, Rahnenführer, Lengauer
2006Attachment IconImproved Scoring of Functional Groups from Gene Expression Data by Decorrelating GO Graph Structure
In: Bioinformatics [22], 1600-1607
Journal Article
1
Hide details for AltmannAltmann
2010Bioinformatical approaches to ranking of anti-HIV combination therapies and planning of treatment schedules
Universität des Saarlandes
Thesis - PhD thesis
1
Hide details for Altmann, Beerenwinkel, Sing, Savenkov, Däumer, Kaiser, Rhee, Fessel, Shafer, LengauerAltmann, Beerenwinkel, Sing, Savenkov, Däumer, Kaiser, Rhee, Fessel, Shafer, Lengauer
2007Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance
In: Antiviral Therapy [12], 169-178
Journal Article
1
Hide details for Altmann, Däumer, Beerenwinkel, Peres, Schülter, Büch, Rhee, Sönnerborg, Fessel, Shafer, Zazzi, Kaiser, LengaueAltmann, Däumer, Beerenwinkel, Peres, Schülter, Büch, Rhee, Sönnerborg, Fessel, Shafer, Zazzi, Kaiser, Lengauer
2009Predicting the Response to Combination Antiretroviral Therapy: Retrospective Validation of
geno2pheno-THEO on a Large Clinical Database
In: The Journal of Infectious Diseases [199], 999-1006
Journal Article
1
Hide details for Altmann, Däumer, Sing, Beerenwinkel, Walter, Kaiser, LengauerAltmann, Däumer, Sing, Beerenwinkel, Walter, Kaiser, Lengauer
2007Validation of geno2pheno and THEO on a large independent clinical dataset
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -
Poster
1
Hide details for Altmann, Pironti, Perner, Büch, LengauerAltmann, Pironti, Perner, Büch, Lengauer
2010Determination of clinically relevant cutoffs for HIV-1 phenotypic resistance estimates through a combined analysis of clinical trial and cohort data
In: Abstract Book. 8th European Drug Resistance Workshop, 46
Poster
1
Hide details for Altmann, Rosen-Zvi, Prosperi, Aharoni, Neuvirth, Schülter, Büch, Peres, Incardona, Sönnerborg, Kaiser, Zazzi, Altmann, Rosen-Zvi, Prosperi, Aharoni, Neuvirth, Schülter, Büch, Peres, Incardona, Sönnerborg, Kaiser, Zazzi, Lengauer
2008The EuResist approach for predicting response to anti HIV-1 therapy
In: Reviews in Antiviral Therapy, 107
Poster
1
Hide details for Altmann, Rosen-Zvi, Prosperi, Aharoni, Neuvirth, Sönnerborg, Schülter, Büch, Struck, Peres, Incardona, Kaiser,Altmann, Rosen-Zvi, Prosperi, Aharoni, Neuvirth, Sönnerborg, Schülter, Büch, Struck, Peres, Incardona, Kaiser, Zazzi, Lengauer
2008Comparison of Classifier Fusion Methods for Predicting Response to Anti HIV-1 Therapy
In: PLoS ONE [3], e3470
Journal Article
1
Hide details for Altmann, Sing, Vermeiren, Winters, Van Craenenbroeck, Van der Borght, Rhee, Shafer, Schülter, Kaiser, Peres, SAltmann, Sing, Vermeiren, Winters, Van Craenenbroeck, Van der Borght, Rhee, Shafer, Schülter, Kaiser, Peres, Sönnerborg, Fessel, Incardona, Zazzi, Bacheler, Van Vlijmen, Lengauer
2009Advantages of Predicted Phenotypes and Statistical Learning Models in Inferring Virological Response to Antiretroviral Therapy from HIV Genotype
In: Antiviral Therapy [14], 273-283
Journal Article
1
Hide details for Altmann, Sing, Vermeiren, Winters, Van Craenenbroeck, Van der Borght, Rhee, Shafer, Schülter, Kaiser, Peres, SAltmann, Sing, Vermeiren, Winters, Van Craenenbroeck, Van der Borght, Rhee, Shafer, Schülter, Kaiser, Peres, Sonnerborg, Fessel, Incardona, Zazzi, Bacheler, Van Vlijmen, Lengauer
2007Inferring virological response from genotype: with or without predicted phenotypes?
In: Proceedings of the 16th International HIV Drug Resistance Workshop, S169
Poster
1
Hide details for Altmann, Tolosi, Sander, LengauerAltmann, Tolosi, Sander, Lengauer
2010Permutation importance: an unbiased feature importance measure
In: Bioinformatics [26], 1340-1347
Journal Article
1
Hide details for AntesAntes
2009Computational Methods for the Investigation of Protein-Ligand Interactions
Universität des Saarlandes
Thesis - Habilitation thesis
1
Hide details for Antes, Chandler, OsterAntes, Chandler, Oster
2002A classical dynamics study of the unbinding of ATP from the F0F1-ATPase
In: Poster book of the European Conference on Computational Biology, Saarbrücken, Germany 2002, -
Poster
1
Hide details for Antes, KleinAntes, Klein
2001The formation of a β-Peptide/DPC-micelle complex studied by MD simulationsMiscellaneous
1
Hide details for Antes, LengauerAntes, Lengauer
2006Refinement of homology modeled protein structures for molecular docking
In: Proceedings of the 367. WE-Heraeus Seminar on Biomolecular Simulations, 1
Poster
1
Hide details for Antes, Lengauer, Mueller, Ulmschneider, HartmannAntes, Lengauer, Mueller, Ulmschneider, Hartmann
2003Docking into the homology models of CYP11B1 and CYP11B2
In: Proceedings of the German Conference on Bioinformatics 2003, 13
Poster
1
Hide details for Antes, Merkwirth, LengauerAntes, Merkwirth, Lengauer
2005POEM: Parameter Optimization using Ensemble Methods: Application to target specific scoring functions
In: Journal of Chemical Information and Modeling [45], 1291-1302
Journal Article
1
Hide details for Antes, Siu, LengauerAntes, Siu, Lengauer
2006Attachment IconDynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequence and conformations
In: Bioinformatics [22], 16-24
Journal Article
1
Hide details for Antes, Thiel, Gunsteren vanAntes, Thiel, Gunsteren van
2002Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation
In: European Biophysics Jounal [31], 504-520
Journal Article
1
Hide details for Antes, Wang, Chandler, OsterAntes, Wang, Chandler, Oster
2003The unbinding of ATP from F1-ATPase
In: Biophysical Journal [85], 695-706
Journal Article
1
Hide details for Apostolakis, Hofmann, LengauerApostolakis, Hofmann, Lengauer
2001Derivation of a scoring function for crystal structure prediction
In: Acta Crystallographica [A57], 442-450
Journal Article
1
Hide details for Aranda, Blankenburg, Kerrien, Brinkman, Ceol, Chautard, Dana, De Las Rivas, Dumousseau, Galeota, Gaulton, GollAranda, Blankenburg, Kerrien, Brinkman, Ceol, Chautard, Dana, De Las Rivas, Dumousseau, Galeota, Gaulton, Goll, Hancock, Isserlin, Jimenez, Kerssemakers, Khadake, Lynn, Michaut, O'Kelly, Ono, Orchard, Prieto, Razick, Rigina, Salwinski, Simonovic, Velankar, Winter, Wu, Bader, Cesareni, Donaldson, Eisenberg, Kleywegt, Overington, Ricard-Blum, Tyers, Albrecht, Hermjakob
2011PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529
Journal Article
1
Hide details for AssenovAssenov
2006Topological Analysis of Biological
Networks
Universität des Saarlandes
Thesis - Masters thesis
1
Hide details for Assenov, Ramírez, Schelhorn, Lengauer, AlbrechtAssenov, Ramírez, Schelhorn, Lengauer, Albrecht
2008Computing topological parameters of biological networks
In: Bioinformatics [24], 282-284
Journal Article
1
Hide details for BaderBader
2012Clustering epigenetic data using a Dirichlet process prior
Universität des Saarlandes
Thesis - Masters thesis
1
Hide details for Balduin, Beerenwinkel, Sierra, Däumer, Rockstroh, Oette, Fätkenheuer, Kupfer, Hoffmann, Selbig, Pfister, KaiseBalduin, Beerenwinkel, Sierra, Däumer, Rockstroh, Oette, Fätkenheuer, Kupfer, Hoffmann, Selbig, Pfister, Kaiser
2005Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy
In: J Clin Virol [34], 277-287
Journal Article
1
Hide details for BastysBastys
2012Attachment IconMAP Kinase Docking Motifs in HIV Proteins
Universität des Saarlandes
Thesis - Masters thesis
2
Hide details for BaumbachBaumbach
2012Integrative computational biology
In: Integrative Biology [4], 713-714
Journal Article
2010On the power and limits of evolutionary conservation - unraveling bacterial gene regulatory networks
In: Nucleic Acids Research [38], 7877-7884
Journal Article
1
Hide details for BayjanovBayjanov
2004Scoring pathway activity from gene
expression data
Universität des Saarlandes
Thesis - Masters thesis
4
Hide details for BeerenwinkelBeerenwinkel
2004Computational Analysis of HIV Drug resistance DataBook
2004Das Arevir-Projekt : neue Wege zur Optimierung von Anti-HIV-Therapien
In: Resistenz in der HIV-Therapie : Diagnostik und Management, 94-98
Part of a Book
2004Methoden zur Interpretation genotypischer Resistenztests
In: Resistenz in der HIV-Therapie : Diagnostik und Management, 66-68
Part of a Book
2003Attachment IconComputational Analysis of HIV Drug Resistance Data
Universität des Saarlandes
Thesis - PhD thesis
1
Hide details for Beerenwinkel, Däumer, Hoffmann, Kaiser, Korn, Lengauer, Schmidt, Walter, SelbigBeerenwinkel, Däumer, Hoffmann, Kaiser, Korn, Lengauer, Schmidt, Walter, Selbig
2001Neue Wege zur Optimierung von Anti-HIV Therapien
In: BIOforum [24], 912-914
Journal Article
1
Hide details for Beerenwinkel, Däumer, Hoffmann, Kaiser, Selbig, LengauerBeerenwinkel, Däumer, Hoffmann, Kaiser, Selbig, Lengauer
2003Bioinformatikmethoden für die Optimierung antiviraler Kombinationstherapien
In: MPG Jahrbuch, 481-486
Part of a Book
1
Hide details for Beerenwinkel, Däumer, Kaiser, Walter, Korn, Hoffmann, Selbig, LengauerBeerenwinkel, Däumer, Kaiser, Walter, Korn, Hoffmann, Selbig, Lengauer
2003Estimating effective drug combinations against drug-resistant mutants from genotypes
In: Proceedings of the 1st European HIV Drug Resistamce Workshop, 18-18
Proceedings Article
1
Hide details for Beerenwinkel, Däumer, Oette, Korn, Hoffmann, Kaiser, Lengauer, Selbig, WalterBeerenwinkel, Däumer, Oette, Korn, Hoffmann, Kaiser, Lengauer, Selbig, Walter
2003Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes
In: Nucleic Acids Research [31], 3850-3855
Journal Article
1
Hide details for Beerenwinkel, Däumer, Sing, Rahnenführer, Lengauer, Selbig, Hoffmann, KaiserBeerenwinkel, Däumer, Sing, Rahnenführer, Lengauer, Selbig, Hoffmann, Kaiser
2005Estimating HIV evolutionary pathways and the genetic barrier to drug resistance
In: The Journal of Infectious Diseases [191], 1953-1960
Journal Article
1
Hide details for Beerenwinkel, Kaiser, Rahnenführer, Däumer, Hoffmann, Selbig, LengauerBeerenwinkel, Kaiser, Rahnenführer, Däumer, Hoffmann, Selbig, Lengauer
2003Tree models for the evolution of drug resistance
In: XII International HIV Drug resistance Workshop, S107-S107
Proceedings Article
1
Hide details for Beerenwinkel, Lengauer, Däumer, Kaiser, Walter, Korn, Hoffmann, SelbigBeerenwinkel, Lengauer, Däumer, Kaiser, Walter, Korn, Hoffmann, Selbig
2003Methods for optimizing antiviral combination therapies
In: Bioinformatics [19], i16-i25
Journal Article
1
Hide details for Beerenwinkel, Lengauer, Däumer, Sierra, Schmidt, Walter, Korn, Oette, Fätkenheuer, Rockstroh, Hoffmann, KaiserBeerenwinkel, Lengauer, Däumer, Sierra, Schmidt, Walter, Korn, Oette, Fätkenheuer, Rockstroh, Hoffmann, Kaiser, Selbig
2002Geno2pheno is predictive of short-term virological response
In: Proceedings from the 5th International Workshop on HIV Drug Resistance & Treatment Strategies, 74-74
Proceedings Article
1
Hide details for Beerenwinkel, Lengauer, Schmidt, Walter, Kaiser, Hoffmann, Korn, SelbigBeerenwinkel, Lengauer, Schmidt, Walter, Kaiser, Hoffmann, Korn, Selbig
2002Quantitative phenotype prediction by support vector machines
In: Proceedings from the 5th International Workshop on HIV Drug resistance & Treatment Strategies, 97
Proceedings Article
2
Hide details for Beerenwinkel, Rahnenführer, Däumer, Hoffmann, Kaiser, Selbig, LengauerBeerenwinkel, Rahnenführer, Däumer, Hoffmann, Kaiser, Selbig, Lengauer
2005Learning multiple evolutionary pathways from cross-sectional data
In: Journal of Computational Biology [12], 584-598
Journal Article
2004Learning multiple evolutionary pathways from cross-sectional data
In: RECOMB 2004 : proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology, 36-44
Proceedings Article
1
Hide details for Beerenwinkel, Rahnenführer, Kaiser, Hoffmann, Selbig, LengauerBeerenwinkel, Rahnenführer, Kaiser, Hoffmann, Selbig, Lengauer
2005Mtreemix: a software package for learning and using mixture models of mutagenetic trees
In: Bioinformatics [21], 2106-2107
Journal Article
2
Hide details for Beerenwinkel, Schmidt, Walter, Kaiser, Lengauer, Hoffmann, Korn, SelbigBeerenwinkel, Schmidt, Walter, Kaiser, Lengauer, Hoffmann, Korn, Selbig
2002Diversity and complexity of HIV-1drug resistance: A bioinformatics approach to predicting phenotype from genotype
In: Proceedings of the National Academy of Sciences [99], 8271-8276
Journal Article
2001Geno2pheno: A system for the interpretation of genotypic HIV Drug resistance tests
In: IEEE Intelligent Systems [16], 35-41
Journal Article
1
Hide details for Beerenwinkel, Sing, Däumer, Kaiser, LengauerBeerenwinkel, Sing, Däumer, Kaiser, Lengauer
2004Computing the genetic barrier
In: XII International HIV Drug resistance Workshop, S125-S125
Proceedings Article
1
Hide details for Beerenwinkel, Sing, Lengauer, Rahnenführer, Roomp, Savenkov, Fischer, Hoffmann, Selbig, Korn, Walter, Berg, BrBeerenwinkel, Sing, Lengauer, Rahnenführer, Roomp, Savenkov, Fischer, Hoffmann, Selbig, Korn, Walter, Berg, Braun, Fätkenheuer, Oette, Rockstroh, Kupfer, Kaiser, Däumer
2005Computational methods for the design of effective therapies against drug resistant HIV strains
In: Bioinformatics [21], 3943-3950
Journal Article
1
Hide details for Beggel, LengauerBeggel, Lengauer
2013Inferring short-range linkage information from sequencing chromatograms
In: PLoS One,
Electronic Journal Article
1
Hide details for Beggel, Münk, Däumer, Hauck, Häussinger, Lengauer, EhrhardtBeggel, Münk, Däumer, Hauck, Häussinger, Lengauer, Ehrhardt
2013Full genome ultra-deep pyrosequencing associates G-to-A-hypermutation of the hepatitis B virus genome with the natural progression of hepatitis B
In: Journal of Viral Hepatitis [12], 882-889
Journal Article
1
Hide details for Beggel, Neumann-Fraune, Doering, Lawyer, Kaiser, Verheyen, LengauerBeggel, Neumann-Fraune, Doering, Lawyer, Kaiser, Verheyen, Lengauer
2012Genotyping hepatitis B virus dual infections using population-based sequence data
In: Journal of General Virology [9], 1899-1907
Journal Article
1
Hide details for Bhadra, Battacharya, Feuerbach, Lengauer, BandyopadhyayBhadra, Battacharya, Feuerbach, Lengauer, Bandyopadhyay
2013DNA Methylation Patterns Facilitate the Identification of Transcription Start Sites: A Brain-specofoc Study
In: PLOSONE [8], xx
Journal Article
1
Hide details for Bhattacharyya, Feuerbach, Bhadra, BandyopadhyayBhattacharyya, Feuerbach, Bhadra, Bandyopadhyay
2012MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection
In: Statistical Applications in Genetics and Molecular Biology [11], 6.1-6.25
Journal Article
1
Hide details for Bickel, Bogojeska, Lengauer, ShefferBickel, Bogojeska, Lengauer, Sheffer
2008Attachment IconMulti-Task Learning for HIV Therapy Screening
In: Proceedings, Twenty-Fifth International Conference on Machine Learning, 56-63
Proceedings Article
2
Hide details for BinslBinsl
2006Feature Prints: A new method for calculating molecular similarities
Universität des Saarlandes
Thesis - Masters thesis
2004Attachment IconImplementation of a Generic Fragment
Based Method for Automated
Calculation of the Octanol-Water
Partition Coefficient
Universität des Saarlandes
Thesis - Bachelor thesis
1
Hide details for BlankenburgBlankenburg
2007A Distributed Annotation System for Molecular Interactions
Ruprecht Karl Universität Heidelberg; Universität Heilbronn
Thesis - other
1
Hide details for Blankenburg, Finn, Prlić, Jenkinson, Ramírez, Emig, Schelhorn, Büch, Lengauer, AlbrechtBlankenburg, Finn, Prlić, Jenkinson, Ramírez, Emig, Schelhorn, Büch, Lengauer, Albrecht
2009DASMI: exchanging, annotating and assessing molecular interaction data
In: Bioinformatics [25], 1321-1328
Journal Article
1
Hide details for Blankenburg, Ramírez, Büch, AlbrechtBlankenburg, Ramírez, Büch, Albrecht
2009DASMIweb: online integration, analysis and assessment of distributed protein interaction data
In: Nucleic Acids Research [37], W122-W128
Electronic Journal Article
1
Hide details for Bleif, Hannemann, Lisurek, von Kries, Zapp, Dietzen, Antes, BernhardtBleif, Hannemann, Lisurek, von Kries, Zapp, Dietzen, Antes, Bernhardt
2011Identification of CYP106A2 as a Regioselective Allylic Bacterial Diterpene Hydroxylase
In: ChemBioChem [12], 576-582
Journal Article
5
Hide details for BockBock
2012Analysing and interpreting DNA methylation data
In: Nature Reviews Genetics [13], 705-719
Journal Article
2009Attachment IconEpigenetic biomarker development
In: Epigenomics [1], 99-110
Journal Article
2008Computational Epigenetics - Bioinformatic methods for epigenome prediction, DNA methylation mapping and cancer epigenetics
Universität des Saarlandes
Thesis - PhD thesis
2008IVF: stars may have to consider the risk of stolen parenthood
In: Nature [454], 938
Journal Article
2006Bioinformatik: Neue Strategien gegen Krebs
In: Deutsches Ärzteblatt PRAXiS [103], 10-11
Journal Article
1
Hide details for Bock, Halachev, Büch, LengauerBock, Halachev, Büch, Lengauer
2009Attachment IconEpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data
In: Genome Biology [10], R14.1-R14.14
Journal Article
1
Hide details for Bock, Halachev, LengauerBock, Halachev, Lengauer
2006Bioinformatisches Data Mining erschließt neue Strategien gegen Krebs
In: Aktuelle Trends in der Softwareforschung, 91-99
Part of a Book
1
Hide details for Bock, HesserBock, Hesser
2006Attachment IconAnalysis and Prediction of Helix Shift Errors in Homology Modeling
In: In Silico Biology [6], 131-145
Journal Article
1
Hide details for Bock, Kiskinis, Verstappen, Gu, Boulting, Smith, Ziller, Croft, Amoroso, Oakley, Gnirke, Eggan, MeissnerBock, Kiskinis, Verstappen, Gu, Boulting, Smith, Ziller, Croft, Amoroso, Oakley, Gnirke, Eggan, Meissner
2011Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines
In: Cell [144], 439-452
Journal Article
4
Hide details for Bock, LengauerBock, Lengauer
2012Epigenom-Karten erstellen und nutzen
In: BIOspektrum [18], 138-141
Journal Article
2012Managing drug resistance in cancer: lessons from HIV therapy
In: Nature Reviews Cancer [12], 494-501
Journal Article
2008Attachment IconComputational epigenetics
In: Bioinformatics [24], 1-10
Journal Article
2007Attachment IconComputational Epigenetics: Bioinformatik für neue Wege in der Krebsforschung
In: Jahrbuch 2007, 271-277
Part of a Book
1
Hide details for Bock, Lengauer, Reither, Mikeska, Paulsen, WalterBock, Lengauer, Reither, Mikeska, Paulsen, Walter
2005Attachment IconBiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing
In: Bioinformatics [21], 4067-4068
Journal Article
1
Hide details for Bock, Paulsen, Tierling, Mikeska, Lengauer, WalterBock, Paulsen, Tierling, Mikeska, Lengauer, Walter
2006Attachment IconCpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure
In: PLoS Genetics [2], 0243-0252
Electronic Journal Article
1
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2010Attachment IconQuantitative comparison of genome-wide DNA methylation mapping technologies
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2008Attachment IconInter-individual variation of DNA methylation and its implications for large-scale epigenome mapping
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2007Attachment IconCpG Island Mapping by Epigenome Prediction
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2011History distribution matching method for predicting effectiveness of HIV combination therapies
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2011Attachment IconStatistical Learning Methods for Bias-aware HIV Therapy Screening
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2007Stability analysis of oncogenetic trees mixture models
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2008Attachment IconRtreemix: an R package for estimating evolutionary pathways and genetic progression scores
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2010Attachment IconDealing with sparse data in predicting outcomes of HIV combination therapies
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2009V3 loop sequence space analysis suggests different evolutionary patterns of CCR5- and CXCR4-tropic HIV.
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2002Automated Grid Alignment for High-Throughput Analysis of Microarray Images (CIIST-02)
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2005Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family
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2007Attachment IconCharacterization and structural analysis of novel mutations in human immunodeficiency virus type 1 reverse transcriptase involved in the regulation of restistance to nonnucleoside inhibitors
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2001FlexE: Efficient Molecular Docking Considering Protein Structure Variations
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2000Age and residual cholesterol efflux affect HDL cholesterol levels and coronary artery disease in ABCA1 heterozygotes
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2011Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects
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2010Short Communication: Selection of Thymidine Analogue Resitance Mutational Patterns in Children from a Common HIV Type 1 Subtype G Source
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2011Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis
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2008Inferring viral tropism from genotype with massively parallel sequencing; qualitative and quantitative analysis
In: Antiviral Therapy, A101
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2005Retinal properties and potential of the adult mammalian ciliary epithelium stem cells
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2005Docking studies to investigate the effect of correlated mutations in the HIV-Protease on the drug resistance of HIV
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2007Inferring Protein Function from Protein Structure
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2003Protein Function from Sequence and Structure Data
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2004Protein Structure Prediction and Databases
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2007Conformational analysis of alternative protein structures
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2004Automated clustering of ensembles of alternative models in protein structure databases
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2012Topological analysis and interactive visualization of biological networks and protein structures
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2012Recent approaches to the prioritization of candidate disease genes
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2011Analyzing and visualizing residue networks of protein structures
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2011Prediction of Thermostability from Amino Acid Attributes by Combination of Clustering with Attribute Weighting: A New Vista in Engineering Enzymes
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2013Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
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2007The Impact of Alternative Splicing on Protein Interaction Networks
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2011Tissue-specific proteins and functional implications
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2008Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks
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2008Integrating expression data with domain interaction networks
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2011Measuring and analyzing tissue specificity of human genes and protein complexes
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2008Visualizing domain interaction networks and the impact of alternative splicing events
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2010AltAnalyze and DomainGraph: analyzing and visualizing exon expression data
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2011Structure collisions between interacting proteins
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2012A DNA methylation fingerprint of 1628 human samples
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2008Towards Comparative Epigenomics: A Software Toolkit For Cross-Species Epigenome Data Analysis
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2012Analyzing epigenome data in context of genome evolution and human diseases
In: Evolutionary Genomics : Statistical and Computational Methods, Volume 2, 431-467
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2009An exhaustive methode for CpG island annotation
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2010Ancestral germline methylation reconstruction of young repeats
In: Transcription, chromatin structure and DNA repair in development and differentiation, 81
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2010Comparative Epigenomiocs - Towards Ancestral Germline Methylome Reconstruction
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2011Reconstructing the ancestral germline methylation state of young repeats
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2008Structure-based prediction of HIV-1 drug resistance
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2007Attachment IconExpression pattern analysis of transcribed HERV sequences is complicated by ex vitvo recombination
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2008Sequence variants in IL10, ARPC2, and multiple other loci contribute to ulcerative colitis
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2010Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL)
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2007Systematic association mapping identifies NELL1 as a novel IBD disease gene
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2002A hypergraph-based method for unification of existing protein structure- and sequence-families
In: In Silico Biology [2], 339 - 349
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2006Development of a
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2009Protein-protein interactions: analysis and prediction
In: Modern Genome Annotation - The Biosapiens Network, 353-410
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2012Applying Lasso regression to related cell types for gene network astimation
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2012Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove
In: Science Signaling [5], ra74,1-ra74,14
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2010GOdot Sequence - function prediction from protein sequence
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2006On the predictability of CpG methylation in human tissue at single basepair resolution
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2006Improving Fold Recognition Using Protein
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2010Attachment IconGenome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
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2005Alternative Binding Modes of Polyproline Peptides Binding to the GYF Domain
In: Biochemistry [44], 6404-6415
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2011Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
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2009Assessing the Conservation of Protein Function on Evolutionary Defined Patches
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2005Confirmation of human protein interaction data by human expression data
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2007BSIFlex: Binding Site Identification including protein flexibility
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2006EpiGRAPHregression: A toolkit for (epi-)genomic correlation analysis and prediction of quantitative attributes
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2013Interactive exploration of large genome and epigenome datasets in real time
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2007A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1
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2002Co-clustering of biological networks and gene expression data
In: Proceedings of the Tenth Conference on Intelligent Systems for Molecular Biology (ISMB 2002), 145-154
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2002ProML - the Protein Markup Language for specification of protein sequences, structures and families
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2004Modelling amorphous Si3B3N7: Structure and elastic properties
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2009Screening for HIV tropism using population-based V3 genotypic analysis: a retrospective outcome analysis using stored plasma screening samples from MOTIVATE-1
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2010Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
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2008Modeling of Flexible Side Chains for Protein-Ligand Docking
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2009Docking and scoring with alternative side-chain conformations
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2007Attachment IconIRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.
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2006Improvement of the fungal enzyme pyranose 2-oxidase using protein engineering
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2012APOBEC3G/F a one possible driving source for co-receptor switch of the human immunodeficiency virus-1
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2011APOBEC3G/F as one possible driving force for co-receptor switch of the human immunodeficiency virus-1
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2006Computational recognition of potassium channel sequences
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2005Multiple-Ligand-Based Virtual Screening: Methods and Applications of the MTree Approach
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2002Flexible docking under pharmacophore type constraints
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2006Docking of monosaccharids into the wild type and mutants of pyranose 2-oxidase
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2002A new method for the fast solution of protein-3D-structures, combining experiments and bioinformatics
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2011Impact of ribavirin on HCV replicon RNA decline during treatment with interferon-α and the protease inhibitors boceprevir or telaprevir
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2007Somatic hypermutation and mRNA expression levels of the BCL-6 gene in patients with hepatitis C virus-associated lymphoproliferative diseases
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2004Association of HCV-related mixed cryoglobulinemia with specific mutational patterns of the HCV E2 protein and CD81 expression on peripheral B lymphocytes
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2007Identification and in silico characterization of a novel compound heterozygosty associated with hereditary aceruloplasminemia
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2008Protein phosphatase and TRAIL receptor genes as new candidate tumor genes on chromosome 8p in prostate cancer
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2006Decomposing Protein Networks Into
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2005A Bayesian Learning Approach to Concept-Based Document Classification
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2004Cellular and Molecular Characterization of Early and Late Retinal Stem Cells/Progenitors: Differential Regulation of Proliferation and Context Dependent Role of Notch Signaling
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2003Identification of rat brahma (rBRM), a subunit of SWI/SNF chromatin remodeling complex: Involvement in the differentiation of retinal stem cells/progenitorsMiscellaneous
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2004Identification of c-Kit receptor as a regulator of adult neural stem cells in the mammalian eye: interactions with Notch signaling
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2003A hazard based approach to dependence tests for bivariate censored models
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2008Integrating biological data - the Distributed Annotation System
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2003New inhibitors of human cathepsin G identified by surface display library screening and peptide-protein docking
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2006Yamada Analyzer - A tool for fast calculation of genomic attributes
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2011Unsupervised dissection of cancer types based on genomic, epigenomic and transciptomic features
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2011Disease gene prioritization by combining network information and functional knowledge
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2010Analysis of protein complexes and tissue-spedific expression
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2002Docking of Bacterial Cell-Wall Fragments into Glycopeptide Antibiotics
In: From Genes to Drugs via Crystallography: 33rd crytallographic course at the E. Majorana Center, 49
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2006Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies
In: Journal of Chemical Information and Modeling [46], 903-911
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2001Docking of Ligands into Artificial ReceptorsMiscellaneous
2001Docking of Ligands into Artificial Receptors
In: Electronically Excited Molecules: Structure and Dynamics, 37th Symposium for Theoretical Chemistry, P76
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2005Efficient conformational analysis of synthetic receptors with macrocyclic and fused ring systems
In: Synthetic Receptors 2005: Second World Congress on Synthetic Receptors, O4
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2003ECLIPPSE: Environment for Chemical Library Inspection, Pre- and Postprocessing, and Screening Evaluation. User GuideManual
2003Virtual Screening for novel Urease Inhibitors
In: Proceedings of the International Workshop on New Approaches in Drug Design & Discovery, 39
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2002Docking of Ligands into Molecular Tweezers and Molecular Clips
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2007Lead Identification by Virtual Screening
In: Bioinformatics - From Genomes to Therapies 2. Getting at the Inner Workings: Molecular Interactions, 651-704
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2005Stable coreceptor usage of HIV-1 in patients with ongoing treatment failure on HAART
In: Proceedings of the 3rd European HIV Drug Resistance Workshop, -
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2012A Phylodynamic Study of HIV Transmission Networks in Europe
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2013Inter-country mixing in HIV transmission clusters: a pan-European phylodynamics study
In: Abstract Book 11th European HIV & Hepatitis Workshop, 9
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2012Computational Identification of Novel Amino-Acid Interactions in HIV Gag via Correlated Evolution
In: PLoS ONE [7], e42468,1-e42468,5
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2013Modelling binding between CCR5 and CXCR4 receptors and their ligands suggests the surface electrostatic potential of the co-receptor to be a key player in the HIV-1 tropism
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2010Decreased HIV diversity after allogeneic stem cell transplantation of an HIV-1 infected patient: a case report.
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2007Detection of Novel Amplicons in Prostate Cancer by Comprehensive Genomic Profiling of Prostate Cancer Cell Lines Using Oligonucleotide-Based ArrayCGH
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2006Automated conformational analysis of macrocyclic ring systems
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2007Attachment IconHyperdiploidy defines a distinct cytogenetic entity of meningiomas
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2007Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas
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2007In silico analysis of microRNA genes on human chromosome 14 and mouse chromosome 12
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2008Attachment IconStructural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region
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2012Automatic Recombination Analysis Using Recoo and Mebitoo
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2011In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing
In: Journal of Virological Methods [71], 329-338
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Universität des Saarlandes
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2010Env-wide analysis of coreceptor determining sites and subtype-specific differences in HIV-1
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2009Impact of a single amino acid in the variable region 2 of the Old World monkey TRIM5alpha SPRY (B30.2) domain on anti-human immunodeficiency virus type 2 activity
In: Virology [388], 160-168
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2007Identification of Symmetries in Molecules and Complexes
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2011RhizoRegNet - A database of rhizobial transcription factors and regulatory networks.
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2010A probabilistic algorithm for matching protein structures - and its application to detecting functionally relevant patterns
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2011Comparative Genomics of Klebsiella pneumoniae Strains with Different Antibiotic Resistance Profiles
In: Antimicrobial Agents and Chemotherapy [55], 4267-4276
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2011Maximal Common Subgraph DAGs: Theory and Application to Virtual Screening in Drug Development
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2007Fifteen years of env C2V3C3 evolution in six individuals clonally infected with human immunodeficiency virus type 1
In: Journal of Medical Virology [79], 1629-1639
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2010A single amino acid substitution of the human immunodeficiency virus type 1 capsid protein affects viral sensitivity to TRIM5 alpha.
In: Retrovirology [7], 58,1-58,10
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2010HLA class I allele associations with HCV genetic variants in patients with chronic HCV genotypes 1a or 1b infection
In: Journal of Hepatology [53], 1022-1028
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2014COMET: Adaptive context-based modeling for ultrafast HIV-1 subtype identification.
In: Nucleic Acids Research [42], e144
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2011HIV-1 mutational pathways under multidrug therapy
In: AIDS Research and Therapy [8], 1-13
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2009Local and covariate-modulated false discovery rates applied in neuroimaging
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2009Grey and white matter proportional relationships in the cerebellar vermis altered in schizophrenia
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2006Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART
In: Journal of Clinical Virology [37], 300-304
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2012Bioinformatical Assistance of Selecting Anti-HIV Therapies: Where Do We Stand?
In: Intervirology [55], 108-112
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2007Bioinformatik
In: Technologiefüher - Grundlagen, Anwendungen, Trends, 4
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2007Introduction
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2007Strategiekonzept "Molekulare Bioinformatik"
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2003Analyzing resistance phenomena in HIV with bioinformatics methods
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2001Bioinformatik an der Schwelle zur postgenomischen Ära
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2011Computermodelle in der Wissenschaft - zwischen Analyse, Vorhersage und SuggestionBook
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2012Computational Biology
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2005Clinical significance of in vitro replication-enhancing mutations of the hepatitis C virus (HCV) replicon in patients with chronic HCV infection.
In: Journal of Infectious Diseases [192], 1710-1719
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2009Bioinformatische Unterstützung der Auswahl von HIV Therapien
In: Informatik Spektrum [32], 320-331
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2010Chasing the AIDS Virus
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2001Geno2pheno: a new machine learning approach to predicting phenotypic drug resistance from genotype
In: Antiviral Therapy [6], 104
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2012Managing drug resistance in cancer: lessons from HIV therapy
In: Nature Reviews Cancer [12], 494-501
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2006Analysis and prediction of protein-protein-interaction types
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2009Computerjagd auf das AIDSVIRUS
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2004Novel technologies for virtual screening
In: Drug Discovery Today [9], 27-34
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2002Proceedings of the European Conference on Computational Biology (ECCB 2002)Proceedings
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2005Automatic Generation of complementary descriptors with molecular graph networks
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2007European Journal of Medical ResearchJournal
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2007Proceedings ISMB2007Proceedings
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2007Bioinformatics prediction of HIV coreceptor usage
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2001Proceedings of the 5th Annual Conference on Research in Computational Molecular Biology (RECOMB2001)Book
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2003Combinatorial Optimization Techniques for Three-Dimensional Arrangement Problems
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2009Resistenzbestimmung
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2006Bioinformatics-assisted anti-HIV therapy
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2013Probabilistic error correction for RNA sequencing
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2002An Extended Set of Haar-like Features for Rapid Object Detection
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2008Theoretical and Experimental Evaluation of a CYP106A2 Low Homology Model and Production of Mutants with Changed Activity and Selectivity of Hydroxylation
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2013Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
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2007Attachment IconThe human genomic melting map
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2010Identifying discriminative motifs for molecular function of proteins
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2007Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates
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2008Novel Aldosterone Synthase Inhibitors with Extended Carbocyclic Skeleton by a Combined Ligand-Based and Structure-Based Drug Design Approach
In: Journal of Medical Chemistry [51], 6138-6149
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2010Processing of high-throughput DNA methylation data
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2011BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing
In: Nucleic Acids Research [39], W551-W556
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2009In Silico Models for the Prediction of Metabolism by Cytochrome P450 Enzymes
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1999Mutations in the ABC1 gene in familial HDL deficiency with defective cholesterol efflux
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2014MIMA - A software for analyte identification in MCC/IMS chromatograms by mapping accompanying GC/MS measurements
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2008Analysis of recombination in Molecular Sequence Data
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2006Recco: recombination analysis using cost optimization
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2002A Fast Method for Training Support Vector Machines With a Very Large Set of Linear Features
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2007Attachment IconComparative Analysis of Protein Structure Alignments
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2010Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies
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2009The role of genomics in tracking the evolution of influenza A virus
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2005Identification of functionally important regions in cytochrome P450 systems and a systematic analysis of various CYP P450 homology models
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2012Erosion of dosage compensation impacts human iPSC disease modeling
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2004Finite iteration DT-CNN - new design and operation principles
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2004Ensemble methods for classification in cheminformatics
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2003Attachment IconStochastic Gradient Descent Training of Ensembles of DT-CNN Classifiers for Digit Recognition
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2009Clinical relevance of the 2'-5'-oligoadenylate synthetase/RNase L system for treatment response in chronic hepatitis C
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2006Amino acid variations in hepatitis C virus p7 and sensitivity to antiviral combination therapy with amantadine in chronic hepatitis C
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2010Effect of ribavirin on the frequency of RNAse L cleavage sites within the hepatitis C viral genome
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2012DNA methylation biomarkers in cancer: Progress towards clinical implementation
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2007Attachment IconOptimization of Quantitative MGMT Promoter Methylation Analysis Using Pyrosequencing and Combined Bisulfite Restriction Analysis
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2008Improved detection of X4 virus by V3 genotyping: application to plasma RNA and proviral DNA
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2011clusterMaker: A Multi-algorithm Clustering Plugin for Cytoscape
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2009Attachment IconFunctional Analysis of a Potassium-Chloride Co-Transporter 3 (SLC12A6) Promoter Polymorphism Leading to an Additional DNA Methylation Site
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2012Extracting pathways from biological networks incorporating omics data, introducing a webinterface for KeyPathwayMiner
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2009Assessing Antibody Neutralization of HIV-1 as an Initial Step in the Search for gp160-based Immunogens
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2008Inferring virological response to antiretroviral combination therapy based on past treatment lines
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2007Using Shape Retrieval Techniques for Identifying Similar Protein Binding Sites
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2011DIDO: a disease-determinants ontology from web sources
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2013High frequency of complex mutational patterns in lamivudine resistant hepatitis B virus isolates
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2006A Fully Computational Model for Predicting Percutaneous Drug Absorption
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2006Prediction of percutaneous drug absorption
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2005Attachment IconGenerating Molecular Hashcodes for
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2002Expression and Functional Analyses of Novel Mutations ot ATP-Binding Cassette Transporter-1 in Japanese Patients with High-Density Lipoprotein Deficiency
In: Biochemical and Biophysical Research Communications [290], 713-721
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2008Determination of HIV-1 co-receptor usage in German patients – comparison of genotypic methods with the TROFILE® phenotypic assay
In: Abstracts of the Ninth International Congress on Drug Therapy in HIV Infection, 123
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2012HIV2EU: supporting standardized HIV-2 drug resistance interpretation in Europe
In: Journal of the International AIDS Society, 135
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2012HIV-GRADE: A Publicly Available, Rules-Based Drug Resistance Interpretation Algorithm Integrating Bioinformatic Knowledge
In: Intervirology [55], 102-107
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2008Determination of HIV-1 coreceptor usage in German patients - comparison of genotypic methods with the TROFILE phenotypic assay
In: Antiviral Therapy, A112
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2004Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures
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2012Efficacy of antiretroviral therapy switch in HIV-infected patients: A 10-year analysis of the EuResist cohort
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2003Lactam hydrolysis catalyzed by mononuclear metallo-beta-lactamases: a density functional study
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2013Genome Signature based Sequence Comparison for Taxonomic Assignment and tree inference
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2012On the trail of EHEC/EAEC - unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria
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2012CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands
In: Nucleic Acids Research [40], D610-D614
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2003Parallel "go with the winners algorithms" in Distributed Memory Models
In: Journal of Parallel and Distributed Processing [63], 801-814
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2010Finding local similarities in gene expression patterns between partially reprogrammed cells and know cell types using a module network approach
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2008Attachment IconSemi-Supervised Learning for Predicting Anti-HIV Drug Resistance
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2006Development of a fast
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2013Association Between HIV-1 Coreceptor Usage and Resistance to Some Broadly Neutralizing Antibodies
In: Proceedings of the AIDS Vaccine Conference 2013, A-1-A-208
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2012Improving coreceptor usage prediction in the clinic using hints from next generation sequencing data
In: Bioinformatics [28], i589-i595
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2012Attachment IconImproving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data
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2013HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure
In: Infection, Genetics and Evolution [19], 349–360
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2009Probabilistic disease gene prioritization
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2011A Computational Method for Predicting First-Line Antiretroviral Therapy Success
In: Abstract Book. 9th Workshop on HIV & Hepatitis Treatment Strategies & Antiviral Drug Resistance, 94
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2012Characterization of HIV-1 Gag Subtype C
In: Abstract Book. 9th Workshop on HIV \& Hepatitis Treatment Strategies \& Antiviral Drug Resistance, 40-41
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2014Simulation of Sanger-sequencing errors in the context of genotypic tropism determination
In: Antiviral Therapy, A81
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2013Effects of sequencing errors on geno2pheno[coreceptor] predictions
In: Abstract Book 11th European Meeting on HIV & Hepatitis, 23-24
Poster
2013In silico analysis of the effects of sequencing errors on geno2pheno[coreceptor]
In: Abstract Book of the International Workshop on HIV&Hepatitis Virus, A142
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3
Hide details for Pironti, Pfeifer, Kaiser, Walter, LengauerPironti, Pfeifer, Kaiser, Walter, Lengauer
2014Accurate prediction of drug-exposure without using established drug-resistance mutations
In: Antiviral Therapy, A75
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2014Improved HIV-1 drug-exposure reconstruction with linear support vector machines
In: Reviews in Antiviral Therapy & Infectious Diseases, 67
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2014Improved therapy-success prediction with GSS estimated from clinical HIV-1 sequences
In: Abstract Supplement of the HIV Drug Therapy Glasgow Congress 2014, 155
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2
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2014Accurate prediction of drug-exposure without using established drug-resistance mutations
In: Antiviral Therapy, A75
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2014Improved HIV-1 drug-exposure reconstruction with linear support vector machines
In: Reviews in Antiviral Therapy & Infectious Diseases, 67
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2014Simulation of Sanger-sequencing errors in the context of genotypic tropism determination
In: Antiviral Therapy, A81
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2006Attachment IconMutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair
In: Nucleic Acids Research [34], 6574-6586
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2004WILMA-automated annotation of protein sequences
In: Bioinformatics [20], 127-128
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2009Investigation of expert rule bases, logistic regression, and non-linear machine learning techniques for predicting response to antiretroviral treatment
In: Antiviral Therapy [14], 433-442
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2010Antiretroviral Therapy Optimisation without Genotype Resistance Testing: A Perspective on Treatment History Based Models
In: PLoS ONE [5], e13753,1-e13753,8
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2013A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227
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2006Statistical methods for the biological interpretation of genome-wide measurements
Universität des Saarlandes
Thesis - Habilitation thesis
2005Clustering algorithms and other exploratory methods for microarray data analysis
In: Methods of Information in Medicine [44], 444-448
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2005Image analysis for cDNA microarrays
In: Methods of Information in Medicine [44], 405-407
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2003Efficient Clustering Methods for Tumor Classification with Microarrays
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2003Statistical Inference for Clustering Microarrays
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2002Hybrid clustering for microarray analysis combining intensity and shape features
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2002Multivariate permutation tests for the k-sample problem with clustered data
In: Computational Statistics [17], 165-184
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2005Estimating cancer survival and clinical outcome based on genetic tumor progression scores
In: Bioinformatics [21], 2438-2446
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2004Hybrid clustering for microarray image analysis combining intensity and shape features
In: BMC Bioinformatics [5], 1-11
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2003Comparative quality analyses for hybrid clustering of microarray images
In: Proceedings of the Sventh Annual International Conference on Computational Biology, -
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2002Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering
In: Bioinformatics [18], 747-756
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2004Calculating the statistical significance of changes in pathway activity from gene expression data
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2003Cost-effective screening for differentially expressed genes in microarray experiments based on normal mixtures
In: Austrian Journal of Statistics [32], 225-238
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2007Analysis of Expression Data: Classification of genes
In: Bioinformatics - From Genomes to Therapies 2. Getting at the Inner Workings: Molecular Interactions, 993-1021
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2005An integrative approach to gain insights into the cellular function of human ataxin-2
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2005Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways
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2012Novel Approaches to the Integration and Analysis of Systems Biology
Universität des Saarlandes
Thesis - PhD thesis
2010Tutorial Cytoscape
In: Bioinformática: Aplicaciones a la genómica y proteómica, 73-98
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2004Evolucion de la Evolucionalidad
In: Biologos lejos del equilibrio: Nuevas metaforas evolutivas, 59-87
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2004Hacia una comprension de la accion de la recombinacion genetica y la mutacion en el origen de la variacion fenotipica, mediante el analisis de la computacion evolutiva
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2010Finding scaffold proteins in interactomes
In: Trends in Cell Biology [20], 2-4
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2000GenLab: Laboratorio virtual de genetica
In: Acta Biologica Colombiana [5], 45-48
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2012Novel search method for the discovery of functional relationships
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2007Computational analysis of human protein interaction networks
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2011Analysis of quality raw data of second generation sequencers with Quality Assessment Software
In: BMC Research Notes [4], 130,1-130,6
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2006Docking studies to investigate the effect of correlated mutations in the HIV-Protease on the drug resistance of HIV
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2011Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment
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2011Estimating and Using the Uncertainty in the Phenotypic Resistance Assay of the Hepatitis B Virus to Improve IC-50 Prediction from Genotype
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2012Risk factors associated with older age in treatment-naive HIV-positive patients
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2011Attachment IconErratum to: Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.
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2011Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients
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2010Attachment IconHepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery
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2013Density Parameter Estimation for Finding Clusters of Homologous Proteins - Tracing Actinobacterial Pathogenicity Life Styles
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2012Online Transitivity Clustering of Biological Data with Missing Values
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2012How Little Do We Actually Know? - On the Size of Gene Regulatory Networks.
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2007Evolution of Drug Resistance in HIV
In: Bioinformatics - From Genomes to Therapies 3. The Holy Grail: Molecular Function, 1457-1496
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2010Predicting MHC class I epitopes in large datasets
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2006Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV
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2011Predicting interactions between T cell receptors and MHC-peptide complexes
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2009Intensive blood glucose control is safe and effective in diabetic cats using home monitoring and treatment with glargine
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2008Selecting anti-HIV therapies based on a variety of genomic and clinical factors
In: Proceedings of the 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008), i399-406
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2008Sustaining lamivudine/emtricitabine, abacavir, zidovudine or atazanavir from a previous treatment shows a clinical benefit
In: Antiviral Therapy, A86
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2012Paving the future: finding suitable ISMB venues
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2011Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
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2011Attachment IconLearning from past treatments and their outcome improves prediction of In Vivo response to anti-HIV therapy
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2010Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism
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2008Iterative Subgraph Mining for Principal Component Analysis.
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2006A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays
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2008Structural Descriptors for the Analysis of Protein Structure, Function, and Evolution
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2004Local sequence-structure relationships in proteins
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2008Computational analysis of covariation and interactions between HIV-1 reverse transcriptase and Integrase
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2008Structural descriptors of protein-protein binding sites
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2006Local protein structure prediction using discriminative models
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2013A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
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2011A singular value decomposition approach for improved taxonomy classification of biological sequences
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2005Clinical significance of in vitro replication-enhancing mutations of the hepatitis C virus (HCV) replicon in patients with chronic HCV infection
In: The Journal of Infectious Diseases [192], 1710-1719
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2001Automated Layout Generation and Wiring Area Estimation for 3D Electronic Modules
In: ASME Journal of Machanical Design [123], 330-336
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2007Prediction of Domain and Motif Interactions from Protein Networks
Universität des Saarlandes
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2013Sensitive detection of viral transcripts in human tumor transcriptomes
In: PLOS Computational Biology [9], xx
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2008An integrative approach for predicting interactions of protein regions
In: Bioinformatics [24], i35-i41
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2011Inferring physical protein contacts from large-scale purification data of protein complexes
In: Molecular & Cellular Proteomics [10], M110.004929,1-M110.004929,15
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2007Identification of PatL1, a human homolog to yeast P body component Pat1
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2010Attachment IconOntology-based Similarity Measures and their Application in Bioinformatics
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2005A Global Approach to Comparative Genomics: Comparison of Functional Annotation over the Taxonomic Tree
Universität des Saarlandes
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2004Attachment IconAutomated Differential Analysis of Proteomes
Universität des Saarlandes
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2010FunSimMat update: new features for exploring functional similarity
In: Nucleic Acids Research [38], D244-D248
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2008Attachment IconFunSimMat: a comprehensive functional similarity database
In: Nucleic Acids Research [36], D434-D439
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2006Attachment IconA new measure for functional similarity of gene products based on Gene Ontology
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2007Attachment IconFunctional evaluation of domain-domain interactions and human protein interaction networks
In: Bioinformatics [23], 859-865
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2006Functional evaluation of domain-domain interactions and human protein interaction networks
In: German Conference on Bioinformatics (GCB 2006), 115-126
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2010Improving disease gene prioritization using the semantic similarity of Gene Ontology terms
In: Bioinformatics [26], i561-i567
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2007Attachment IconGOTax: investigating biological processes and biochemical activities along the taxonomic tree
In: Genome Biology [8], R33.1-10
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2013An Integrative Clinical Database and Diagnostics Platform for Biomarker Identification and Analysis in Ion Mobility Spectra of Human Exhaled Air
In: Journal of Integrative Bioinformatics [10],
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2005Genetics of Crohn disease, an archetypal inflammatory barrier disease
In: Nature Reviews Genetics [6], 376-388
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2008MethMarker – A toolkit for design, optimization and validation of DNA methylation biomarkers for cancer diagnosis and therapy optimization
Universität des Saarlandes
Thesis - Masters thesis
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2009Attachment IconMethMarker: User-friendly design and optimization of gene-specific DNA methylation assays
In: Genome Biology [10], R105:1-R105:10
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2012Etravirine in protease inhibitor-free antiretroviral combination therapies
In: Journal of the International AIDS Society, 155-156
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1
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2011HIV prevalence and route of transmission in Turkish immigrants
living in North-Rhine Westphalia, Germany
In: Medical Microbiology and Immunology [200], 219-223
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2007Attachment IconFactor interaction analysis for chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer
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2013Reconstructing dynamic microRNA-regulated interaction networks
In: Proceedings of the National Academy of Sciences of the United States [110], 15686–15691
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2011High Concordance between the Position-Specific Scoring Matrix and Geno2pheno Algorithms for Genotypic Interpretation of HIV-1 Tropism: V3 Length as the Major Cause of Disagreement
In: Journal of Clinical Microbiology [49], 3380-3382
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2012Multi-scale computational modeling of developmental biology
In: Bioinformatics [28], 2022-2028
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2011Protease Inhibitor-Resistant Hepatitis C Virus Mutants With Reduced Fitness From Impaired Production of Infectious Virus
In: Gastroenterology [140], 667-675
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2009Evolution of raltegravir resistance during therapy
In: Journal of antimicrobial chemotherapy [64], 25-32
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2012Optimisation of baseline genotypic testing for safe and efficient maraviroc administration
In: Journal of the International AIDS Society, 101-102
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1
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2011Prediction of HIV-1 coreceptor usage (tropism) by sequence analysis using a genotypic approach
In: Journal of Visualized Experiments [58], e3264,1-e3264,9
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2007Attachment IconGenotypic coreceptor analysis.
In: European Journal of Medical Research [12], 453-462
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2008Genotypic Analysis of HIV Co-Receptor Usage
In: Entry Inhibitoren - Neue Formen der HIV-Therapie, 31-39
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2013Comparative genome-wide DNA methylation analysis of colorectal tumor and matched human tissue
In: Epigenetics [7], 1355-1367
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2012Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues
In: Epigenetics [7], 1355-1367
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2008Model-Based Anti HIV Therapy
Universität des Saarlandes
Thesis - PhD thesis
2004Learning localized rule mixtures by maximizing the area under the ROC curve, with an application to the prediction of HIV-1 coreceptor usage
Universität Freiburg
Thesis - Masters thesis
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2007Attachment IconMutagenetic tree Fisher kernel improves prediction of HIV drug resistance from viral genotype
In: Advances in Neural Information Processing Systems 19, 1-9
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2005Geno2pheno[coreceptor]: a tool for predicting coreceptor usage from genotype and for monitoring coreceptor-associated sequence alterations
In: Proceedings of the 3rd European HIV Drug Resistance Workshop, -
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2004Learning mixtures of localized rules by maximizing the area under the ROC curve
In: ROCAI-2004: 1st International Workshop on ROC Analysis in Artificial Intelligence, 89-96
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2007Predicting HIV coreceptor usage on the basis of genetic and clinical covariates
In: Antiviral Therapy [12], 1097-1106
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2006ROCR: Visualizing classifier performance in R
In: Bioinformatics [21], 3940-3941
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2005Characterization of novel HIV Drug Resistance Mutations using clustering, multidimensional scaling and SVM-based feature ranking
In: Knowledge Discovery in Databases: PKDD 2005., 285-296
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2005Computational prediction of MHC-peptide interactions
Universität des Saarlandes
Thesis - Masters thesis
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2007Attachment IconDetermining human immunodeficiency virus coreceptor use in a clinical setting: Degree of correlation between two phenotypic assays and a bioinformatic model
In: Journal of Clinical Microbiology [45], 279-284
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2014Current breathomics – A review on data pre-processing techniques and machine learning in metabolomics breath analysisUnpublished/Draft
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2012PIPS: Pathogenicity Island Prediction Software
In: PLoS One [7], e30848,1-e30848,10
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2007Attachment IconVariants in a novel epidermal collagen gene (COL29A1) are associated with atopic dermatitis
In: PLoS Biology [5], e242.1952-1961
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2009Attachment IconFrom Protein Structure to Function
Universität des Saarlandes
Thesis - Habilitation thesis
2007Protein Fold Recognition Based on Distant Homologs
In: Bioinformatics - From Genomes to Therapies 1. The Building Blocks: Molecular Sequences and Structures, 351-388
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2007Moment invariants as shape recognition technique for comparing protein binding sites
In: Bioinformatics [23], 3139-3146
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2004Predicting Protein Structure Classes from Function Predictions
In: Bioinformatics [20], 770-776
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2006Improving the quality of protein structure models by selecting from alignment alternatives
In: BMC Bioinformatics [7], 1-11
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2002Confidence measures for protein fold recognition
In: Bioinformatics [18], 802-812
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2009Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740
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2012Towards the identification of cancer subtypes by integrative clustering of molecular data
Universität des Saarlandes
Thesis - Masters thesis
2010Network analysis of viral host factors
Universität des Saarlandes
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2008Computational Approaches in Supramolecular Chemistry with a special Focus on Virtual Screening
Universität des Saarlandes
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2006Flexible Docking of Ligands into Synthetic Receptors Using a Two-Sided Incremental Construction Algorithm
In: Journal of Chemical Information and Modeling [46], 1695-1703
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In: Biosensors 2006: The ninth world congress on biosensors, O66
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In: Synthetic Receptors 2005: Second World Congress on Synthetic Receptors, O7
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In: Proceedings of the 2nd Summer School Medicinal Chemistry Regensburg 2004, 83
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2004FlexR - Predicting the structure of host-guest complexes
In: Proceedings of the Annual Meeting of the German Pharmaceutical Society - Joint Meeting 2004 (DPhG 2004), 130
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2007Combined similarity and QSPR virtual screening for guest molecules of $\beta$-cyclodextrin
In: New Journal of Chemistry [31], 1941-1949
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2007Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening
In: Chemistry [13], 6801-6809
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2013Assessment of transcript reconstruction methods for RNA-seq
In: Nature Methods [10], 1177-84
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2010History Based HIV Therapy Outcome Prediction
Universität des Saarlandes
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2008Protein Surface Remeshing and Characterisation Using Morse-Smale Complexes
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1995Genomic organization of the human tissue inhibitor of metalloproteinases-3 (TIMP3)
In: Genome Research [5], 483-7
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2004Genetic variation in DLG5 is associated with inflammatory bowel disease
In: Nature Genetics [36], 376-380
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2009Characterization of resistance to the protease inhibitor boceprevir in hepatitis C virus-infected patients.
In: Hepatology [50], 1709-1718
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2011Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975–983
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2005Additional Mutations in HIV-1 Reverse Transcriptase are Involved in the Highly Ordered Regulation of NRTI Resistance
In: Proceedings of the 3rd European HIV Drug Resistance Workshop, -
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2005A highly ordered network of HIV-1 RT mutations regulates the continuous escape from antiviral drugs
In: International Workshop in HIV Dynamics and Evolution, -
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2011Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975-983
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2006Involvement of novel HIV-1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors
In: Journal of Virology [80], 7186-7198
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