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MPI-INF D3 Publications , MPG Format, generated: Wednesday, 23. April 2014

Scientific Publications for 2012

Adams, D., L. Altucci, S.E. Antonarakis, J. Ballesteros, S. Beck, A. Bird, C. Bock, B. Boehm, E. Campo, A. Caricasole, F. Dahl, E.T. Dermitzakis, T. Enver, M. Esteller, X. Estivill, A. Ferguson-Smith, J. Fitzgibbon, P. Flicek, C. Giehl, T. Graf, F. Grosveld, R. Guigó, I. Gut, K. Helin, J. Jarvius, R. Küppers, H. Lehrach, T. Lengauer, Å. Lernmark, D. Leslie, M. Loeffler, E. Macintyre, A. Mai, J.H.A. Martens, S. Minucci, W.H. Ouwehand, P.G. Pelicci, H. Pendeville, B. Porse, V. Rakyan, W. Reik, M. Schrappe, D. Schübeler, M. Seifert, R. Siebert, D. Simmons, N. Soranzo, S. Spicuglia, M. Stratton, H.G. Stunnenberg, A. Tanay, D. Torrents, A. Valencia, E. Vellenga, M. Vingron, J. Walter and S. Willcocks: BLUEPRINT to decode the epigenetic signature written in blood. Nature Biotechnology 30, 224-226 (2012).

Alcaraz, N., H. Kucuk, J. Weile, A. Wipat and J. Baumbach: KeyPathwayMiner - detecting case-specific biological pathways by using expression data. Internet Mathematics 7, 299-313 (2012).

Baumbach, J.: Integrative computational biology. Integrative Biology 4, 713-714 (2012).

Beggel, B., M. Neumann-Fraune, M. Doering, G. Lawyer, R. Kaiser, J. Verheyen and T. Lengauer: Genotyping hepatitis B virus dual infections using population-based sequence data. Journal of General Virology 9, 1899-1907 (2012).

Bhattacharyya, M., L. Feuerbach, T. Bhadra and S. Bandyopadhyay: MicroRNA transcription start site prediction with multi-objective feature selection. Statistical Applications in Genetics and Molecular Biology 11, 6.1-6.25 (2012).

Bock, C.: Analysing and interpreting DNA methylation data. Nature Reviews Genetics 13, 705-719 (2012).

Bock, C. and T. Lengauer: Epigenom-Karten erstellen und nutzen. BIOspektrum 18, 138-141 (2012).

- Managing drug resistance in cancer: lessons from HIV therapy. Nature Reviews Cancer 12, 494-501 (2012).

Bogojeska, J. and T. Lengauer: Hierarchical Bayes model for predicting effectiveness of HIV combination therapies. Statistical Applications in Genetics and Molecular Biology 11, 11.1-11.19 (2012).

Bogojeska, J., D. Stöckel, M. Zazzi, R. Kaiser, F. Incardona, M. Rosen-Zvi and T. Lengauer: History-alignment models for bias-aware prediction of virological response to HIV combination therapy. In: Proc. Fifteenth Int. Conf. on Artificial Intelligence and Statistics (AISTATS 2012), JMLR Workshop and Conference Proceedings 22, (Eds.) N. Lawrence, M. Girolami. Journal of Machine Learning Research, Brookline 2012, 118-126.

Bozek, K., M. Eckhardt, S. Sierra, R. Kaiser, H.-G. Kräusslich, B. Müller and T. Lengauer: An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data. Retrovirology 9, 60.1-60.15 (2012).

Calvanese, V., A.F. Fernandez, R.G. Urdinguio, B. Suarez-Álvarez, C. Mangas, V. Pérez-García, C. Bueno, R. Montes, V. Ramos-Mejía, P. Martínez-Camblor, C. Ferrero, Y. Assenov, C. Bock, P. Menendez, A.C. Carrera, C. Lopez-Larrea and M.F. Fraga: A promoter DNA demethylation landscape of human hematopoietic differentiation. Nucleic Acids Research 40, 116-131 (2012).

Dietzen, M., E. Zotenko, A. Hildebrandt and T. Lengauer: On the applicability of elastic network normal modes in small-molecule docking. Journal of Chemical Information and Modeling 52, 844-856 (2012).

Doncheva, N.T., Y. Assenov, F.S. Domingues and M. Albrecht: Topological analysis and interactive visualization of biological networks and protein structures. Nature Protocols 7, 670-685 (2012).

Doncheva, N.T., T. Kacprowski and M. Albrecht: Recent approaches to the prioritization of candidate disease genes. Wiley Interdisciplinary Reviews: Systems Biology and Medicine 4, 429-442 (2012).

Emig, D., H. Blankenburg, F. Ramírez and M. Albrecht: Functional characterization of human genes from exon expression and RNA interference results. In: Bioinformatics and Drug Discovery, Methods in Molecular Biolog 910, (Ed.) R.S. Larson. Humana Press, New York 2012, 33-53.

Fernandez, A.F., Y. Assenov, J.I. Martin-Subero, B. Balint, R. Siebert, H. Taniguchi, H. Yamamoto, M. Hidalgo, A.-C. Tan, O. Galm, I. Ferrer, M. Sanchez-Cespedes, A. Villanueva, J. Carmona, J.V. Sanchez-Mut, M. Berdasco, V. Moreno, G. Capella, D. Monk, E. Ballestar, S. Ropero, R. Martinez, M. Sanchez-Carbayo, F. Prosper, X. Agirre, M.F. Fraga, O. Gran˜a, L. Perez-Jurado, J. Mora, S. Puig, J. Prat, L. Badimon, A.A. Puca, S.J. Meltzer, T. Lengauer, J. Bridgewater, C. Bock and M. Esteller: A DNA methylation fingerprint of 1628 human samples. Genome Research 22, 407-419 (2012).

Feuerbach, L., K. Halachev, Y. Assenov, F. Mueller, C. Bock and T. Lengauer: Analyzing epigenome data in context of genome evolution and human diseases. In: Evolutionary Genomics : Statistical and Computational Methods, Volume 2, Methods in Molecular Biology 856, (Ed.) M. Anisimova. Springer, New York 2012, 431-467.

Garai, Á., A. Zeke, G. Gógl, I. Töro, F. Fördos, H. Blankenburg, T. Bárkai, J. Varga, A. Alexa, D. Emig, M. Albrecht and A. Reményi: Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove. Science Signaling 5, ra74,1-ra74,14 (2012).

Halachev, K., H. Bast, F. Albrecht, T. Lengauer and C. Bock: EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biology 13, R96,1-R96,14 (2012).

Heger, E., A. Thielen, R. Gilles, M. Obermeier, T. Lengauer, R. Kaiser and S. Trapp: APOBEC3G/F a one possible driving source for co-receptor switch of the human immunodeficiency virus-1. Medical Microbiology and Immunology 201, 7-16 (2012).

Lawyer, G., E. Schülter, R. Kaiser, S. Reuter, M. Oette and T. Lengauer: Endogenous or exogenous spreading of HIV-1 in Nordrhein-Westfalen, Germany, investigated by phylodynamic analysis of the RESINA Study cohort. Medical Microbiology and Immunology 201, 259-269 (2012).

Lengauer, T.: Bioinformatical assistance of selecting Anti-HIV therapies: Where do we stand?. Intervirology 55, 108-112 (2012).

Lengauer, T., M. Albrecht and F.S. Domingues: Computational biology. In: Encyclopedia of Molecular Cell Biology and Molecular Medicine, (Ed.) R.A. Meyers. Wiley-VCH, Weinheim 2012, 1-71.

Lengauer, T. and C. Bock: Managing drug resistance in cancer: lessons from hiv therapy. Nature Reviews Cancer 12, 494-501 (2012).

Mekhubad, S., C. Bock, A.S. de Boer, E. Kiskinis, A. Meissner and K. Eggan: Erosion of dosage compensation impacts human iPSC disease modeling. Cell Stem Cell 10, 595-609 (2012).

Mikeska, T., C. Bock, H. Do and A. Dobrovic: DNA methylation biomarkers in cancer: progress towards clinical implementation. Expert Reviews of Molecular Diagnostics 12, 473-487 (2012).

Obermeier, M., R. Camacho, C. Charpentier, D. Deschamps, J. Eberle, L. Gürtler, J. Ruelle, A. Pironti, F. Brun-Veziet, M. Stürmer and R. Kaiser: HIV2EU: supporting standardized HIV-2 drug resistance interpretation in europe.

Obermeier, M., A. Pironti, T. Berg, P. Braun, M. Däumer, J. Eberle, R. Ehret, R. Kaiser, N. Kleinkauf, K. Korn, C. Kücherer, H. Müller, C. Noah, M. Stürmer, A. Thielen, E. Wolf and H. Walter: HIV-GRADE: A publicly available, rules-based drug resistance interpretation algorithm integrating bioinformatic knowledge. Intervirology 55, 102-107 (2012).

Oette, M., E. Schulter, M. Rosen-Zvi, Y. Peres, M. Zazzi, A. Sonnerborg, D. Struck, A. Altmann and R. Kaiser: Efficacy of antiretroviral therapy switch in HIV-infected patients: A 10-year analysis of the EuResist cohort. Intervirology 55, 160-166 (2012).

Pauling, J., R. Röttger, A. Neuner, H. Salgado, J. Collado-Vides, P. Kalaghatgi, V. Azevedo, A. Tauch, A. Pühler and J. Baumbach: On the trail of EHEC/EAEC - unraveling the gene regulatory networks of human pathogenic escherichia coli bacteria. Integrative Biology 4, 728-733 (2012).

Pauling, J., R. Röttger, A. Tauch, V. Azevedo and J. Baumbach: CoryneRegNet 6.0 - updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Research 40, D610-D614 (2012).

Pfeifer, N. and T. Lengauer: Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data. Bioinformatics 28, i589-i595 (2012).

Pironti, A., T. Lengauer, R. Kaiser, E. Schülter and J. Verheyen: Characterization of HIV-1 Gag subtype C.

Ramírez, F., G. Lawyer and M. Albrecht: Novel search method for the discovery of functional relationships. Bioinformatics 28, 269-276 (2012).

Reppas, A. and G. Lawyer: Low k-shells identify bridge elements critical to disease flow in small-world networks. In: Numerical Analysis and Applied Mathematics (ICNAAM 2012), AIP Conference Proceedings 1479, (Eds.) T. Simos, G. Psihoyios, C. Tsitouras, Z. Anastassi. AIP, New York 2012, 1426-1429.

Reuter, S., M. Oette, R. Kaiser, T. Lengauer, G. Fätkenheuer, J. Rockstroh, H. Knechten and D. Häussinger: Risk factors associated with older age in treatment-naive HIV-positive patients. Intervirology 55, 147-153 (2012).

Rost, B., T. Gaasterland, T. Lengauer, M. Linial, S. Markel, B.J.M. McKay, R. Schneider, P. Horton and J. Kelso: Paving the future: finding suitable ISMB venues. Bioinformatics 28, 2556-2559 (2012).

Röttger, R., U. Rueckert, J. Taubert and J. Baumbach: How little do we actually know? - On the size of gene regulatory networks.. IEEE/ACM transactions on computational biology and bioinformatics 9, 1293-1300 (2012).

Schuelter, E., N. Lübcke, B. Jensen, M. Zazzi, A. Sönnerborg, T. Lengauer, F. Incardona, R. Camacho, J. Schmit, B. Clotet, R. Kaiser and A. Pironti: Etravirine in protease inhibitor-free antiretroviral combination therapies.

Setty, Y.: Multi-scale computational modeling of developmental biology. Bioinformatics 28, 2022-2028 (2012).

Sierra, S., J.N. Dzbowski, A. Pironti, L. Gueney, A. Thielen, S. Reuter, S. Esser, G. Fätkenheuer, T. Lengauer, D. Hider, D. Hoffmann, H. Pfister, B. Jensen and R. Kaiser: Optimisation of baseline genotypic testing for safe and efficient maraviroc administration.

Simmer, F., A.B. Brinkman, Y. Assenov, F. Matarese, A. Kaan, L. Sabatino, A. Villanueva, D. Huertas, M. Esteller, T. Lengauer, C. Bock, V. Colantuoni, L. Altucci and H.G. Stunnenberg: Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues. Epigenetics 7, 1355-1367 (2012).

Thielen, A. and T. Lengauer: Geno2pheno[454]: A web server for the prediction of HIV-1 coreceptor usage from next-generation sequencing data. Intervirology 55, 113-117 (2012).

Welsch, C., S. Schweizer, T. Shimakami, F.S. Domingues, S. Kim, S.M. Lemon and I. Antes: Ketoamide resistance and hepatitis C virus fitness in Val55 variants of the NS3 serine protease. Antimicrobial Agents and Chemotherapy 56, 1907-1915 (2012).

Welsch, C., T. Shimakami, C. Hartmann, Y. Yang, F.S. Domingues, T. Lengauer, S. Zeuzem and S.M. Lemon: Peptidomimetic escape mechanisms arise via genetic diversity in the ligand-binding site of the hepatitis C virus NS3/4A serine protease. Gastroenterology 142, 654-663 (2012).

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 (2012).

Zazzi, M., F. Incardona, M. Rosen-Zvi, M. Prosperi, T. Lengauer, A. Altmann, A. Sonnerborg, T. Lavee, E. Schülter and R. Kaiser: Predicting response to antiretroviral treatment by machine learning: the EuResist project. Intervirology 55, 123-127 (2012).

Publikationen im Internet

Faria, D., A. Schlicker, C. Pesquita, H. Bastos, A.E.N. Ferreira, M. Albrecht and A.O. Falcão: Mining GO annotations for improving annotation consistency. PLoS ONE 7, e40519,1-e40519,7 (2012). Internet: <>

Halachev, K., H. Bast, F. Albrecht, T. Lengauer and C. Bock: EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biology 13, R96,1-R96,14 (2012). Internet: <>

Hauschild, A.-C., J.I. Baumbach and J. Baumbach: Integrated statistical learning of metabolic ion mobility spectrometry profiles for pulmonary disease identification. Genetics and Molecular Research 11, 2733-2744 (2012). Internet: <>

Hauschild, A.-C., T. Schneider, J. Pauling, K. Rupp, M. Jang, J.I. Baumbach and J. Baumbach: Computational methods for metabolomic data analysis of ion mobility spectrometry data - reviewing the state of the art. Metabolites 2, 733-755 (2012). Internet: <>

Kalinina, O.V., H. Oberwinkler, B. Glass, H.-G. Kräusslich, R.B. Russell and J.A.G. Briggs: Computational identification of novel amino-acid interactions in HIV gag via correlated evolution. PLoS ONE 7, e42468,1-e42468,5 (2012). Internet: <>

Röttger, R., C. Kreutzer, T. Duong Vu, T. Wittkop and J. Baumbach: Online transitivity clustering of biological data with missing values. In: German Conf. on Bioinformatics 2012 (GCB 2012), (Eds.) S. Böcker, F. Hufsky, K. Scheubert, J. Schleicher, S. Schuster, OASIcs: OpenAccess Series in Informatics 26. Schloss Dagstuhl / Leizbniz-Zentrum für Informatik, Dagstuhl 2012, 57-68 Internet: <>.

Soares, S.C., V.A.C. Abreu, R.T.J. Ramos, L. Cerdeira, A. Silva, J. Baumbach, E. Trost, A. Tauch, R. Hirata, A.L. Mattos-Guaraldi, A. Miyoshi and V. Azevedo: PIPS: pathogenicity island prediction software. PLoS One 7, e30848,1-e30848,10 (2012). Internet: <>

Bachelor Thesis

Galata, V.: Applying Lasso regression to related cell types for gene network astimation. Universität des Saarlandes 2012.

Klingen, T.: Automatic recombination analysis using Recoo and Mebitoo. Universität des Saarlandes 2012.

Zeidler, M.: Cloudbasierte Analyse von viralen Sequenzdaten der neuesten Generation. Universität des Saarlandes 2012.

Master's thesis

Bader, M.: Clustering epigenetic data using a Dirichlet process prior. Universität des Saarlandes 2012.

Bastys, T.: MAP kinase docking motifs in HIV proteins. Universität des Saarlandes 2012.

Eldarov, N.: Modeling influenza evolution in response to immune system pressure. Universität des Saarlandes 2012.

Kalaghatgi, P.: A phylodynamic study of HIV transmission networks in europe. Universität des Saarlandes 2012.

König, E.: Automatic detection of loss of heterozygosity in cancer. Universität des Saarlandes 2012.

Koser, S.: Reconstructing anecestral methylation states in phylogenetic trees. Universität des Saarlandes 2012.

Müller, J.: Extracting pathways from biological networks incorporating omics data, introducing a webinterface for KeyPathwayMiner. Universität des Saarlandes 2012.

Speicher, N.: Towards the identification of cancer subtypes by integrative clustering of molecular data. Universität des Saarlandes 2012.

Doctoral dissertation

Ramirez, F.: Novel approaches to the integration and analysis of systems biology. Universität des Saarlandes 2012.

Tolosi, L.: Finding regions of aberrant DNA copy number associated with tumor phenotype. Universität des Saarlandes 2012.