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Number of items: 24.

Singer, Jochen; Ruscheweyh, Hans-Joachim; Hofmann, Ariane L; Thurnherr, Thomas; Singer, Franziska; Toussaint, Nora C; Ng, Charlotte K Y; Piscuoglio, Salvatore; Beisel, Christian; Christofori, Gerhard; Dummer, Reinhard; Hall, Michael N; Krek, Wilhelm; Levesque, Mitchell; Manz, Markus G; Moch, Holger; Papassotiropoulos, Andreas; Stekhoven, Daniel J; Wild, Peter; Wüst, Thomas; Rinn, Bernd; Beerenwinkel, Niko (2018). NGS-pipe: a flexible, easily extendable, and highly configurable framework for NGS analysis. Bioinformatics, 34(1):107-108.

Prakash, Meher K; Lang, Brian; Heinrich, Henriette; Valli, Piero V; Bauerfeind, Peter; Sonnenberg, Amnon; Beerenwinkel, Niko; Misselwitz, Benjamin (2017). CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies. BMC Medical Informatics and Decision Making, 17(1):80.

Hofmann, Ariane L; Behr, Jonas; Singer, Jochen; Kuipers, Jack; Beisel, Christian; Schraml, Peter; Moch, Holger; Beerenwinkel, Niko (2017). Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. BMC Bioinformatics, 18(1):8.

Montazeri, Hesam; Kuipers, Jack; Kouyos, Roger; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Günthard, Huldrych F; Beerenwinkel, Niko (2016). Large-scale inference of conjunctive Bayesian networks. Bioinformatics, 32(17):i727-i735.

Seifert, David; Di Giallonardo, Francesca; Töpfer, Armin; Singer, Jochen; Schmutz, Stefan; Günthard, Huldrych F; Beerenwinkel, Niko; Metzner, Karin J (2016). A comprehensive analysis of primer IDs to study heterogeneous HIV-1 populations. Journal of Molecular Biology, 428(1):238-250.

Andritschke, Daniel; Dilling, Sabrina; Emmenlauer, Mario; Welz, Tobias; Schmich, Fabian; Misselwitz, Benjamin; Rämö, Pauli; Rottner, Klemens; Kerkhoff, Eugen; Wada, Teiji; Penninger, Josef M; Beerenwinkel, Niko; Horvath, Peter; Dehio, Christoph; Hardt, Wolf-Dietrich (2016). A genome-wide siRNA screen implicates Spire1/2 in SipA-driven salmonella typhimurium host cell invasion. PLoS ONE, 11(9):e0161965.

Erzinger, Melanie M; Bovet, Cédric; Hecht, Katrin M; Senger, Sabine; Winiker, Pascale; Sobotzki, Nadine; Cristea, Simona; Beerenwinkel, Niko; Shay, Jerry W; Marra, Giancarlo; Wollscheid, Bernd; Sturla, Shana J (2016). Sulforaphane preconditioning sensitizes human colon cancer cells towards the bioreductive anticancer prodrug PR-104A. PLoS ONE, 11(3):e0150219.

Levesque, Mitchell P; Dummer, Reinhard; Beerenwinkel, Niko (2015). Perturbing resistance: a network perspective. Pigment Cell & Melanoma Research, 29(1):5-7.

Montazeri, Hesam; Günthard, Huldrych F; Yang, Wan-Lin; Kouyos, Roger; Beerenwinkel, Niko (2015). Estimating the dynamics and dependencies of accumulating mutations with applications to HIV drug resistance. Biostatistics, 16(4):713-726.

Siebourg-Polster, Juliane; Mudrak, Daria; Emmenlauer, Mario; Rämö, Pauli; Dehio, Christoph; Greber, Urs; Fröhlich, Holger; Beerenwinkel, Niko (2015). NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation. PLoS Computational Biology, 11(4):e1004078.

Seifert, David; Di Giallonardo, Francesca; Metzner, Karin J; Günthard, Huldrych F; Beerenwinkel, Niko (2015). A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory. Genetics, 199(1):191-203.

Vongrad, Valentina; Imig, Jochen; Mohammadi, Pejman; Kishore, Shivendra; Jaskiewicz, Lukasz; Hall, Jonathan; Günthard, Huldrych F; Beerenwinkel, Niko; Metzner, Karin J (2015). HIV-1 RNAs are not part of the argonaute 2 associated RNA interference pathway in macrophages. PLoS ONE, 10(7):e0132127.

Schmich, Fabian; Szczurek, Ewa; Kreibich, Saskia; Dilling, Sabrina; Andritschke, Daniel; Casanova, Alain; Low, Shyan Huey; Eicher, Simone; Muntwiler, Simone; Emmenlauer, Mario; Rämö, Pauli; Conde-Alvarez, Raquel; von Mering, Christian; Hardt, Wolf-Dietrich; Dehio, Christoph; Beerenwinkel, Niko (2015). gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens. Genome Biology, 16:220.

Rämö, Pauli; Drewek, Anna; Arrieumerlou, Cécile; Beerenwinkel, Niko; Ben-Tekaya, Houchaima; Cardel, Bettina; Casanova, Alain; Conde-Alvarez, Raquel; Cossart, Pascale; Csúcs, Gábor; Eicher, Simone; Emmenlauer, Mario; Greber, Urs; Hardt, Wolf-Dietrich; Helenius, Ari; Kasper, Christoph; Kaufmann, Andreas; Kreibich, Saskia; Kühbacher, Andreas; Kunszt, Peter; Low, Shyan Huey; Mercer, Jason; Mudrak, Daria; Muntwiler, Simone; Pelkmans, Lucas; Pizarro-Cerdá, Javier; Podvinec, Michael; Pujadas, Eva; Rinn, Bernd; Rouilly, Vincent; Schmich, Fabian; Siebourg-Polster, Juliane; Snijder, Berend; Stebler, Michael; Studer, Gabriel; Szczurek, Ewa; Truttmann, Matthias; von Mering, Christian; Vonderheit, Andreas; Yakimovich, Artur; Bühlmann, Peter; Dehio, Christoph (2014). Simultaneous analysis of large-scale RNAi screens for pathogen entry. BMC Genomics, 15:1162.

Di Giallonardo, Francesca; Töpfer, Armin; Rey, Melanie; Prabhakaran, Sandhya; Duport, Yannick; Leemann, Christine; Schmutz, Stefan; Campbell, Nottania K; Joos, Beda; Lecca, Maria Rita; Patrignani, Andrea; Däumer, Martin; Beisel, Christian; Rusert, Peter; Trkola, Alexandra; Günthard, Huldrych F; Roth, Volker; Beerenwinkel, Niko; Metzner, Karin J (2014). Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. Nucleic Acids Research, 42(14):e115.

Constantinescu, Simona; Hecht, Katrin; Sobotzki, Nadine; Erzinger, Melanie M; Bovet, Cédric; Shay, Jerry W; Wollscheid, Bernd; Sturla, Shana J; Marra, Giancarlo; Beerenwinkel, Niko (2014). Transcriptomic responses of cancerous and noncancerous human colon cells to sulforaphane and selenium. Chemical Research in Toxicology, 27(3):377-386.

Mohammadi, Pejman; Desfarges, Sébastien; Bartha, István; Joos, Beda; Zangger, Nadine; Muñoz, Miguel; Günthard, Huldrych F; Beerenwinkel, Niko; Telenti, Amalio; Ciuffi, Angela (2013). 24 hours in the life of HIV-1 in a T cell line. PLoS Pathogens, 9(1):e1003161.

Di Giallonardo, Francesca; Zagordi, Osvaldo; Duport, Yannick; Leemann, Christine; Joos, Beda; Künzli-Gontarczyk, Marzanna; Bruggmann, Rémy; Beerenwinkel, Niko; Günthard, Huldrych F; Metzner, Karin J (2013). Next-Generation Sequencing of HIV-1 RNA Genomes: Determination of Error Rates and Minimizing Artificial Recombination. PLoS ONE, 8(9):e74249.

Beerenwinkel, Niko; Montazeri, Hesam; Schuhmacher, Heike; Knupfer, Patrick; von Wyl, Viktor; Furrer, Hansjakob; Battegay, Manuel; Hirschel, Bernard; Cavassini, Matthias; Vernazza, Pietro; Bernasconi, Enos; Yerly, Sabine; Böni, Jürg; Klimkait, Thomas; Cellerai, Cristina; Günthard, Huldrych F (2013). The individualized genetic barrier predicts treatment response in a large cohort of HIV-1 infected patients. PLoS Computational Biology, 9(8):e1003203.

Beerenwinkel, Niko; Günthard, Huldrych F; Roth, Volker; Metzner, Karin J (2012). Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data. Frontiers in Microbiology, 3:329.

Beerenwinkel, Niko; Siebourg, Juliane (2012). Probability, Statistics, and Computational Science. Methods in Molecular Biology, 855:77-110.

Gerstung, Moritz; Beisel, Christian; Rechsteiner, Markus; Wild, Peter; Schraml, Peter; Moch, Holger; Beerenwinkel, Niko (2012). Reliable detection of subclonal single-nucleotide variants in tumour cell populations. Nature Communications, 3:811.

Siebourg, Juliane; Merdes, Gunter; Misselwitz, Benjamin; Hardt, Wolf-Dietrich; Beerenwinkel, Niko (2012). Stability of gene rankings from RNAi screens. Bioinformatics, 28(12):1612-1618.

Delgado-Eckert, Edgar; Ojosnegros, Samuel; Beerenwinkel, Niko (2011). The Evolution of Virulence in RNA Viruses under a Competition–Colonization Trade-Off. Bulletin of Mathematical Biology, 73(8):1881-1908.

This list was generated on Thu Sep 20 03:05:53 2018 CEST.