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MPI-INF D3 Publications , MPG Format, generated: Friday, 25. July 2014

Scientific Publications for 2013

Dietz, J., S.-E. Schelhorn, D. Fitting, U. Mihm, S. Susser, M.-.W. Welker, C. Füller, M. Däumer, G. Teuber, H. Wedemeyer, T. Berg, T. Lengauer, S. Z., E. Herrmann and C. Sarrazin: Deep sequencing reveals mutagenic effects of ribavirin during monotherapy of hcv genotype 1-infected patients. Journal of Virology 87, 6172-6181 (2013).

Ellinghaus, D., H. Zhang, S. Zeissig, S. Lipinski, A. Till, T. Jiang, B. Stade, Y. Bromberg, E. Ellinghaus, A. Keller, M.A. Rivas, J. Skieceviciene, N.T. Doncheva, X. Liu, Q. Liu, F. Jiang, M. Forster, G. Mayr, M. Albrecht, R. Häsler, B.O. Boehm, J. Goodall, C.R. Berzuini, J. Lee, V. Andersen, U. Vogel, L. Kupcinskas, M. Kayser, M. Krawczak, S. Nikolaus, R.K. Weersma, C.Y. Ponsioen, M. Sans, C. Wijmenga, D.P. Strachan, W.L. McArdle, S. Vermeire, P. Rutgeerts, J.D. Sanderson, C.G. Mathew, M.H. Vatn, J. Wang, M.M. Nöthen, R.H. Duerr, C. Büning, S. Brand, J. Glas, J. Winkelmann, T. Illig, A. Latiano, V. Annese, J. Halfvarson, M. D'Amato, M.J. Daly, M. Nothnagel, T.H. Karlsen, S. Subramani, P. Rosenstiel, S. Schreiber, M. Parkes and A. Franke: Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies. Gastroenterology 145, 339-347 (2013).

Hauschild, A.-C., J.I. Baumbach and J. Baumbach: Paving the way for automated clinical breath analysis and biomarker detection.

Kacprowski, T., N.T. Doncheva and M. Albrecht: NetworkPrioritizer: a versatile tool for network-based prioritization of candidate disease genes or other molecules. Bioinformatics 29, 1471-1473 (2013).

Kalaghatgi, P. and G. Lawyer: Inter-country mixing in hiv transmission clusters: a pan-european phylodynamics study.

Kalinina, O., N. Pfeifer and T. Lengauer: Modelling 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. Retrovirology 10, 130 (2013).

Le, H.-S., M.H. Schulz, B.M. McCauley, V.F. Hinman and Z. Bar-Joseph: Probabilistic error correction for RNA sequencing. Nucleic Acids Researcb 41, e109 (2013).

Liu, J.Z., J.R. Hov, T. Folseraas, E. Ellinghaus, S.M. Rushbrook, N.T. Doncheva, O.A. Andreassen, R.K. Weersma, T.J. Weismuller, B. Eksteen, P. Invernizzi, G.M. Hirschfield, D.N. Gotthardt, A. Pares, D. Ellinghaus, T. Shah, B.D. Juran, P. Milkiewicz, C. Rust, C. Schramm, T. Muller, B. Srivastava, G. Dalekos, M.M. Nothen, S. Herms, J. Winkelmann, M. Mitrovic, F. Braun, C.Y. Ponsioen, P.J.P. Croucher, M. Sterneck, A. Teufel, A.L. Mason, J. Saarela, V. Leppa, R. Dorfman, D. Alvaro, A. Floreani, S. Onengut-Gumuscu, S.S. Rich, W.K. Thompson, A.J. Schork, S. Naess, I. Thomsen, G. Mayr, I.R. Konig, K. Hveem, I. Cleynen, J. Gutierrez-Achury, I. Ricano-Ponce, D. van Heel, E. Bjornsson, R.N. Sandford, P.R. Durie, E. Melum, M.H. Vatn, M.S. Silverberg, R.H. Duerr, L. Padyukov, S. Brand, M. Sans, V. Annese, J.-P. Achkar, K.M. Boberg, H.-U. Marschall, O. Chazouilleres, C.L. Bowlus, C. Wijmenga, E. Schrumpf, S. Vermeire, M. Albrecht, The UK-PSCSC Consortium, The International IBD Genetics Consortium, J.D. Rioux, G. Alexander, A. Bergquist, J. Cho, S. Schreiber, M.P. Manns, M. Farkkila, A.M. Dale, R.W. Chapman, K.N. Lazaridis, The International PSC Study Group, A. Franke, C.A. Anderson and T.H. Karlsen: Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis. Nature Genetics 45, 670-677 (2013).

Pfeifer, N. and T. Lengauer: Association between hiv-1 coreceptor usage and resistance to some broadly neutralizing antibodies.

Pironti, A.: HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure. Infection, Genetics and Evolution 19, 349–360 (2013).

Pironti, A., T. Lengauer and N. Pfeifer: Effects of sequencing errors on geno2pheno[coreceptor] predictions.

- In silico analysis of the effects of sequencing errors on geno2pheno[coreceptor].

Radivojac, P., W.T. Clark, T.R. Oron, A.M. Schnoes, T. Wittkop, A. Sokolov, K. Graim, C. Funk, K. Verspoor, A. Ben-Hur, G. Pandey, J.M. Yunes, A.S. Talwalkar, S. Repo, M.L. Souza, D. Piovesan, R. Casadio, Z. Wang, J. Cheng, H. Fang, J. Gough, P. Koskinen, P. T\"{o}r\"{o}nen, J. Nokso-Koivisto, L. Holm, D. Cozzetto, D.W.A. Buchan, K. Bryson, D.T. Jones, B. Limaye, H. Inamdar, A. Datta, S.K. Manjari, R. Joshi, M. Chitale, D. Kihara, A.M. Lisewski, S. Erdin, E. Venner, O. Lichtarge, R. Rentzsch, H. Yang, A.E. Romero, P. Bhat, A. Paccanaro, T. Hamp, R. Ka\ss ner, S. Seemayer, E. Vicedo, C. Schaefer, D. Achten, F. Auer, A. Boehm, T. Braun, M. Hecht, M. Heron, P. H\"{o}nigschmid, T.A. Hopf, S. Kaufmann, M. Kiening, D. Krompass, C. Landerer, Y. Mahlich, M. Roos, J. Bj\"{o}rne, T. Salakoski, A. Wong, H. Shatkay, F. Gatzmann, I. Sommer, M.N. Wass, M.J.E. Sternberg, N. Skunca, F. Supek, M. Bo\v{s}njak, P. Panov, S. D\v{z}eroski, T. Smuc, Y.A.I. Kourmpetis, A.D.J. van Dijk, C.J.F.T. Braak, Y. Zhou, Q. Gong, X. Dong, W. Tian, M. Falda, P. Fontana, E. Lavezzo, B. {Di Camillo}, S. Toppo, L. Lan, N. Djuric, Y. Guo, S. Vucetic, A. Bairoch, M. Linial, P.C. Babbitt, S.E. Brenner, C. Orengo, B. Rost, S.D. Mooney and I. Friedberg: A large-scale evaluation of computational protein function prediction. Nature Methods 10, 221-227 (2013).

Röttger, R., P. Kalaghatgi, P. Sun, S. de Castro Soares, V. Azevedo, T. Wittkop and J. Baumbach: Density parameter estimation for finding clusters of homologous proteins - tracing actinobacterial pathogenicity life styles. Bioinformatics 29, 215-222 (2013).

Sandoval, J., J. Mendez-Gonzales, E. Nadal, G. Chen, F.J. Carmona, S. Sayols, S. Moran, H. Heyn, M. Vizoso, A. Gomez, M. Sanchez-Cespedes, Y. Assenov, F. Müller, C. Bock, M. Taron, J. Mora, L.A. Muscarella, T. Liloglou, M. Davies, M. Pollan, M.J. Pajares, W. Torre, L.M. Montuenga, E. Brambilla, J.K. Field, L. Roz, M. Lo Iacono, G.V. Scagliotti, R. Rosell, D.G. Beer and M. Esteller: A prognostic dna methylation signature for stage I non-small-cell lung cancer. Journal of Clinical Oncology 31, 4140-4147 (2013).

Schelhorn, S.-E., M. Fischer, L. Tolosi, J. Altmüller, P. Nürnberg, H. Pfister, T. Lengauer and F. Berthold: Sensitive detection of viral transcripts in human tumor transcriptomes. PLOS Computational Biology 9, xx (2013).

Schulz, M.H., K.V. Pandit, C.L. Lino Cardenas, N. Ambalavanan, N. Kaminski and Z. Bar-Joseph: Reconstructing dynamic microRNA-regulated interaction networks. Proceedings of the National Academy of Sciences of the United States 110, 15686–15691 (2013).

Simmer, F., A.B. Brinkmann, Y. Assenov, F. Matarese, A. Kaan, T. Lengauer, C. Bock, V. Colantuoni, L. Altucci and H.G. Stunnenberg: Comparative genome-wide dna methylation analysis of colorectal tumor and matched human tissue. Epigenetics 7, 1355-1367 (2013).

Steijger, T., J. Abril, P. Engström, F. Kokocinski, J. Abril, M. Akerman, T. Alioto, G. Ambrosini, S. Antonarakis, J. Behr, R. Bohnert, P. Bucher, N. Cloonan, T. Derrien, S. Djebali, J. Du, S. Dudoit, P. Engström, M. Gerstein, T. Gingeras, D. Gonzalez, S. Grimmond, L. Habegger, C. Iseli, G. Jean, A. Kahles, F. Kokocinski, J. Lagarde, J. Leng, G. Lefebvre, S. Lewis, A. Mortazavi, P. Niermann, G. Rätsch, A. Reymond, P. Ribeca, H. Richard, J. Rougemont, J. Rozowsky, M. Sammeth, A. Sboner, M.H. Schulz, S. Searle, N. Solorzano, V. Solovyev, M. Stanke, T. Steijger, B. Stevenson, H. Stockinger, A. Valsesia, D. Weese, S. White, B. Wold, J. Wu, T. Wu, G. Zeller, D. Zerbino, M. Zhang, T. Hubbard, R. Guigó, J. Harrow and P. Bertone: Assessment of transcript reconstruction methods for RNA-seq. Nature Methods 10, 1177-84 (2013).

Tolosi, L., J. Theißen, K. Halachev, B. Hero, F. Berthold and T. Lengauer: A method for finding consensus breakpoints in the cancer genome from copy number data. Bioinformatics 29, 1793-1800 (2013).

Zanon, A., A. Rakovic, H. Blankenburg, N.T. Doncheva, C. Schwienbacher, A. Serafin, A. Alexa, C.X. Weichenberger, M. Albrecht, C. Klein, A.A. Hicks, P.P. Pramstaller, F.S. Domingues and I. Pichler: Profiling of parkin-binding partners using tandem affinity purification. PLoS ONE 8, 1-17 (2013).

Ziller, M.J., H. Gu, F. Müller, J. Donaghey, L.T.-.Y. Tsai, O. Kohlbacher, P.L. De Jager, E.D. Rosen, D.A. Bennett, B.E. Bernstein, A. Gnirke and A. Meissner: Charting a dynamic dna methylation landscape of the human genome. Nature 500, 477–481 (2013).

Publikationen im Internet

Beggel, B. and T. Lengauer: Inferring short-range linkage information from sequencing chromatograms. PLoS One [***Warning: Volume missing!], [***Warning: Pages missing!] (2013).

Hauschild, A.-C., D. Kopczynski, M. D'Addario, J.I. Baumbach, S. Rahmann and J. Baumbach: Peak detection method evaluation for ion mobility spectrometry by using machine learning approaches. Metabolites 3, 277-293 (2013).

Schneider, T., A.-C. Hauschild, J.I. Baumbach and J. Baumbach: An integrative clinical database and diagnostics platform for biomarker identification and analysis in ion mobility spectra of human exhaled air. Journal of Integrative Bioinformatics 10, [***Warning: Pages missing!] (2013).

Doctoral dissertation

Patil, K.R.: Genome signature based sequence comparison for taxonomic assignment and tree inference. Universität des Saarlandes 2013.