Forschungsgruppe "Bioinformatik für Hochdurchsatz-Methoden"

Andrzej J. Rutkowski, Florian Erhard, Anne L’Hernault, Thomas Bonfert, Markus Schilhabel, Colin Crump, Philip Rosenstiel, Stacey Efstathiou, Ralf Zimmer, Caroline C. Friedel, Lars Dölken. Wide-spread disruption of host transcription termination in HSV-1 infection. Nature Communications, vol 6, no. 7126, 2015.

Thomas Bonfert, Evelyn Kirner, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel. ContextMap 2: fast and accurate context-based RNA-seq mapping.. BMC bioinformatics, vol 16, pp. 122, 2015.

Sabine Hünten, Markus Kaller, Friedel Drepper, Silke Oeljeklaus, Thomas Bonfert, Florian Erhard, Anne Dueck, Norbert Eichner, Caroline C. Friedel, Gunter Meister, Ralf Zimmer, Bettina Warscheid, Heiko Hermeking. p53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses.. Molecular & cellular proteomics : MCP, 2015 Jul 16 2015.

Andreas Osterman, Thorsten Stellberger, Anna Gebhardt, Marisa Kurz, Caroline C. Friedel, Peter Uetz, Hans Nitschko, Armin Baiker, Maria G. Vizoso-Pinto. The Hepatitis E virus intraviral interactome.. Scientific reports, vol 5, pp. 13872, 2015 2015.

Yasuhiro Murakawa, Michael Hinz, Janina Mothes, Anja Schuetz, Michael Uhl, Emanuel Wyler, Tomoharu Yasuda, Guido Mastrobuoni, Caroline C. Friedel, Lars Dölken, Stefan Kempa, Marc Schmidt-Supprian, Nils Blüthgen, Rolf Backofen, Udo Heinemann, Jana Wolf, Claus Scheidereit, Markus Landthaler. RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway.. Nature communications, vol 6, pp. 7367, 2015 2015.

Caroline C. Friedel. Treatment of Noise and Artifacts in Affymetrix Arrays. Luis Rueda (ed.): Microarray Image and Data Analysis: Theory and Practice, pp. 251-276, CRC Press, 2014.

Caroline C. Friedel. Bioinformatics methods for the biological interpretation of high-throughput experiments. Habilitation, Ludwig-Maximilians-Universität München, 2014.

Bernd Rädle, Andrzej Rutkoswki, Zsolt Ruzsics, Caroline C. Friedel, Ulrich H. Koszinowski, Lars Dölken. Metabolic labeling of newly transcribed RNA for high resolution gene expression profiling of RNA synthesis, processing and decay in cell culture. J. Vis. Exp., vol 78, pp. e50195, 2013.

Herbert B. Schiller, Michaela-Rosemarie Hermann, Julien Polleux, Timothée Vignaud, Sara Zanivan, Caroline C. Friedel, Zhiqi Sun, Aurelia Raducanu, Kay-E Gottschalk, Manuel Théry, Matthias Mann, Reinhard Fässler. β1- and αv-class integrins cooperate to regulate myosin II during rigidity sensing of fibronectin-based microenvironments. Nature cell biology, vol 15, pp. 625-36, Jun 2013.

Samantha J. Griffiths, Manfred Koegl, Chris Boutell, Helen L. Zenner, Colin Crump, Orland Gonzalez, Caroline C. Friedel, Gerald Barry, Kimberley Martin, Marie H. Craigon, Rui Chen, Lakshmi N. Kaza, Even Fossum, John K. Fazakerley, Stacey Efstathiou, Ralf Zimmer, Peter Ghazal, Jürgen Haas. A systematic analysis of host factors reveals a Med23-interferon-lambda regulatory axis against Herpes simplex virus Type 1 replication. PLoS Pathogens, vol 9, no. 8, pp. e1003514, 2013.

Mirko Trilling, Nicolas Bellora, Andrzej J. Rutkowski, deMiranda Graaf, Paul Dickinson, Kevin Robertson, daOlivia Prazeres Costa, Peter Ghazal, Caroline C. Friedel, Mar M. Alba, Lars Dölken. Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis. Nucleic Acids Research, 2013.

Roland H. Friedel, Caroline C. Friedel, Thomas Bonfert, Roland Rad, Philippe Soriano. Clonal expansion of transposon insertions identifies candidate cancer genes in a PiggyBac mutagenesis screen. PLoS ONE, vol 8, no. 8, pp. e72338, 2013.

Caroline C. Friedel. Computational analysis of virus-host interactomes. Methods in molecular biology, vol 1064, pp. 115-30, 2013 2013.

Kaspar Burger, Bastian Mühl, Markus Kellner, Michaela Rohrmoser, Anita Gruber-Eber, Lukas Windhager, Caroline C. Friedel, Lars Dölken, Dirk Eick. 4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response. RNA biology, vol 10, 2013 Sep 4 2013.

Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel. Mining RNA-Seq Data for Infections and Contaminations. PloS one, vol 8, pp. e73071, Sep 2013.

Milan Spasic, Caroline C. Friedel, Johanna Schott, Jochen Kreth, Kathrin Leppek, Sarah Hofmann, Sevim Ozgur, Georg Stoecklin. Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm. PLoS Genet, vol 8, no. 1, pp. e1002433, 01 2012.

Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel. A context-based approach to identify the most likely mapping for RNA-seq experiments. BMC Bioinformatics, vol 13(Suppl 6), pp. S9, 2012.

Tobias Petri, Evi Berchtold, Ralf Zimmer, Caroline C. Friedel. Detection and correction of probe-level artefacts on microarrays. BMC Bioinformatics, vol 13, pp. 114, 2012.

Lisa Marcinowski, Michael Lidschreiber, Lukas Windhager, Martina Rieder, Jens B. Bosse, Bernd Rädle, Thomas Bonfert, Ildiko Györy, deMiranda Graaf, daOlivia Prazeres Costa, Philip Rosenstiel, Caroline C. Friedel, Ralf Zimmer, Zsolt Ruzsics, Lars Dölken. Real-time Transcriptional Profiling of Cellular and Viral Gene Expression during Lytic Cytomegalovirus Infection. PLoS Pathog, vol 8, no. 9, pp. e1002908, 2012.

Robert Lindner, Caroline C. Friedel. A comprehensive evaluation of alignment algorithms in the context of RNA-Seq. PLoS ONE, vol 7, no. 12, pp. e52403, 2012.

Lukas Windhager, Thomas Bonfert, Kaspar Burger, Zsolt Ruzsics, Stefan Krebs, Stefanie Kaufmann, Georg Malterer, Anne L'Hernault, Markus Schilhabel, Stefan Schreiber, Philip Rosenstiel, Ralf Zimmer, Dirk Eick, Caroline C. Friedel, Lars Dölken. Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution.. Genome research, vol 22, pp. 2031-42, 2012 Oct 2012.

Herbert B. Schiller, Caroline C. Friedel, Cyril Boulegue, Reinhard Fässler. Quantitative proteomics of the integrin adhesome reveals a myosin II-dependent recruitment of LIM domain proteins. EMBO Reports, vol 12, no. 3, pp. 259-66, 2011.

Caroline C. Friedel, Jürgen Haas. Virus-host interactomes and global models of virus-infected cells. Trends in Microbiology , vol 19, no. 10, pp. 501-8, 2011.

Susanne Pfefferle, Julia Schöpf, Manfred Kögl, Caroline C. Friedel, Marcel A. Müller, Javier Carbajo-Lozoya, Thorsten Stellberger, vonEkatarina Dall'Armi, Petra Herzog, Stefan Kallies, Daniela Niemeyer, Vanessa Ditt, Thomas Kuri, Roland Züst, Ksenia Pumpor, Rolf Hilgenfeld, Frank Schwarz, Ralf Zimmer, Imke Steffen, Friedemann Weber, Volker Thiel, Georg Herrler, Heinz-Jürgen Thiel, Christel Schwegmann-Weßels, Stefan Pöhlmann, Jürgen Haas, Christian Drosten, Albrecht von Brunn. The SARS-Coronavirus-Host Interactome: Identification of Cyclophilins as Target for Pan-Coronavirus Inhibitors. PLoS Pathog, vol 7, no. 10, pp. e1002331, 10 2011.

Florian Erhard, Caroline C. Friedel, Ralf Zimmer. FERN - Stochastic Simulation and Evaluation of Reaction Networks. Sangdun Choi (ed.): Systems Biology for Signaling Networks, Systems Biology, vol 1, Part 4, pp. 751-775, Springer, 2010.

Caroline C. Friedel, Stefanie Kaufmann, Lars Dölken, Ralf Zimmer. HALO - A Java framework for precise transcript half-life determination. Bioinformatics, vol 26, no. 9, pp. 1264-1266, May 2010.

Lars Dölken, Georg Malterer, Florian Erhard, Sheila Kothe, Caroline C. Friedel, Guillaume Suffert, Lisa Marcinowski, Natalie Motsch, Stephanie Barth, Michaela Beizinger, Diana Lieber, Susanne M. Bailer, Reinhard Hoffmann, Zsolt Ruzsics, Elisabeth Kremmer, Sebastien Pfeffer, Ralf Zimmer, Ulrich H. Koszinowski, Friedrich Grässer, Gunter Meister, Jürgen Haas. Systemic Analysis of Viral and Cellular miRNA Targets in Cells Latently Infected with Human gamma-Herpesviruses through RISC Immunoprecipitation Assays. Cell Host & Microbe, vol 7, no. 4, pp. 324-334, April 2010.

Caroline C. Friedel. Analysis of High-throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life. Ausgezeichnete Informatikdissertationen 2009, GI-Edition Lecture Notes in Informatics, 2010.

Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer. Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. Journal of Computational Biology, vol 16, no. 8, pp. 1-17, 2009.

Caroline C. Friedel, Ralf Zimmer. Identifying the topology of protein complexes from affinity purification assays. Bioinformatics, vol 25, no. 16, pp. 2140-2146, August 2009.

Caroline C. Friedel, Lars Dölken, Zsolt Ruzsics, Ulrich Koszinowski, Ralf Zimmer. Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Research, vol 37, no. 17, pp. e115, Sep 2009.

Caroline C. Friedel, Lars Dölken. Metabolic tagging and purification of nascent RNA: Implications for transcriptomics. Molecular BioSystems, vol 5, no. 11, pp. 1271-8, Nov 2009.

Even Fossum, Caroline C. Friedel, Seesandra V. Rajagopala, Björn Titz, Armin Baiker, Tina Schmidt, Theo Kraus, Thorsten Stellberger, Christiane Rutenberg, Silpa Suthram, Sourav Bandyopadhyay, Dietlind Rose, Albrecht von Brunn, Mareike Uhlmann, Christine Zeretzke, Yu-An Dong, Hélène Boulet, Manfred Koegl, Susanne M. Bailer, Ulrich Koszinowski, Trey Ideker, Peter Uetz, Ralf Zimmer, Jürgen Haas. Evolutionarily conserved herpesviral protein interaction networks.. PLoS Pathog, vol 5, no. 9, pp. e1000570, Sep 2009.

Fabian Birzele, Gergely Csaba, Florian Erhard, Caroline C. Friedel, R. Küffner, Tobias Petri, Lukas Windhager, Ralf Zimmer. Algorithmische Systembiologie mit Petrinetzen – Von qualitativen zu quantitativen Systemmodellen. Informatik-Spektrum, vol 32, no. 4, pp. 310-319, 2009.

Caroline C. Friedel. Analysis of High-Throughput Data - Protein-Protein Interactions, Protein Complexes and RNA Half-life. PhD Thesis, LMU München, February 2009.

Caroline C. Friedel, Ralf Zimmer. Identifying the topology of protein complexes from affinity purification assays. Proceedings of the German Conference on Bioinformatics (GCB 2008), September 9-12, 2008, Dresden, Germany, Lecture Notes in Informatics, vol P-136, pp. 30-43, GI, 2008.

Florian Erhard, Caroline C. Friedel, Ralf Zimmer. FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinformatics, vol 9, no. 1, pp. 356, 2008.

Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer. Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. Sorin Istrail, Pavel Pevzner, Michael Waterman (eds.): Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2008, Singapore, March 30 - April 2, 2008, Lecture Notes in Computer Science, vol 4955, pp. 3-16, Springer, 2008.

Lars Dölken, Zsolt Ruzsics, Bernd Rädle, Caroline C. Friedel, Ralf Zimmer, Jörg Mages, Reinhard Hoffmann, Paul Dickinson, Thorsten Forster, Peter Ghazal, Ulrich H. Koszinowski. High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA, vol 14, no. 9, pp. 1959–1972, Sep 2008.

Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer. ProCope–protein complex prediction and evaluation. Bioinformatics, vol 24, no. 18, pp. 2115–2116, Sep 2008.

Albrecht von Brunn, Carola Teepe, Jeremy C. Simpson, Rainer Pepperkok, Caroline C. Friedel, Ralf Zimmer, Rhonda Roberts, Jürgen Haas. Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. PLoS ONE, vol 2, no. 5, pp. e459, 2007.

Caroline C. Friedel, Ralf Zimmer. Influence of degree correlations on network structure and stability in protein-protein interaction networks. BMC Bioinformatics, vol 8, pp. 297, 2007.

Caroline C. Friedel, Ralf Zimmer. Toward the complete interactome. Nat Biotechnol, vol 24, no. 6, pp. 614-615, Jun 2006.

Caroline C. Friedel, Ralf Zimmer. Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics, vol 7, pp. 519, Nov 2006.

Caroline C. Friedel, Ulrich Rückert, Stefan Kramer. Cost Curves for Abstaining Classifiers. Proceedings of the third Workshop on ROC Analysis in Machine Learning, Pittsburgh, USA, 2006.

Chad A. Davis, Fabian Gerick, Volker Hintermair, Caroline C. Friedel, Katrin Fundel, R. Küffner, Ralf Zimmer. Reliable gene signatures for microarray classification: assessment of stability and performance. Bioinformatics, vol 22, no. 19, pp. 2356-2363, 2006.

Caroline C. Friedel, Katharina H.V. Jahn, Selina Sommer, Stephen Rudd, Hans W. Mewes, Igor V. Tetko. Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage. Bioinfomatics, vol 21, no. 8, pp. 1383-1388, 2005.

Caroline C. Friedel. On Abstaining Classifiers. Master Thesis, TU München, 2005.

Caroline C. Friedel. Automatische Generierung und Verbesserung von Synonymlisten und Entwicklung eines geeigneten Benchmarksystems. Bachelor Thesis, LMU München, June 2003.