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MPI-INF D3 Publications

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BibTeX cite keyAuthor/EditorYearTitleType
Rahnenf2001aRahnenführer, Jörg2003Statistical Inference for Clustering Microarrays
In: Proceedings of the MSRI Workshop: Nonlinear Estimation and Classification, 323-332
Proceedings Article
Rahnenf2002aRahnenführer, Jörg
Bozinov, Daniel
2002Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering
In: Bioinformatics [18], 747-756
Journal Article
Rahnenf2002bRahnenführer, Jörg2002Multivariate permutation tests for the k-sample problem with clustered data
In: Computational Statistics [17], 165-184
Journal Article
Rahnenf2002cBozinov, Daniel
Rahnenführer, Jörg
Burson, Cathy
Spiegelstein, Ofer
2002Automated Grid Alignment for High-Throughput Analysis of Microarray Images (CIIST-02)
In: Proceedings of the 2002 International Conference on Imaging Science, Systems, and Technology, 161-167
Proceedings Article
Rahnenf2002dRahnenführer, Jörg2002Hybrid clustering for microarray analysis combining intensity and shape features
In: Poster book of the European Conference on Computational Biology, Saarbrücken, Germany 2002, -
Poster
Rahnenf2003aRahnenführer, Jörg2003On preferences of general two-sided tests with applications to Kolmogorov-Smirnov-type tests
In: Statistics & Decisions [21], 115-136
Journal Article
Rahnenf2003bJanssen, A.
Rahnenführer, Jörg
2003A hazard based approach to dependence tests for bivariate censored models
In: Mathematical Methods in Statistics [11], 297-322
Journal Article
Rahnenf2003cRahnenführer, Jörg2003Efficient Clustering Methods for Tumor Classification with Microarrays
In: Proceedings of the 26th Annual Conference of the Gesellschaft für Klassifikation, 670-679
Proceedings Article
Rahnenf2003dRahnenführer, Jörg
Bozinov, Daniel
2003Comparative quality analyses for hybrid clustering of microarray images
In: Proceedings of the Sventh Annual International Conference on Computational Biology, -
Poster
Rahnenfuehrer2003eRahnenführer, Jörg
Futschik, Andreas
2003Cost-effective screening for differentially expressed genes in microarray experiments based on normal mixtures
In: Austrian Journal of Statistics [32], 225-238
Journal Article
Rahnenfuehrer2003fJames, Jackson
Das, Ani V.
Rahnenführer, Jörg
Leon, FAS
Ahmad, Iqbal
2003Identification of rat brahma (rBRM), a subunit of SWI/SNF chromatin remodeling complex: Involvement in the differentiation of retinal stem cells/progenitorsMiscellaneous
Rahnenfuehrer2004aRahnenführer, Jörg
Domingues, Francisco S.
Maydt, Jochen
Lengauer, Thomas
2004Calculating the statistical significance of changes in pathway activity from gene expression data
In: Statistical Applications in Genetics and Molecular Biology [3], Article 16
Electronic Journal Article
Rahnenfuehrer2004bJames, Jackson
Das, Ani V.
Rahnenführer, Jörg
Ahmad, Iqbal
2004Cellular and Molecular Characterization of Early and Late Retinal Stem Cells/Progenitors: Differential Regulation of Proliferation and Context Dependent Role of Notch Signaling
In: Journal of Neurobiology [61], 359-376
Journal Article
Rahnenfuehrer2004cJames, Jackson
Das, Ani V.
Zhao, Xing
Rahnenführer, Jörg
Ahmad, Iqbal
2004Identification of c-Kit receptor as a regulator of adult neural stem cells in the mammalian eye: interactions with Notch signaling
In: Developmental Biology [273], 87-105
Journal Article
Rahnenfuehrer2004dRahnenführer, Jörg
Bozinov, Daniel
2004Hybrid clustering for microarray image analysis combining intensity and shape features
In: BMC Bioinformatics [5], 1-11
Journal Article
Rahnenfuehrer2005aRahnenführer, Jörg
Beerenwinkel, Niko
Schulz, Wolfgang A.
Hartmann, Christian
von Deimling, Andreas
Wullich, Bernd
Lengauer, Thomas
2005Estimating cancer survival and clinical outcome based on genetic tumor progression scores
In: Bioinformatics [21], 2438-2446
Journal Article
Rahnenfuehrer2005bRahnenführer, Jörg2005Image analysis for cDNA microarrays
In: Methods of Information in Medicine [44], 405-407
Journal Article
Rahnenfuehrer2005cRahnenführer, Jörg2005Clustering algorithms and other exploratory methods for microarray data analysis
In: Methods of Information in Medicine [44], 444-448
Journal Article
Rahnenfuehrer2005dDas, Ani V.
James, Jackson
Rahnenführer, Jörg
Thoresona, Wallace B.
Bhattacharyaa, Sumitra
Zhao, Xing
Ahmad, Iqbal
2005Retinal properties and potential of the adult mammalian ciliary epithelium stem cells
In: Vision Research [45], 1653-1666
Journal Article
Rahnenfuehrer2006HabilRahnenführer, Jörg2006Statistical methods for the biological interpretation of genome-wide measurements
Universität des Saarlandes
Thesis - Habilitation thesis
Rahnenfuehrer2007aRahnenführer, Jörg
Lengauer, Thomas
2007Analysis of Expression Data: Classification of genes
In: Bioinformatics - From Genomes to Therapies 2. Getting at the Inner Workings: Molecular Interactions, 993-1021
Part of a Book
Rahnenfuehrer2007cSchulz, Wolfgang A.
Alexa, Adrian
Jung, Volker
Hader, Christiane
Hoffmann, Michele J.
Yamanaka, Masanori
Fritzsche, Sandy
Wlazlinski, Agnes
Müller, Mirko
Lengauer, Thomas
Engers, Rainer
Florl, Andrea R.
Wullich, Bernd
Rahnenführer, Jörg
2007Attachment IconFactor interaction analysis for chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer
In: Molecular Cancer [6], 1-16
Journal Article
Rahnenfuehrer2007dKetter, Ralf
Kim, Yoo-Jin
Storck, Simone
Rahnenführer, Jörg
Romeike, Bernd F.M.
Steudel, Wolf-Ingo
Zang, Klaus D.
Henn, Wolfram
2007Attachment IconHyperdiploidy defines a distinct cytogenetic entity of meningiomas
In: Journal of Neuro-Oncology [83], 213-221
Journal Article
RahnenführerTolosi2007Kamradt, Jörn
Jung, Volker
Wahrheit, Kerstin
Tolosi, Laura
Rahnenführer, Jörg
Schilling, Martin
Walker, Robert
Davis, Sean
Stöckle, Michael
Meltzer, Paul
Wullich, Bernd
2007Detection of Novel Amplicons in Prostate Cancer by Comprehensive Genomic Profiling of Prostate Cancer Cell Lines Using Oligonucleotide-Based ArrayCGH
In: PLoS ONE [2], e769
Electronic Journal Article
Ramirez2000Ramírez, Fidel
Garcia, Sergio
2000GenLab: Laboratorio virtual de genetica
In: Acta Biologica Colombiana [5], 45-48
Journal Article
Ramirez2004Ramírez, Fidel2004Evolucion de la Evolucionalidad
In: Biologos lejos del equilibrio: Nuevas metaforas evolutivas, 59-87
Part of a Book
Ramirez2004_thesisRamírez, Fidel2004Hacia 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
Universidad Nacional de Colombia
Thesis - Masters thesis
Ramirez2010Ramirez, Fidel2010Tutorial Cytoscape
In: Bioinformática: Aplicaciones a la genómica y proteómica, 73-98
Part of a Book
Ramirez2012thRamirez, Fidel2012Novel Approaches to the Integration and Analysis of Systems Biology
Universität des Saarlandes
Thesis - PhD thesis
Ray2003Jose, Joachim
Betschieder, Dirk
Ray, Somak
Lengauer, Thomas
Zangen, D
2003New inhibitors of human cathepsin G identified by surface display library screening and peptide-protein docking
In: 7th International Symposium on Pharmaceutical Sciences (ISOPS-7), 46-49
Proceedings Article
Reimer2006Reimer, Daniela2006Docking studies to investigate the effect of correlated mutations in the HIV-Protease on the drug resistance of HIV
Universität des Saarlandes
Thesis - Bachelor thesis
Reppas2012Reppas, Andreas
Lawyer, Glenn
2012Attachment IconLow k-shells identify bridge elements critical to disease flow in small-world networks
In: Numerical Analysis and Applied Mathematics (ICNAAM 2012), 1426-1429
Proceedings Article
Reuter2010aReuter, Stefan
Oette, Mark
Wilhelm, Frank Clemens
Beggel, Bastian
Kaiser, Rolf
Balduin, Melanie
Schweitzer, Finja
Verheyen, Jens
Adams, Ortwin
Lengauer, Thomas
Faetkenheuer, Gerd
Pfister, Herbert
Haeussinger, Dieter
2011Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients
In: Medical Microbiology and Immunology [200], 39-49
Journal Article
Reuter2010bReuter, Stefan
Oette, Mark
Wilhelm, Frank Clemens
Beggel, Bastian
Kaiser, Rolf
Balduin, Melanie
Schweitzer, Finja
Verheyen, Jens
Adams, Ortwin
Lengauer, Thomas
Faetkenheuer, Gerd
Pfister, Herbert
Haeussinger, Dieter
2011Attachment IconErratum to: Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.
In: Medical Microbiology and Immunology [200], 51-51
Journal Article
Reuter2011Reuter, Kerstin2011Estimating and Using the Uncertainty in the Phenotypic Resistance Assay of the Hepatitis B Virus to Improve IC-50 Prediction from Genotype
Universität des Saarlandes
Thesis - Bachelor thesis
Reuter2012aReuter, Stefan
Oette, Mark
Kaiser, Rolf
Lengauer, Thomas
Fätkenheuer, Gerd
Rockstroh, Jürgen
Knechten, Heribert
Häussinger, Dieter
2012Risk factors associated with older age in treatment-naive HIV-positive patients
In: Intervirology [55], 147-153
Journal Article
Rhee2010Rhee, Soo-Yon
Margeridon-Thermet, Severin
Nguyen, Mindie
Liu, Tommy
Kagan, Ron
Beggel, Bastian
Verheyen, Jens
Kaiser, Rolf
Shafer, Robert
2010Attachment IconHepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery
In: Antiviral Research [88], 269-275
Journal Article
roettger2012densityRöttger, Richard
Kalaghatgi, Prabhav
Sun, Peng
de Castro Soares, Siomar
Azevedo, Vasco
Wittkop, Tobias
Baumbach, Jan
2013Density Parameter Estimation for Finding Clusters of Homologous Proteins - Tracing Actinobacterial Pathogenicity Life Styles
In: Bioinformatics [29], 215-222
Journal Article
roettger2012littleRöttger, Richard
Rueckert, Ulrich
Taubert, Jan
Baumbach, Jan
2012How Little Do We Actually Know? - On the Size of Gene Regulatory Networks.
In: IEEE/ACM transactions on computational biology and bioinformatics [9], 1293-1300
Journal Article
roettger2012onlineRöttger, Richard
Kreutzer, Christoph
Duong Vu, Thuy
Wittkop, Tobias
Baumbach, Jan
2012Online Transitivity Clustering of Biological Data with Missing Values
In: German Conference on Bioinformatics 2012 (GCB 2012), 57-68
Electronic Proceedings Article
Roomp1995aStohr, H.
Roomp, Kirsten
Felbor, U.
Weber, B. H.
1995Genomic organization of the human tissue inhibitor of metalloproteinases-3 (TIMP3)
In: Genome Research [5], 483-7
Journal Article
Roomp1999aBrooks-Wilson, A
Marcil, Michel
Clee, Susanne M.
Zhang, Lin-Hua
Roomp, Kirsten
van Dam, M
Yu, L
Brewer, C
Collins, Jennifer A.
Molhuizen, H.O.
Loubser, O
Ouelette, B.F.
Fichter, K
Ashbourne-Excoffon, K.J.
Sensen, C.W.
Scherer, S
Mott, S
Denis, M
Martindale, D
Frohlich, J
Morgan, K
Koop, B
Pimstone, S
Kastelein, J.J.P.
Hayden, Michael R.
1999Mutations in ABC1 in Tangier disease and familial high-density lipoprotein
In: Nature Genetics [22], 336-45
Journal Article
Roomp1999bMarcil, Michel
Brooks-Wilson, A.
Clee, Susanne M.
Roomp, Kirsten
Zhang, Lin-Hua
Yu, L.
Collins, Jennifer A.
van Dam, M.
Molhuizen, H. O.
Loubser, O.
Ouelette, B. F.
Sensen, C. W.
Fichter, K.
Mott, S.
Denis, M.
Boucher, B.
Pimstone, S.
Genest, Jacques
Kastelein, J. J. P.
Hayden, Michael R.
1999Mutations in the ABC1 gene in familial HDL deficiency with defective cholesterol efflux
In: The Lancet [354], 1341-6
Journal Article
Roomp2000aClee, Susanne M.
Kastelein, J.J.P.
van Dam, M
Marcil, Michel
Roomp, Kirsten
Zwarts, K.Y.
Collins, Jennifer A.
Roelants, R
Tamasawa, N
Stulc, T
Suda, T
Ceska, R
Boucher, B
Rondeau, C
DeSouich, C
Brooks-Wilson, A
Molhuizen, H.O.
Frohlich, J
Genest, Jacques Jr
Hayden, Michael R.
2000Age and residual cholesterol efflux affect HDL cholesterol levels and coronary artery disease in ABCA1 heterozygotes
In: Journal of Clinical Investigation [106], 1263-70
Journal Article
Roomp2001aClee, Susanne M.
Zwinderman, A.H.
Engert, J.C.
Zwarts, K.Y.
Molhuizen, H.O.
Roomp, Kirsten
Jukema, J.W.
van Wijland, M
van Dam, M
Hudson, T.J.
Brooks-Wilson, A
Genest, Jacques Jr
Kastelein, J.J.P.
Hayden, Michael R.
2001Common genetic variation in ABCA1 is associated with altered lipoprotein levels and a modified risk for coronary artery disease
In: Circulation [103], 1198-205
Journal Article
Roomp2002aWellington, Cheryl L.
Yang, Yu-Zhou
Zhou, Stephen
Clee, Susanne M.
Tan, Bing
Hirano, Kenichi
Zwarts, K.Y.
Kwok, Anita
Gelfer, Allison
Marcil, Michel
Newman, Scott
Roomp, Kirsten
Singaraja, Roshni
Collins, Jennifer A.
Zhang, Lin-Hua
Groen, Albert K.
Hovingh, Kees
Brownlie, Alison
Tafuri, Sherrie
Genest, Jacques Jr
Kastelein, J.J.P.
Hayden, Michael R.
2002Truncation mutations in ABCA1 suppress normal upregulation of full-length ABCA1 by 9-cis-retinoic acid and 22-R-hydroxycholesterol
In: Journal of Lipid Research [43], 1939-1949
Journal Article
Roomp2002bZwarts, K.Y.
Clee, Susanne M.
Zwinderman, A.H.
Engert, J.C.
Singaraja, Roshni
Loubser, O
James, E
Roomp, Kirsten
Hudson, T.J.
Jukema, J.W.
Kastelein, J.J.P.
Hayden, Michael R.
2002ABCA1 regulatory variants influence coronary artery disease independent of effects on plasma lipid levels
In: Clinical Genetics [61], 115-125
Journal Article
Roomp2002cNishida, Yoshiharu
Hirano, Kenichi
Tsukamoto, Kosuke
Nagano, Makoto
Ikegami, Chiaki
Roomp, Kirsten
Ishihara, Mitsuaki
Sakane, Naoki
Zhang, Zhongyan
Tsujii, Ken-ichi
Matsuyama, Akifumi
Ohama, Tohru
Matsuura, Fumihiko
Ishigami, Masato
Sakai, Naohiko
Hiraoka, Hisatoyo
Hattori, Hiroaki
Wellington, Cheryl L.
Yoshida, Yoshihide
Misugi, Susumu
Hayden, Michael R.
Egashira, Toru
Yamashita, Shizuya
Matsuzawa, Yuji
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
Journal Article
Roomp2006Roomp, Kirsten
Beerenwinkel, Niko
Sing, Tobias
Schülter, Eugen
Büch, Joachim
Sierra-Aragon, Saleta
Däumer, Martin
Hoffmann, Daniel
Kaiser, Rolf
Lengauer, Thomas
Selbig, Joachim
2006Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV
In: Lecture Notes in Computer Science [4075], 185-194
Journal Article
Roomp2007dRoomp, Kirsten2007Evolution of Drug Resistance in HIV
In: Bioinformatics - From Genomes to Therapies 3. The Holy Grail: Molecular Function, 1457-1496
Part of a Book
Roomp2009Roomp, Kirsten
Rand, Jacquie
2009Intensive blood glucose control is safe and effective in diabetic cats using home monitoring and treatment with glargine
In: Journal of feline medicine and surgery [11], 668-682
Journal Article
Roomp2010aRoomp, Kirsten
Antes, Iris
Lengauer, Thomas
2010Predicting MHC class I epitopes in large datasets
In: BMC Bioinformatics [11], 90,1-90,11
Electronic Journal Article
Roomp2011aRoomp, Kirsten
Domingues, Francisco S.
2011Predicting interactions between T cell receptors and MHC-peptide complexes
In: Molecular Immunology [48], 553-562
Journal Article
RoompLengauer2010bLange, Christian Markus
Roomp, Kirsten
Dragan, Anette
Nattermann, Jacob
Michalk, Monika
Spengler, Ulrich
Weich, Viola
Lengauer, Thomas
Zeuzem, Stefan
Berg, Thoma
Sarrazin, Christoph
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
Journal Article
Rosen2008aRosen-Zvi, Michal
Altmann, Andre
Prosperi, Mattia
Aharoni, Ehud
Neuvirth, Hani
Sönnerborg, Anders
Schülter, Eugen
Struck, Daniel
Peres, Yardena
Incardona, Francesca
Kaiser, Rolf
Zazzi, Maurizio
Lengauer, Thomas
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
Proceedings Article
RosenZvi2008IDRWRosen-Zvi, Michal
Schülter, Eugen
Altmann, Andre
Sierra-Aragon, Saleta
Zazzi, Maurizio
Sönnerborg, Anders
Oette, Mark
Lengauer, Thomas
Kaiser, Rolf
2008Sustaining lamivudine/emtricitabine, abacavir, zidovudine or atazanavir from a previous treatment shows a clinical benefit
In: Antiviral Therapy, A86
Poster
Rost2012Rost, Burkhard
Gaasterland, Terry
Lengauer, Thomas
Linial, Michal
Markel, Scott
McKay, B. J. Morrison
Schneider, Reinhard
Horton, Paul
Kelso, Janet
2012Paving the future: finding suitable ISMB venues
In: Bioinformatics [28], 2556-2559
Journal Article
Saigo2008aSaigo, Hiroto
Tsuda, Koji
2008Iterative Subgraph Mining for Principal Component Analysis.
In: Proceedings of the IEEE International Conference on Data Mining (ICDM2008), DM934
Proceedings Article
SAIGO2010Saigo, Hiroto
Hattori, Masahiro
Kashima, Hisashi
Tsuda, Koji
2010Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism
In: BMC Bioinformatics [11], S31,1-S31,7
Electronic Journal Article
Saigo2011Saigo, Hiroto
Altmann, André
Bogojeska, Jasmina
Müller, Fabian
Nowozin, Sebastian
Lengauer, Thomas
2011Attachment IconLearning from past treatments and their outcome improves prediction of In Vivo response to anti-HIV therapy
In: Statistical Applications in Genetics and Molecular Biology [10], 1-32
Electronic Journal Article
Sander2004Sander, Oliver2004Local sequence-structure relationships in proteins
Friedrich-Alexander-Universität Erlangen-Nürnberg
Thesis - other
Sander2006Sander, Oliver
Sommer, Ingolf
Lengauer, Thomas
2006Local protein structure prediction using discriminative models
In: BMC Bioinformatics [7], 1-13
Electronic Journal Article
Sander2007Sander, Oliver
Sing, Tobias
Sommer, Ingolf
Low, Andrew J.
Cheung, Peter K.
Harrigan, P. Richard
Lengauer, Thomas
Domingues, Francisco S.
2007Attachment IconStructural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage
In: PLoS Computational Biology [3], 555-564
Journal Article
Sander2008Sander, Oliver
Domingues, Francisco S.
Zhu, Hongbo
Lengauer, Thomas
Sommer, Ingolf
2008Structural descriptors of protein-protein binding sites
In: Proceedings of 6th Asia-Pacific Bioinformatics Conference, 79-88
Proceedings Article
Sander2008EDRWSander, Oliver
Altmann, Andre
Lengauer, Thomas
2008Computational analysis of covariation and interactions between HIV-1 reverse transcriptase and Integrase
In: Reviews in Antiviral Therapy, 113-114
Poster
SanderDiss2008Sander, Oliver2008Structural Descriptors for the Analysis of Protein Structure, Function, and Evolution
Universität des Saarlandes
Thesis - PhD thesis
Sandoval2013Sandoval, Juan
Mendez-Gonzales, Jesus
Nadal, Ernest
Chen, Guoan
Carmona, F. Javier
Sayols, Sergi
Moran, Sebastian
Heyn, Holger
Vizoso, Miguel
Gomez, Antonio
Sanchez-Cespedes, Montse
Assenov, Yassen
Müller, Fabian
Bock, Christoph
Taron, Miquel
Mora, Josefina
Muscarella, Lucia A.
Liloglou, Triantafillos
Davies, Michael
Pollan, Marina
Pajares, Maria J.
Torre, Wenceslao
Montuenga, Luis M.
Brambilla, Elisabeth
Field, John K.
Roz, Luca
Lo Iacono, Marco
Scagliotti, Giorgio V.
Rosell, Rafael
Beer, David G.
Esteller,Manel
2013A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147
Journal Article
Schelhorn2007Schelhorn, Sven-Eric2007Prediction of Domain and Motif Interactions from Protein Networks
Universität des Saarlandes
Thesis - Masters thesis
Schlicker2004aSchlicker, Andreas2004Attachment IconAutomated Differential Analysis of Proteomes
Universität des Saarlandes
Thesis - Bachelor thesis
Schlicker2005Schlicker, Andreas2005A Global Approach to Comparative Genomics: Comparison of Functional Annotation over the Taxonomic Tree
Universität des Saarlandes
Thesis - Masters thesis
Schlicker2007Schlicker, Andreas
Rahnenführer, Jörg
Albrecht, Mario
Lengauer, Thomas
Domingues, Francisco S.
2007Attachment IconGOTax: investigating biological processes and biochemical activities along the taxonomic tree
In: Genome Biology [8], R33.1-10
Electronic Journal Article
Schlicker2010Schlicker, Andreas2010Attachment IconOntology-based Similarity Measures and their Application in Bioinformatics
Universität des Saarlandes
Thesis - PhD thesis
Schlicker_BMCBioinformatics_2006Schlicker, Andreas
Domingues, Francisco S.
Rahnenführer, Jörg
Lengauer, Thomas
2006Attachment IconA new measure for functional similarity of gene products based on Gene Ontology
In: BMC Bioinformatics [7], 1-16
Electronic Journal Article
Schüffler2008Schüffler, Peter2008MethMarker – A toolkit for design, optimization and validation of DNA methylation biomarkers for cancer diagnosis and therapy optimization
Universität des Saarlandes
Thesis - Masters thesis
Schulter2011Schülter, Eugen
Oette, Mark
Balduin, Melanie
Reuter, Stefan
Rockstroh, Jürgen
Fätkenheuer, Gerd
Esser, Stefan
Lengauer, Thomas
Agacfidan, Ali
Pfister, Herbert
Kaiser, Rolf
Akgul, Baki
2011HIV prevalence and route of transmission in Turkish immigrants
living in North-Rhine Westphalia, Germany
In: Medical Microbiology and Immunology [200], 219-223
Journal Article
SchulzA2013Le, Hai-Son
Schulz, Marcel Holger
McCauley, Brenna MM
Hinman, Veronica F
Bar-Joseph, Ziv
2013Probabilistic error correction for RNA sequencing
In: Nucleic Acids Researcb [41], e109
Journal Article
SchulzB2013Schulz, Marcel Holger
Pandit, Kusum V
Lino Cardenas, Christian L
Ambalavanan,Namasivayam
Kaminski, Naftali
Bar-Joseph, Ziv
2013Reconstructing dynamic microRNA-regulated interaction networks
In: Proceedings of the National Academy of Sciences of the United States [110], 15686–15691
Journal Article
SchulzC2013Steijger, T
Abril, JF
Engström,PG
Kokocinski, F
Abril, JF
Akerman, M
Alioto, T
Ambrosini, G
Antonarakis, SE
Behr, J
Bohnert, R
Bucher, P
Cloonan, N
Derrien, T
Djebali, S
Du, J
Dudoit, S
Engström, PG
Gerstein, M
Gingeras, TR
Gonzalez, D
Grimmond, SM
Habegger, L
Iseli, C
Jean, G
Kahles, A
Kokocinski, F
Lagarde, J
Leng, J
Lefebvre, G
Lewis, S
Mortazavi, A
Niermann, P
Rätsch, G
Reymond, A
Ribeca, P
Richard, H
Rougemont, J
Rozowsky, J
Sammeth, M
Sboner, A
Schulz, Marcel Holger
Searle, SM
Solorzano, ND
Solovyev, V
Stanke, M
Steijger, T
Stevenson, BJ
Stockinger, H
Valsesia, A
Weese, D
White, S
Wold, BJ
Wu, J
Wu, TD
Zeller, G
Zerbino, D
Zhang, MQ
Hubbard, TJ
Guigó, R
Harrow, J
Bertone, P
2013Assessment of transcript reconstruction methods for RNA-seq
In: Nature Methods [10], 1177-84
Journal Article
Seclen2011Seclen, Eduardo
Soriano, Vincente
González, Maria M
Gómez, Sagrario
Thielen, Alexander
Poveda, Eva
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
Journal Article
Settyr2012Setty, Yaki2012Multi-scale computational modeling of developmental biology
In: Bioinformatics [28], 2022-2028
Journal Article
Shimakami2011Shimakami, Tetsuro
Welsch, Christoph
Yamane, Daisuke
McGivern, David R.
Yi, MinKyung
Zeuzem, Stefan
Lemon, Stanley M.
2011Protease Inhibitor-Resistant Hepatitis C Virus Mutants With Reduced Fitness From Impaired Production of Infectious Virus
In: Gastroenterology [140], 667-675
Journal Article
Sichtig2009Sichtig, Nadine
Sierra, Saleta
Kaiser, Rolf
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Pfister, Herbert
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Lengauer, Thomas
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Beerenwinkel, Niko
Lengauer, Thomas
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Däumer, Martin
Lengauer, Thomas
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Sing2005pkddSing, Tobias
Svicher, Valentina
Beerenwinkel, Niko
Ceccherini-Silberstein, Francesca
Däumer, Martin
Kaiser, Rolf
Walter, Hauke
Korn, Klaus
Hoffmann, Daniel
Oette, Mark
Rockstroh, Jürgen K.
Fätkenheuer, Gerd
Perno, Carlo-Federico
Lengauer, Thomas
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Low, Andrew J.
Beerenwinkel, Niko
Sander, Oliver
Cheung, Peter K.
Domingues, Francisco S.
Büch, Joachim
Däumer, Martin
Kaiser, Rolf
Lengauer, Thomas
Harrigan, P. Richard
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sing2008Sing, Tobias2008Model-Based Anti HIV Therapy
Universität des Saarlandes
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Ceccherini-Silberstein, Francesca
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Ortuso, Francesco
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Parrotta, Lucia
Flandre, Philippe
Descamps, Diane
Calvez, Vincent
Marcelin, Anne-Genevieve
Perno, Carlo Federico
Sing, Tobias
Svicher, Valentina
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Beerenwinkel, Niko
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Siu2005Siu, Shirley Weng-In2005Computational prediction of MHC-peptide interactions
Universität des Saarlandes
Thesis - Masters thesis
Skrabal2007Skrabal, Katharina
Low, Andrew J.
Dong, Winnie
Sing, Tobias
Cheung, Peter K.
Mammano, Fabrizio
Harrigan, P. Richard
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Hirata, Raphael
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Müller, Oliver
Domingues, Francisco S.
Sander, Oliver
Weickert, Joachim
Lengauer, Thomas
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Sommer2010Sommer, Ingolf2009Attachment IconFrom Protein Structure to Function
Universität des Saarlandes
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Speicher2010Speicher, Nora K.2010Network analysis of viral host factors
Universität des Saarlandes
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SpeicherMaster2012Speicher, Nora2012Towards the identification of cancer subtypes by integrative clustering of molecular data
Universität des Saarlandes
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Steffen2004Steffen, Andreas
Kämper, Andreas
Lengauer, Thomas
2004FlexR - Predicting the structure of host-guest complexes
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Steffen2004aSteffen, Andreas
Kämper, Andreas
Lengauer, Thomas
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Steffen2005Steffen, Andreas
Kämper, Andreas
Lengauer, Thomas
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Steffen2006aSteffen, Andreas
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Lengauer, Thomas
2006Flexible Docking of Ligands into Synthetic Receptors Using a Two-Sided Incremental Construction Algorithm
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Steffen2006bSteffen, Andreas
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Lengauer, Thomas
2006Virtual screening for guest molecules of a biosensor
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steffen2008aSteffen, Andreas2008Computational Approaches in Supramolecular Chemistry with a special Focus on Virtual Screening
Universität des Saarlandes
Thesis - PhD thesis
Stöckel2008Stöckel, Daniel2008Protein Surface Remeshing and Characterisation Using Morse-Smale Complexes
Universität des Saarlandes
Thesis - Bachelor thesis
StoeckelMaster2010Stöckel, Daniel2010History Based HIV Therapy Outcome Prediction
Universität des Saarlandes
Thesis - Masters thesis
Struck2014Lawyer, Glenn2014COMET: Adaptive context-based modeling for ultrafast HIV-1 subtype identification.
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Susser2009Susser, Simone
Welsch, Christoph
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Tong, Xiao
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Sarrazin, Christoph
2009Characterization of resistance to the protease inhibitor boceprevir in hepatitis C virus-infected patients.
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Svicher2005aSvicher, Valentina
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Santoro, Maria Mercedes
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2005A highly ordered network of HIV-1 RT mutations regulates the continuous escape from antiviral drugs
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Bellocchi, M. C.
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Antinori, A.
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2005Additional Mutations in HIV-1 Reverse Transcriptase are Involved in the Highly Ordered Regulation of NRTI Resistance
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Svicher2011Svicher, Valentina
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Mercurio, Fabio
Fraune, Maria
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Bertoli, Ada
Micheli, Valeria
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Longo, Roberta
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Jensen, Mark A.
Wynhoven, Brian
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Glascock, Christopher
Harrigan, P. Richard
2010Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA
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Swenson2011Swenson, Luke C.
Mo, Theresa
Dong, Winnie W. Y.
Zhong, Xiaoyin
Woods, Conan K.
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Thielen, Alexander
Chapman, Douglass
Lewis, Marilyn
James, Ian
Heera, Jayvant
Valdez, Hernan
Harrigan, P. Richard
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Mo, Theresa
Dong, Winnie WY
Zhong, Xiaoyin
Woods, Conan K
Thielen, Alexander
Jensen, Mark A
Knapp, David JHF
Chapman, Douglass
Lewis, Marilyn
James, Ian
Heera, Jayvant
Valdez, Hernan
Harrigan, P Richard
2011Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc.
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S.Domingues2006Domingues, Francisco S.
Lengauer, Thomas
2007Inferring Protein Function from Protein Structure
In: Bioinformatics - From Genomes to Therapies 3. The Holy Grail: Molecular Function, 1211-1252
Part of a Book
Talwar2003Talwar, Priti
Lengauer, Thomas
Wittmann, Christoph
Mangadu, Vidya
Heinzle, Elmar
2003Towards cellular function through metabolite screening
In: Proceedings of the 3rd Annual Conference on Metabolic Profiling: Pathways in Discovery, 7
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Talwar2003aTalwar, Priti
Wittmann, Christoph
Lengauer, Thomas
Heinzle, Elmar
2003Software tool for automated processing of 13C labeling data from mass spectrometry data
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Talwar2004aTalwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
Velagapudi, VR
Wittmann, Christoph
Heinzle, Elmar
2004Computational Methods For Metabolite Screening
In: Proceedings of the 12th International Conference on Intelligent Systems for Molecular Biology + 3rd European Conference on Computational Biology (ISMB/ECCB 2004), 1
Poster
Talwar2004bTalwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
Velagapudi, VR
Wittmann, Christoph
Heinzle, Elmar
2004Computational Methods For Metabolite Screening
In: Proceedings of the 5th International Conference on Systems Biology (ICSB 2004), 1
Poster
Talwar2005Talwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
Wittmann, Christoph
Velagapudi, VR
Heinzle, Elmar
2005Computational Methods for Protein Function Prediction using Metabolomics Data
In: Proceedings of International Workshop on Systems Biology 2005, 1
Poster
Talwar2006Talwar, Priti
Lengauer, Thomas
Wittmann, Christoph
Velagapudi, V. R.
Heinzle, Elmar
2006Development of Computational Methods for Analysis of Metabolic Profiling Data
In: Proceedings of International Conference on Systems Biology (ICSB 2006), Japan, 42-42
Proceedings Article
Talwar2006aTalwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
Heinzle, Elmar
Velagapudi, VR
Wittmann, Christoph
2005Towards computational analysis of metabolic profiling data for protein function prediction.
In: Proceedings of the Yeast Systems Biology, 6th International Conference on Systems Biology (ICSB 2005), 1
Poster
talwar2008Talwar, Priti2008Development of Computational Methods for Metabolic Network Analysis based on Metabolomics Data
Universität des Saarlandes
Thesis - PhD thesis
Thielen2006Thielen, Alexander2006Prediction of linear B-cell epitopes and MHC class II binding peptides
Eberhardt-Karls-Universität Tübingen
Thesis - Masters thesis
Thielen2008EDRWThielen, Alexander
Sichtig, Nadine
Braun, Patrick
Däumer, Martin
Walter, Hauke
Noah, Christian
Wolf, Eva
Müller, Harm
Stürmer, Martin
Lengauer, Thomas
Kaiser, Rolf
Obermeier, Martin
2009Performance of genotypic coreceptor measurement using geno2pheno[coreceptor] in B- and non-B HIV subtypes in a large cohort of therapy-experienced patients in Germany
In: Reviews in Antiviral Therapy, 99-99
Poster
Thielen2008EntryThielen, Alexander
Kaiser, Rolf
Lengauer, Thomas
2008Improving HIV-1 coreceptor usage prediction from genotype with regions outside of V3
In: Reviews in Antiviral Therapy, 81-82
Poster
Thielen2008IDRWThielen, Alexander
Harrigan, P Richard
Low, Andrew J.
Moores, A
Altmann, Andre
Bozek, Kasia
Heger, Eva
Sichtig, Nadine
Kaiser, Rolf
Lengauer, Thomas
2008Improved genotypic prediction of HIV-1 coreceptor usage by incorporating V2 loop sequence variation
In: Antiviral Therapy, A100
Poster
Thielen2009IDRWThielen, Alexander
Altmann, André
Bogojeska, Jasmina
Kaiser, Rolf
Lengauer, Thomas
2009Estimating evolutionary pathways to 7CXCR4 usage from cross-sectional data
In: Abstracts presented at the XVIII International HIV Drug Resistance Workshop : Basic Principles & Clinical Implications, A16-A16
Poster
Thielen2010Thielen, Alexander
Sichtig, Nadine
Kaiser, Rolf
Lam, Jeffrey
Harrigan, P. Richard
Lengauer, Thomas
2010Improved prediction of HIV-1 coreceptor usage with sequence information from the second hypervariable loop of gp120
In: Journal of Infectious Diseases [202], 1435-1443
Journal Article
Thielen2010EDRWThielen, Alexander
Lengauer, Thomas
Harrigan, P Richard
Swenson, Luke
Dong, Winnie WY
McGovern, Rachel A
Lewis, Marilyn
James, Ian
Heera, Jayvant
Valdez, Hernan
2010Mutations within GP41 are correlated with coreceptor tropism but do not substantially improve coreceptor usage prediction
In: Reviews in Antiviral Therapy & Infectious Diseases, 47-47
Poster
Thielen2010gp41Thielen, Alexander
Lengauer, Thomas
Swenson, Luke C
Dong, Winnie W.Y.
McGovern, Rachel A
Lewis, Marilyn
James, Ian
Heera, Jayvant
Valdez, Hernan
Harrigan, P Richard
2011Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially
In: Antiviral Therapy [16], 319-328
Journal Article
Thielen2011Thielen, Alexander
Lengauer, Thomas
2012Geno2pheno[454]: A Web Server for the Prediction of HIV-1 Coreceptor Usage from Next-Generation Sequencing Data
In: Intervirology [55], 113-117
Journal Article
Thielen2011dissThielen, Alexander2011Genotypic Analysis of HIV-1 Coreceptor Usage
Universität des Saarlandes
Thesis - PhD thesis
Tolosi2006Tolosi, Laura2006Analysis of Array CGH Data for the Estimation of Genetic Tumor Progression
Universität des Saarlandes
Thesis - Masters thesis
tolosi2009Sos, Martin L.
Michel, Kathrin
Zander, Thomas
Weiss, Jonathan
Frommolt, Peter
Pfeifer, Martin
Li, Danan
Ullrich, Roland
Koker, Mirjam
Fischer, Florian
Shimamura, Takeshi
Rauh, Daniel
Mermel, Craig
Fischer, Stefanie
Stückrath, Isabel
Heynck, Stefanie
Beroukhim, Rameen
Lin, William
Winckler, Wendy
Shah, Kinjal
LaFramboise, Thomas
Moriarty, Whei F.
Hanna, megan
Tolosi, Laura
Rahnenführer, Jörg
Verhaak, Roel
Chiang, Derek
Getz, Gad
Hellmich, Martin
Wolf, Jürgen
Girard, Luc
Peyton, Michael
Weir, Barbara A.
Chen, Tzu-Hsiu
Greulich, Heidi
Barretina, Jordi
Shapiro, Geoffrey I.
Garraway, Levi A.
Gazdar, Adi F.
Minna, John D.
Meyerson, Matthew
Wong, Kwok-Kin
Thomas, Roman K.
2009Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740
Journal Article
Tolosi2011Tolosi, Laura
Lengauer, Thomas
2011Classification with correlated features: unreliability of feature ranking and solutions
In: Bioinformatics [27], 1986-1994
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Tolosi2012thTolosi, Laura2012Finding Regions of Aberrant DNA Copy Number Associated With Tumor Phenotype
Universität des Saarlandes
Thesis - PhD thesis
Trajkovski2004Trajkovski, Igor2004Analysis of protein binding pocket flexibility
Universität des Saarlandes
Thesis - Masters thesis
Verheyen2006Verheyen, Jens
Litau, Elena
Sing, Tobias
Däumer, Martin
Balduin, Melanie
Oette, Mark
Fätkenheuer, Gerd
Rockstroh, Jürgen K.
Schuldenzucker, Ulrike
Hoffmann, Daniel
Pfister, Herbert
Kaiser, Rolf
2006Compensatory mutations at the HIV cleavage sites p7/p1 and p1/p6-gag in therapy-naive and therapy-experienced patients
In: Antiviral Therapy [11], 879-887
Journal Article
Verheyen2008aVerheyen, Jens
Altmann, Andre
Knops, Elena
Schülter, Eugen
Sichtig, Nadine
Reuter, Stefan
Fätkenheuer, Gerd
Pfister, Herbert
Kaiser, Rolf
2008Relevance of HIV gag cleavage site mutations in failures of protease inhibitor therapies
In: Antiviral Therapy, A53
Poster
Volkamer2006aVolkamer, Andrea2005Attachment IconImplementation of a method to filter
out compounds with toxic, reactive
and unsuitable functional groups
Universität des Saarlandes
Thesis - Bachelor thesis
Volkamer2007Volkamer, Andrea2007Automated generation of pharmacophore type constraints to improve FlexX docking
Universität des Saarlandes
Thesis - Masters thesis
vonOehsen2003von Öhsen, Niklas
Sommer, Ingolf
Zimmer, Ralf
2003Profile-Profile Alignment: A Powerful Tool For Protein Structure Prediction
In: Pacific Symposium on Biocomputing, PSB 2003, 252-263
Proceedings Article
Weimann2009aWeimann, Aaron2009Using multidimensional Scaling for visualizing similarities of proteins
Universität des Saarlandes
Thesis - Bachelor thesis
Weimann2011aWeimann, Aaron2011Functional Profiling in Metagenomics
Universität des Saarlandes
Thesis - Masters thesis
Weinhold2006Weinhold, Nils2006Inference of Protein Function based on Functionally Conserved Regions in Sequence and Structure Space
Universität des Saarlandes
Thesis - Masters thesis
Weinhold2008Weinhold, Nils
Sander, Oliver
Domingues, Francisco S.
Lengauer, Thomas
Sommer, Ingolf
2008Attachment IconLocal function conservation in sequence and structure space
In: PLoS Computational Biology [4], e1000105
Journal Article
Weiss2005aWeiss, Julia2005Attachment IconGenerating Frequency Profiles from Multiple
Structure Alignments
Universität des Saarlandes
Thesis - Bachelor thesis
Weisser2007Weisser, Hendrik2007Estimating the local variance of protein structure models
Universität des Saarlandes
Thesis - Masters thesis
Weisser2010aWeisser, Hendrik
Altmann, André
Sierra, Saleta
Incardona, Francesca
Struck, Daniel
Sönnerborg, Anders
Kaiser, Rolf
Zazzi, Maurizio
Tschochner, Monika
Walter, Hauke
Lengauer, Thomas
2010Only Slight Impact of Predicted Replicative Capacity for Therapy Response Prediction
In: PLoSOne [5], e9044,1-e9044,10
Electronic Journal Article
Welker2011Welker, M.-W.
Welsch, Christoph
Ochs, D.
Hofmann, W. P.
Herrmann, E.
Piiper, A.
Hartmann, R. W.
Zeuzem, S.
Sarrazin, C.
Kronenberger, Bernd
2011Comparison of Envelope 2 CD81 binding regions in PBMC-derived versus serum-derived hepatitis C virus isolates: higher conservation of CD81 region 2 in PBMC isolates
In: Journal of Viral Hepatitis [18], 181-192
Journal Article
Welsch2011Hofmann, Wolf Peter
Chung, Tje Lin
Osbahr, Carola
Susser, Simone
Karey, Ursel
Mihm, Ulrike
Welsch, Christoph
Lötsch, Jörn
Sarrazin, Christoph
Zeuzem, Stefan
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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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