Florian Erhard

E-Mail:	Florian.Erhard * at * bio.ifi.lmu.de
Phone:	+49-89-2180-4066
Fax:	+49-89-2180-99-4066
Address:	Teaching and Research Unit Bioinformatics Institut für Informatik Ludwig-Maximilians-Universität München
	Amalienstr. 17, 80333 Munich, Germany
Raum:	3-07, 3. Etage

Research

Stochastic simulation of biochemical networks (mehr)
miRNA target prediction
Function of viral miRNA
Massspectrometry

Teaching

SS 2011	Tutor for the lecture Algorithmic Bioinformatics Trees and Graphs
WS 2010 / 2011	Tutor for the GoBi
	Tutor for the practical programming course
	Tutor for the lecture Algorithmic Bioinformatics II
WS 2009 / 2010	Tutor for the GoBi
	Tutor for the practical programming course
	Tutor for the seminar
SS 2009	Tutor for the lecture Algorithmic Bioinformatics Trees and Graphs
	Tutor for the seminar
WS 2008 / 2009	Tutor for the lecture Algorithmic Bioinformatics II
	Tutor for the practical programming course

Publications

Submitted

Papers

Florian Erhard, Ralf Zimmer. Context-dependent rescoring of Tandem-MS spectra dramatically increases peptide identiﬁcation rates. ISMB 2011, submitted, Submitted.

BibTex

2015

Papers

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.

BibTex

Florian Erhard, Ralf Zimmer. Count ratio model reveals bias affecting NGS fold changes. Nucleic Acids Research, pp. pii: gkv696. , Jul 8 2015.

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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.

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2014

Papers

Florian Erhard, Jürgen Haas, Diana Lieber, Georg Malterer, Lukasz Jaskiewicz, Mihaela Zavolan, Lars Dölken, Ralf Zimmer. Widespread context-dependency of microRNA-mediated regulation.. Genome research, 2014 Mar 25 2014.

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Theses

Florian Erhard. Algorithmic Methods for Systems Biology of Herpes-viral microRNAs. PhD Thesis, LMU München, 2014.

E-Diss

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2013

Papers

Florian Erhard, Lars Dölken, Ralf Zimmer. RIP-chip enrichment analysis. Bioinformatics, vol 29, no. 1, pp. 77--83, September 2012, Basel, Switzerland, Jan 2013.

BibTex

Harth-Hertle ML, Scholz BA, Florian Erhard, Glaser LV, Dölken L, Ralf Zimmer, Bettina Kempkes. Inactivation of intergenic enhancers by EBNA3A initiates and maintains polycomb signatures across a chromatin domain encoding CXCL10 and CXCL9. PLoS Pathogens, vol 9, no. 9, pp. e1003638, 2013.

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Florian Erhard, Lars Dölken, Lukasz Jaskiewicz, Ralf Zimmer. PARma: identification of microRNA target sites in AGO-PAR-CLIP data.. Genome biology, vol 14, pp. R79, 2013 Jul 29 2013.

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2012

Papers

Florian Erhard, Ralf Zimmer. Detecting outlier peptides in quantitative high-throughput mass spectrometry data. Journal of Proteomics, vol 75, no. 11, pp. 3230-9, 2012 Jun 18 2012.

BibTex

Marcinowski L, Tanguy M, Krmpotic A, Rädle B, Lisnić VJ, Tuddenham L, Chane-Woon-Ming B, Ruzsics Z, Florian Erhard, Benkartek C, Babic M, Ralf Zimmer, Trgovcich J, Koszinowski UH, Jonjic S, Pfeffer S, Lars Dölken. Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo. PLoS Pathogens, vol 8, no. 2, pp. e1002510, 2012.

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2011

Papers

Florian Erhard, Ralf Zimmer. Detecting outlier peptides in quantitative high-throughput mass spectrometry data. Detecting outlier peptides in quantitative high-throughput mass spectrometry data, September 2011, Weihenstephan, Germany, 2011.

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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.

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Florian Erhard, Ralf Zimmer. Classification of ncRNAs using position and size information in deep sequencing data. Bioinformatics, vol 26, no. 18, pp. i426-i432, September 2010.

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Lukas Windhager, Florian Erhard, Ralf Zimmer. Fuzzy modeling. Ina Koch, Wolfgang Reisig, Falk Schreiber (eds.): Modeling in Systems Biology: The Petri Net Approach, Springer, 2010.

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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

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2008

Papers

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.

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Theses

Florian Erhard. Petri Net Based System for Spatio-Temporal Simulation of Gene Regulation. Diploma Thesis, LFE Bioinformatik/LMU München, July 2008.

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Software

FERN	Java framework for stochastic simulation and analysis of reaction networks (available as java library, Cytoscape or CellDesigner plugin)
ALPS	Alignment of Pattern Matrices Score
PNMA	Petri Net Modeling Application - currently under development

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