Prof. Dr. Caroline Friedel

E-Mail:	Caroline.Friedel * at * bio.ifi.lmu.de
Phone:	+49-89-2180-4056
Fax:	+49-89-2180-99-4056
Address:	Teaching and Research Unit Bioinformatics Institut für Informatik Ludwig-Maximilians-Universität München
	Amalienstr. 17, 80333 Munich, Germany
Office:	306

Office Hours

*General Office Hours*	Monday 2pm-3pm or by appointment
No regular Office Hours on:

Research

RNA sequencing (RNA-seq), ChIP-sequencing (ChIP-seq)
Protein - Protein Interactions (more)
Protein Komplexe (more)
Stochastic simulation of biochemical networks (more)
Gene expression data analysis (more)

Group

Thomas Bonfert	Ph.D. student	since 10/2010
Karolina Worf	student assistant	since 02/2012

Funding

Time period	Funding agency	Topic
2010-2013	DFG (1 PhD student 100%, 1 Student assistant)	Analysis of RNA decay for alternatively spliced transcripts by RNA tagging.

Teaching

WS 2011	Lecture Algorithmic Systems Biology
	Lecture Mathematics/Informatics A for Molecular Biotechnologists
SS 2011	Lecture Mathematics/Informatics B for Molecular Biotechnologists
WS 2010	Lecture Mathematics/Informatics A for Molecular Biotechnologists
SS 2010	Lecture Algorithmic Bioinformatics: Systems and Networks
WS 2009 / 2010	Tutor for the lecture Algorithms on sequences
	Tutor for the Programming Course Bioinformatics
SS 2009	Tutor for the lecture Algorithmic Bioinformatics I
	Tutor for the seminar Current Problems in Bioinformatics II
WS 2008 / 2009	Tutor for the lecture Algorithmic Bioinformatics II
	Tutor for the seminar Current Problems in Bioinformatics II
	Tutor for the Programming Course Bioinformatics
SS 2008	Tutor for the lecture Algorithmic Bioinformatics I
	Tutor for the seminar Current Problems in Bioinformatics II
WS 2007 / 2008	Tutor for the lecture Algorithmic Bioinformatics II
	Tutor for the seminar Current Problems in Bioinformatics II
	Tutor for the Programming Course Bioinformatics
SS 2007	Tutor for the lecture Algorithmic Systems Biology
	Tutor for the seminar Current Problems in Bioinformatics II
WS 2006 / 2007	Tutor for the lecture Algorithmic Bioinformatics II
	Tutor for the Programming Course Bioinformatics
SS 2006	Tutor for the lecture Algorithmic Systems Biology
WS 2005 / 2006	Tutor for the Programming Course Bioinformatics
SS 2005	Tutor for the Advanced Lab Course Bioinformatics: Expression Data Analysis II

Publications

2012

Papers

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.

BibTex

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.

BibTex

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. Ultra short and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution. Genome Research, 2012.

BibTex

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

BibTex

2011

Papers

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, 2011.

BibTex

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.

BibTex

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.

BibTex

2010

Papers

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.

BibTex

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.

BibTex

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.

BibTex

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.

BibTex

2009

Papers

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.

DOI
Journal version

BibTex

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.

BibTex

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.

BibTex

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.

BibTex

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.

BibTex

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.

BibTex

Theses

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

BibTex

2008

Papers

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.

BibTex

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.

BibTex

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.

BibTex

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

BibTex

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.

BibTex

2007

Papers

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.

BibTex

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.

BibTex

2006

Papers

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

BibTex

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

BibTex

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.

BibTex

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.

BibTex

2005

Papers

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.

BibTex

Theses

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

BibTex

2003

Theses

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

BibTex

Software

ProCope	Java library for the prediction and evaluation of protein complexes from purification data experiments.
FERN	Java framework for stochastic simulation and analysis of reaction networks (available as java library, Cytoscape or CellDesigner plugin)
HALO	HALO is a software for the precise determination of transcript half-lives from measurements of RNA de novo transcription. In addition, methods for quality control, filtering and normalization are supplied as well as a graphical user interface, command line tools and a well-documented Java API.

Curriculum Vitae

Since 11/2011	Assistant professor for bioinformatics (complex biological networks) at LMU Munich.
08/2011	Offered an assistant professorship (W1) with tenure track for bioinformatics (complex biological networks) at LMU Munich.
10/2010-11/2011	Assistant professor (W1) for molecular biology and theoretical bioinformatics at Heidelberg University
08/2010	Offered an assistant professorship (W1) for bioinformatics at Jena University.
06/2010	Offered an assistant professorship (W1) for molecular biology and theoretical bioinformatics at Heidelberg University
2010	Nominated for the GI Dissertationprize 2009
2009	Dissertation prize of the University of Munich (LMU Munich)
03/2009-10/2010	Postdoc, Bioinformatics Group, University of Munich (LMU Munich)
05/2005-02/2009	PhD-Student, Bioinformatics Group, University of Munich (LMU Munich)
10/2003-05/2005	Bioinformatics course, University of Munich (LMU Munich) and Technical University of Munich (TU Munich), M. Sc.
2002-2004	Student assistant, Bioinformatics Group, University of Munich (LMU Munich)
August-September 2002	Internship at 4SC AG, Martinsried
10/2000-09/2003	Bioinformatics course, University of Munich (LMU Munich) and Technical University of Munich (TU Munich), B. Sc.
1990-1999	Abitur, Max-Born Gymnasium Germering

News

People

Benjamin Albrecht

Thomas Bonfert

Gergely Csaba

Florian Erhard

Caroline Friedel

Mathematik/Informatik A (2011)

Mathematik/Informatik B (2011)

Mathematik/Informatik A (2010)

Ludwig Geistlinger

Orland Gonzalez

Volker Heun

Robert Küffner

Haroon Naeem

Robert Pesch

Tobias Petri

Franziska Schneider

Konrad Schreiber

Frank Steiner

Pegah Tavakkolkhah

Lukas Windhager

Ralf Zimmer

Alumni

Studies

Publications

Research

Funding

Software/Services

Contact