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Alcaro, S., C. Alteri, A. Artese, F. Ceccherini-Silberstein, G. Costa, F. Ortuso, F. Forbici, M.M. Santoro, L. Parrotta, P. Flandre, D. Descamps, V. Calvez, A.-G. Marcelin, C.F. Perno, T. Sing and V. Svicher: Docking analysis and resistance evaluation of clinically relevant mutations associated with the HIV-1 nonnucleoside reverse transcriptase inhibitors nevirapine, efavirenz and etravirine. ChemMedChem 6, 2203-2213 (2011).
Aranda, B., H. Blankenburg, S. Kerrien, F.S. Brinkman, A. Ceol, E. Chautard, J.M. Dana, J. De Las Rivas, M. Dumousseau, E. Galeota, A. Gaulton, J. Goll, R.E.W. Hancock, R. Isserlin, R.C. Jimenez, J. Kerssemakers, J. Khadake, D.J. Lynn, M. Michaut, G. O'Kelly, K. Ono, S. Orchard, C. Prieto, S. Razick, O. Rigina, L. Salwinski, M. Simonovic, S. Velankar, A. Winter, G. Wu, G.D. Bader, G. Cesareni, I.M. Donaldson, D. Eisenberg, G.J. Kleywegt, J. Overington, S. Ricard-Blum, M. Tyers, M. Albrecht and H. Hermjakob: PSICQUIC and psiscore: accessing and scoring molecular interactions. Nature Methods 8, 528-529 (2011).
Bleif, S., F. Hannemann, M. Lisurek, J.P. von Kries, J. Zapp, M. Dietzen, I. Antes and R. Bernhardt: Identification of CYP106A2 as a regioselective allylic bacterial diterpene hydroxylase. ChemBioChem 12, 576-582 (2011).
Bock, C., E. Kiskinis, G. Verstappen, H. Gu, G. Boulting, Z.D. Smith, M. Ziller, G.F. Croft, M.W. Amoroso, D.H. Oakley, A. Gnirke, K. Eggan and A. Meissner: Reference maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell 144, 439-452 (2011).
Cerdeira, L.T., A.R. Carneir, R.T.J. Ramos, S.S. de Almeida, V. D'Afonseca, M.P.C. Schneider, J. Baumbach, A. Tauch, J.A. McCulloch, V.A.C. Azevedo and A. Silva: Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis i19 as a case study. Journal of Microbiological Methods 86, 218-223 (2011).
Doncheva, N.T., K. Klein, F.S. Domingues and M. Albrecht: Analyzing and visualizing residue networks of protein structures. Trends in Biochemical Sciences 36, 179-182 (2011).
Emig, D. and M. Albrecht: Tissue-specific proteins and functional implications. Journal of Proteome Research 10, 1893-1903 (2011).
Emig, D., T. Kacprowski and M. Albrecht: Measuring and analyzing tissue specificity of human genes and protein complexes. EURASIP Journal on Bioinformatics and Systems Biology 2011, 5,1-5,6 (2011).
Feuerbach, L., R.B. Lyngso, T. Lengauer and J. Hein: Reconstructing the ancestral germline methylation state of young repeats. Molecular Biology and Evolution 28, 1777-1784 (2011).
Gu, H., Z.D. Smith, C. Bock, P. Boyle, A. Gnirke and A. Meissner: Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nature Protocols 6, 468-481 (2011).
Heger, E., A. Thielen, R. Gilles, M. Obermeier, T. Lengauer, R. Kaiser and S. Trapp: APOBEC3G/F as one possible driving force for co-receptor switch of the human immunodeficiency virus-1. Medical Microbiology and Immunology 201, 7-16 (2011).
Hofmann, W.P., T.L. Chung, C. Osbahr, S. Susser, U. Karey, U. Mihm, C. Welsch, J. Lötsch, C. Sarrazin, S. Zeuzem and E. Herrmann: Impact of ribavirin on HCV replicon RNA decline during treatment with interferon-α and the protease inhibitors boceprevir or telaprevir. Antiviral Therapy 16, 695-704 (2011).
Knoepfel, S., F. Di Giallonardoc, M. Däumer, A. Thielen and K.J. Metzner: In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing. Journal of Virological Methods 71, 329-338 (2011).
Krol, E., J. Blom, J. Winnebald, A. Berhörster, M.J. Barnett, A. Goesmann, J. Baumbach and A. Becker: RhizoRegNet - A database of rhizobial transcription factors and regulatory networks.. Journal of Biotechnology 155, 127-134 (2011).
Kumar, V., P. Sun, J. Vamathevan, Y. Li, K. Ingraham, L. Palmer, J. Huang and J.R. Brown: Comparative genomics of Klebsiella pneumoniae strains with different antibiotic resistance profiles. Antimicrobial Agents and Chemotherapy 55, 4267-4276 (2011).
Lawyer, G., A. Altmann, A. Thielen, M. Zazzi, A. Sönnerborg and T. Lengauer: HIV-1 mutational pathways under multidrug therapy. AIDS Research and Therapy 8, 1-13 (2011).
Lengauer, T.: (Ed.): Computermodelle in der Wissenschaft - zwischen Analyse, Vorhersage und Suggestion. . Wissenschaftliche Verlagsgeselleschaft, Stuttgart 2011, 358 p.
Lutsik, P., L. Feuerbach, J. Arand, T. Lengauer, J. Walter and C. Bock: BiQ analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Research 39, W551-W556 (2011).
Morris, J.H., L. Apeltsin, A.M. Newman, J. Baumbach, T. Wittkop, G. Su, G.D. Bader and T.E. Ferrin: clusterMaker: A multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics 12, 436,1-436,14 (2011).
Nebot, V., M. Ye, M. Albrecht, J.-H. Eom and G. Weikum: DIDO: a disease-determinants ontology from web sources. In: Proc. 20th Int. Conf. on World Wide Web (WWW 2011). ACM, New York 2011, 237-240.
Pironti, A., A. Altmann, J. Büch and T. Lengauer: A computational method for predicting first-line antiretroviral therapy success.
Ramos, R.T.J., A.R. Carneiro, J. Baumbach, V. Azevedo, M.P.C. Schneider and A. Silva: Analysis of quality raw data of second generation sequencers with quality assessment software. BMC Research Notes 4, 130,1-130,6 (2011).
Reiss, S., I. Rebhan, P. Backes, I. Romero-Brey, H. Erfle, P. Matula, L. Kaderali, M. Poenisch, H. Blankenburg, M.-S. Hiet, T. Longerich, S. Diehl, F. Ramírez, T. Balla, K. Rohr, A. Kaul, S. Bühler, R. Pepperkok, T. Lengauer, M. Albrecht, R. Eils, P. Schirmacher, V. Lohmann and R. Bartenschlager: Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host & Microbe 9, 32-45 (2011).
Reuter, S., M. Oette, F.C. Wilhelm, B. Beggel, R. Kaiser, M. Balduin, F. Schweitzer, J. Verheyen, O. Adams, T. Lengauer, G. Faetkenheuer, H. Pfister and D. Haeussinger: Erratum to: prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.. Medical Microbiology and Immunology 200, 51-51 (2011).
- Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve hiv-infected patients. Medical Microbiology and Immunology 200, 39-49 (2011).
Roomp, K. and F.S. Domingues: Predicting interactions between T cell receptors and MHC-peptide complexes. Molecular Immunology 48, 553-562 (2011).
Santos, A.R., M.A. Santos, J. Baumbach, J.A. McCulloch, G.C. Oliveira, A. Silva, A. Miyoshi and V. Azevedo: A singular value decomposition approach for improved taxonomy classification of biological sequences. BMC Genomics 12, S11,1-S11,15 (2011).
Schülter, E., M. Oette, M. Balduin, S. Reuter, J. Rockstroh, G. Fätkenheuer, S. Esser, T. Lengauer, A. Agacfidan, H. Pfister, R. Kaiser and B. Akgul: HIV prevalence and route of transmission in Turkish immigrants living in North-Rhine Westphalia, Germany. Medical Microbiology and Immunology 200, 219-223 (2011).
Seclen, E., V. Soriano, M.M. González, S. Gómez, A. Thielen and E. Poveda: High 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. Journal of Clinical Microbiology 49, 3380-3382 (2011).
Shimakami, T., C. Welsch, D. Yamane, D.R. McGivern, M. Yi, S. Zeuzem and S.M. Lemon: Protease inhibitor-resistant hepatitis C virus mutants with reduced fitness from impaired production of infectious virus. Gastroenterology 140, 667-675 (2011).
Svicher, V., V. Cento, R. Salpini, F. Mercurio, M. Fraune, B. Beggel, Y. Han, C. Gori, L. Wittkop, A. Bertoli, V. Micheli, G. Gubertini, R. Longo, S. Romano, M. Visca, V. Gallinaro, N. Marino, F. Mazzotta, G.M. De Sanctis, H. Fleury, P. Trimoulet, M. Angelico, G. Cappiello, X.X. Zhang, J. Verheyen, F. Ceccherini-Silberstein and C.F. Perno: Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development. Digestive and Liver Disease 43, 975-983 (2011).
Swenson, L.C., T. Mo, W.W.Y. Dong, X. Zhong, C.K. Woods, M.A. Jensen, A. Thielen, D. Chapman, M. Lewis, I. James, J. Heera, H. Valdez and P.R. Harrigan: Deep sequencing to infer HIV-1 co-receptor usage: Application to three clinical trials of maraviroc in treatment-experienced patients. The Journal of Infectious Diseases 203, 237-245 (2011).
Swenson, L.C., T. Mo, W.W. Dong, X. Zhong, C.K. Woods, A. Thielen, M.A. Jensen, D.J. Knapp, D. Chapman, M. Lewis, I. James, J. Heera, H. Valdez and P.R. Harrigan: Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc.. Clinical Infectious Diseases 53, 732-742 (2011).
Thielen, A., T. Lengauer, L.C. Swenson, W.W.Y. Dong, R.A. McGovern, M. Lewis, I. James, J. Heera, H. Valdez and P.R. Harrigan: Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially. Antiviral Therapy 16, 319-328 (2011).
Tolosi, L. and T. Lengauer: Classification with correlated features: unreliability of feature ranking and solutions. Bioinformatics 27, 1986-1994 (2011).
Welker, M.-.W., C. Welsch, D. Ochs, W.P. Hofmann, E. Herrmann, A. Piiper, R.W. Hartmann, S. Zeuzem, C. Sarrazin and B. Kronenberger: Comparison 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. Journal of Viral Hepatitis 18, 181-192 (2011).
Wittkop, T., D. Emig, A. Truss, M. Albrecht, S. Böcker and J. Baumbach: Comprehensive cluster analysis with Transitivity Clustering. Nature Protocols 6, 285-295 (2011).
Wittkop, T., S. Rahmann, R. Roettger, S. Boecker and J. Baumbach: Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis. Internet Mathematics 7, 255-273 (2011).
Xi, Y., C. Bock, F. Müller, D. Sun, A. Meissner and W. Li: RRBSMAP: A fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. Bioinformatics 28, 430-432 (2011).
Yamanishi, Y., E. Pauwels, H. Saigo and V. Stovent: Extracting sets of chemical substructures and protein domains governing drug-target interactions. Journal of Chemical Information and Modeling 51, 1183-1194 (2011).
Zacharek, S.J., C.M. Fillmore, A.N. Lau, D.W. Gludish, a. Chou, J.W.K. Ho, R. Zamponi, R. Gazit, C. Bock, N. Jäger, Z.D. Smith, T.-m. Kim, A.H. Saunders, J. Wong, J.-H. Lee, R.R. Roach, D.J. Rossi, A. Meissner, A.A. Gimelbrant, P.J. Park and C.F. Kim: Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci. Cell Stem Cell 9, 272-280 (2011).
Zazzi, M., R. Kaiser, A. Sönnerborg, D. Struck, A. Altmann, M. Prosperi, M. Rosen-Zvi, A. Petroczi, Y. Peres, E. Schülter, C.A. Boucher, F. Brun-Vezinet, R. Harrigan, L. Morris, M. Obermeier, C.-.F. Perno, P. Phanuphak, D. Pillay, R.W. Shafer, A.-.M. Vandamme, K. Van Laethem, A. Wensing, T. Lengauer and F. Incardona: Prediction of response to antiretroviral therapy by human experts and by the EuResist data-driven expert system (the EVE study). HIV Medicine 12, 211-218 (2011).
Bogojeska, J.: History distribution matching method for predicting effectiveness of HIV combination therapies. In: Neural Information Processing Systems (NIPS 2011), (Eds.) J. Shawe-Taylor, R.S. Zemel, P. Bartlett, F. Pereira, K.Q. Weinberger, Advances in Neural Information Processing Systems 24. Neural Information Processing Systems Foundation, [s.l.] 2011, 424-432 Internet: <http://books.nips.cc/papers/files/nips24/NIPS2011_0316.pdf>.
Codoner, F., C. Pou, A. Thielen, F. García, R. Delgado, D. Dalmau, M. Álvarez-Tejado, L. Ruiz, B. Clotet and R. Paredes: Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects. PLoS One 6, e19461,1-e19461,5 (2011). Internet: <http://dx.doi.org/10.1371/journal.pone.0019461>
Däumer, M., R. Kaiser, R. Klein, T. Lengauer, B. Thiele and A. Thielen: Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis. BMC Medical Informatics and Decision Making 11, 30,1-30,8 (2011). Internet: <http://dx.doi.org/10.1186/1472-6947-11-30>
Ebrahimi, M., A. Lakizadeh, E. Agha-Golzadeh and M. Ebrahimi: Prediction of thermostability from amino acid attributes by combination of clustering with attribute weighting: A new vista in engineering enzymes. PLoS One 6, e23146,1-e23146,11 (2011). Internet: <http://dx.doi.org/10.1371/journal.pone.0023146>
Emig, D., O. Sander, G. Mayr and M. Albrecht: Structure collisions between interacting proteins. PLoS ONE 6, e19581,1-e19581,7 (2011). Internet: <http://dx.doi.org/10.1371/journal.pone.0019581>
Ruiz, J.C., V. D'Afonseca, A. Silva, A. Ali, A.C. Pinto, A.R. Santos, A.A.M.C. Rocha, D.O. Lopes, F.A. Dorella, L.G.C. Pacheco, M.P. Costa, M.Z. Turk, N. Seyffert, P.M.R.O. Moraes, S.C. Soares, S.S. Almeida, T.L.P. Castro, V.A.C. Abreu, E. Trost, J. Baumbach, A. Tauch, M.P.C. Schneider, J. McCulloch, L.T. Cerdeira, R.T.J. Ramos, A. Zerlotini, A. Dominitini, D.M. Resende, E.M. Coser, L.M. Oliveira, A.L. Pedrosa, C.U. Vieira, C.T. Guimaraes, D.C. Bartholomeu, D.M. Oliveira, F.R. Santos, E.M. Rabelo, F.P. Lobo, G.R. Franco, A.F. Costa, I.M. Castro, S.R. Dias, J.A. Ferro, J.M. Ortega, L.V. Paiva, L.R. Goulart, J.F. Almeida, M.I. Ferro, N.P. Carneiro, P.R.K. Falcao, P. Grynberg, S.M.R. Teixeira, S. Brommonschenkel, S.C. Oliveira, R. Meyer, R.J. Moore, A. Miyoshi, G.C. Oliveira and V. Azevedo: Evidence for reductive genome evolution and lateral acquisition of virulence functions in two corynebacterium pseudotuberculosis strains. PLoS One 6, e18551 (2011). Internet: <http://dx.doi.org/10.1016/j.jbiotec.2010.11.004>
Saigo, H., A. Altmann, J. Bogojeska, F. Müller, S. Nowozin and T. Lengauer: Learning from past treatments and their outcome improves prediction of in vivo response to anti-HIV therapy. Statistical Applications in Genetics and Molecular Biology 10, 1-32 (2011). Internet: <http://dx.doi.org/10.2202/1544-6115.1604>
Schelhorn, S.-E., J. Mestre, E. Zotenko and M. Albrecht: Inferring physical protein contacts from large-scale purification data of protein complexes. Molecular & Cellular Proteomics 10, M110.004929,1-M110.004929,15 (2011). Internet: <http://dx.doi.org/10.1074/mcp.M110.004929>
Sierra, S., R. Kaiser, N. Lübke, A. Thielen, E. Schuelter, E. Heger, M. Däumer, S. Reuter, S. Esser, G. Fätkenheuer, H. Pfister, M. Oette and T. Lengauer: Prediction of HIV-1 coreceptor usage (tropism) by sequence analysis using a genotypic approach. Journal of Visualized Experiments 58, e3264,1-e3264,9 (2011). Internet: <http://www.jove.com/video/3264/>
Ziller, M.J., F. Müller, J. Liao, Y. Zhang, H. Gu, C. Bock, P. Boyle, C.B. Epstein, B.E. Bernstein, T. Lengauer, A. Gnirke and A. Meissner: Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genetics 17, e1002389,1-e1002389,15 (2011). Internet: <http://dx.doi.org/10.1371/journal.pgen.1002389>
Döring, M.: Web implementation of the HBV dual infection model. Universität des Saarlandes 2011.
Junge, A.: Unsupervised dissection of cancer types based on genomic, epigenomic and transciptomic features. Universität des Saarlandes 2011.
Reuter, K.: Estimating and using the uncertainty in the phenotypic resistance assay of the hepatitis B virus to improve IC-50 prediction from genotype. Universität des Saarlandes 2011.
Hauschild, A.-C.: Modeling HIV neutralization. Universität des Saarlandes 2011.
Hoinka, J.-M.: Finding the hairpin in the haystack: Towards an high throughput in silico pipeline for aptamer motif identification using SELEX data. Universität des Saarlandes 2011.
Ivanova, V.: Comparison of methods for discovering genomic aberrations relevant for cancer. Universität des Saarlandes 2011.
Jing, C.: A comprehensive analysis of the illumina infinium assay. Universität des Saarlandes 2011.
Kacprowski, T.: Disease gene prioritization by combining network information and functional knowledge. Universität des Saarlandes 2011.
Weimann, A.: Functional profiling in metagenomics. Universität des Saarlandes 2011.
Bogojeska, J.: Statistical learning methods for bias-aware HIV therapy screening. Universität des Saarlandes 2011.
Bozek, K.: Analysis of HIV-host interaction on different scales.. Universität des Saarlandes 2011.
Emig, D.: Novel analysis approaches to context-dependent molecular networks. Universität des Saarlandes 2011.
Kunert, L.: Maximal common subgraph DAGs: Theory and application to virtual screening in drug development. Universität des Saarlandes 2011.
Thielen, A.: Genotypic analysis of HIV-1 coreceptor usage. Universität des Saarlandes 2011.