Thomas Bonfert

E-Mail:	bonfert * at * bio.ifi.lmu.de
Phone:	+49-89-2180-4057
Fax:	+49-89-2180-99-4057
Address:	Teaching and Research Unit Bioinformatics Institut für Informatik Ludwig-Maximilians-Universität München
	Amalienstr. 17, 80333 Munich, Germany
Raum:	202 2. Etage

Research

Mapping of RNA-seq data
RNA decay

Software

ContextMap

RNA-seq mapping software for identifying the most likely mapping for each read based on the context of all other reads.

Teaching

SS 2016	Tutor for the lecture Algorithmic Bioinformatics: Trees and graphs
WS 2015	Tutor for the lecture Algorithmic Systems Biology
	Tutor for the seminar course Current methods for the bioinformatics analysis of NGS data
SS 2015	Tutor for the lecture Algorithmic Bioinformatics: Systems and Networks
WS 2014	Tutor for the lecture Algorithmic Systems Biology
	Tutor for the practical course Bioinformatics programming course
SS 2014	Tutor for the lecture Algorithmic Bioinformatics: Systems and Networks
WS 2013	Tutor for the lecture Algorithmic Bioinformatics II
	Tutor for the practical course Bioinformatics programming course
SS 2013	Tutor for the lecture Algorithmic Bioinformatics I
	Lecture and Excercise, Bioinformatics Pearls
WS 2012	Tutor for the lecture Algorithmic Systems Biology
	Lecture and Excercise, Bioinformatics Pearls
	Tutor for the practical course Bioinformatics programming course
SS 2012	Tutor for the lecture Algorithmic Bioinformatics: Systems and Networks

Publications

2016

Theses

Thomas Bonfert. Context-based RNA-seq mapping. PhD Thesis, LMU München, 2016.

E-Diss

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

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.

BibTex

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.

BibTex

2013

Papers

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.

BibTex

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.

BibTex

2012

Papers

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

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.

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. Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution.. Genome research, vol 22, pp. 2031-42, 2012 Oct 2012.

BibTex

2010

Theses

Thomas Bonfert. Phylogenetic networks from multi-labeled trees. Diploma Thesis, Eberhard Karls Universität Tübingen, 2010.

BibTex

Supervised Work

2014

Theses

Yvonne Awaloff. Reconstruction of microbial transcripts from RNA-seq experiments. Bachelor Thesis, LMU München, September 2014.

BibTex

Julia Söllner. Evaluation of RNA-seq mapping methods for newly transcribed RNA measurements. Bachelor Thesis, LMU München, September 2014.

BibTex

Elisabeth Frank. Evaluation of transcript reconstruction methods for newly transcribed RNA measurements. Bachelor Thesis, LMU München, November 2014.

BibTex

Curriculum Vitae

Education
2004-2010	Studies in Bioinformatics, University of Tübingen, Degree: Diploma
1995-2004	Abitur, Graf-Eberhard-Gymnasium Bad Urach
Working experience
Since 2010	Research assistant, Bioinformatics Group, University of Munich (LMU Munich)
2008-2010	Student assistant at University of Tübingen
2008-2009	Student research project at Max Planck Institute for Developmental Biology in Tübingen
2001	Trainee at SAP in Walldorf

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