Dr. Ludwig Geistlinger

eMail:	Ludwig.Geistlinger * at * bio.ifi.lmu.de
Phone:	+49-89-2180-4067
Address:	Teaching and Research Unit Bioinformatics Institute for Informatics University of Munich
	Amalienstr. 17, 80333 Munich, Germany
Room:	2-01, 2nd Floor

Research

Network-based analysis of gene expression data:

Construction of gene regulatory network models
Detection of significant subnetworks
Systematic biological interpretation of detected subnetworks

Teaching

SS 2016	Excercises Networks, graphs and systems
WS 2015/16	Excercises Algorithmic Bioinformatics II Supervision Praktikum GoBi NGS toolbox
SS 2015	Excercises Algorithmic Bioinformatics I Supervision Proseminar Where in the Genome does DNA Replication Begin? Supervision Master-Praktikum NEAP Network and expression data analysis
SS 2014	Excercises Systems Biology
SS 2013	Excercises Networks, graphs and systems Lecture & Excercise Gene Definition Bioinformatics Pearls
WS 2012/13	Excercises Systems Biology Lecture & Excercise Gene Definition Bioinformatics Pearls
WS 2011/12	Excercises Systems Biology

Supervised Theses

2015

Theses

Vinicius H. Silva. Metabolic pathways and meat tenderness: from CNVs to gene expression in Nelore cattle breed. Master Thesis, Escola Superior de Agricultura Luiz de Queiroz (ESALQ) / Universidade de São Paulo (USP), 2015.

Link

BibTex

Conference Talks

13 Jan 2015	European Bioconductor Developers Meeting, Bioc Europe 2015 (Heidelberg, Germany) Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis (Session VI)
30 Aug 2013	26th International Conference on Yeast Genetics and Molecular Biology, YEAST 2013 (Frankfurt a.M., Germany) A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae (Workshop 4 - Systems biology and bioinformatics)
19 Jul 2011	19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology, ISMB/ECCB 2011 (Vienna, Austria) From Sets to Graphs: Towards a Realistic Enrichment Analysis of Transcriptomic Systems (Proceedings Track, PT40)

Publications

2016

Papers

Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer. Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. BMC Bioinformatics, vol 17, pp. 45, January 2016.

BibTex

Vinicius Henrique Silva, Luciana Correia Almeida Regitano, Ludwig Geistlinger, Fábio Pértille, Poliana Fernanda Giachetto, Ricardo Augusto Brassaloti, Natália Silva Morosini, Ralf Zimmer, Luiz Lehmann Coutinho. Genome-wide detection of CNVs and their association with meat tenderness in Nelore cattle. PLOS ONE, vol 11, no. 6, pp. e0157711, June 2016.

BibTex

Theses

Ludwig Geistlinger. Network-based analysis of gene expression data. PhD Thesis, LMU München, 2016.

E-Diss

BibTex

2015

Papers

Tobias Petri, Stefan Altmann, Ludwig Geistlinger, Ralf Zimmer, Robert Küffner. Addressing false discoveries in network inference. Bioinformatics, vol 31, no. 17, pp. 2836-43, September 2015.

BibTex

2013

Papers

Mayuko Kurome, Ludwig Geistlinger, Barbara Keßler, Valeri Zakhartchenko, Nikolai Klymiuk, Annegret Wünsch, Anne Richter, Andrea Bähr, Katrin Krähe, Katinka Burkhardt, Krzysztof Flisikowski, Tatiana Flisikowska, Claudia Merkl, Martina Landmann, Marina Durkovic, Alexander Tschukes, Simone Kraner, Dirk Schindelhauer, Tobias Petri, Alexander Kind, Hiroshi Nagashima, Angelika Schnieke, Ralf Zimmer, Eckhard Wolf. Factors Influencing the Efficiency of Generating Genetically Engineered Pigs by Nuclear Transfer: Multi-Factorial Analysis of a Large Data Set. BMC Biotechnology, vol 13, no. 43, May 2013.

BibTex

Ludwig Geistlinger, Gergely Csaba, Simon Dirmeier, Robert Küffner, Ralf Zimmer. A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae. Nucleic Acids Research, vol 41, no. 18, pp. 8452-8463, July 2013.

BibTex

2011

Papers

Zhen Wang, Guohui Ding, Ludwig Geistlinger, Hong Li, Lei Liu, Rong Zeng, Yoshio Tateno, Yixue Li. Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes. Molecular Biology and Evolution, vol 28, no. 3, pp. 1131-40, March 2011.

BibTex

Ludwig Geistlinger, Gergely Csaba, Robert Küffner, Nicola Mulder, Ralf Zimmer. From Sets to Graphs: Towards a Realistic Enrichment Analysis of Transcriptomic Systems. Bioinformatics, Bioinformatics, vol 27, no. 13, pp. i366-i373, July 2011.

BibTex

2010

Papers

Carola Marzi, Eva Albrecht, Pirro G. Hysi, Vasiliki Lagou, Melanie Waldenberger, Anke Tönjes, Inga Prokopenko, Katharina Heim, Hannah Blackburn, Janina S. Ried, Marcus E. Kleber, Massimo Mangino, Barbara Thorand, Annette Peters, Christopher J. Hammond, Harald Grallert, Bernhard O. Boehm, Peter Kovacs, Ludwig Geistlinger, Holger Prokisch, Bernhard R. Winkelmann, Tim D. Spector, H.-Erich Wichmann, Michael Stumvoll, Nicole Soranzo, Winfried März, Wolfgang Koenig, Thomas Illig, Christian Gieger. Genome-wide association study identifies two novel regions at 11p15.5-p13 and 1p31 with major impact on acute-phase serum amyloid A. PLoS Genetics, vol 6, no. 11, pp. e1001213, November 2010.

BibTex

Theses

Ludwig Geistlinger. Gene Graph Enrichment Analysis (GGEA): Mapping of Gene Expression Data onto Networks of Biochemical Processes. Diploma Thesis, LFE Bioinformatik, LMU München, September 2010.

BibTex

2008

Papers

Christian Gieger, Ludwig Geistlinger, Elisabeth Altmaier, Martin Hrabé-de-Angelis, Florian Kronenberg, Thomas Meitinger, Hans-Werner Mewes, H.-Erich Wichmann, Klaus M. Weinberger, Jerzy Adamski, Thomas Illig, Karsten Suhre. Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genetics, vol 4, no. 11, pp. e1000282, November 2008.

BibTex

Peer-reviewed Work

Verified Peer-Review Record

Software/Services

EnrichmentBrowser	A Bioconductor package for the enrichment analysis of gene expression data, including GGEA
DiauxicGRN	Comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae

Curriculum Vitae

Education
since Apr 2016	Post-Doc @ LFE Bioinfo, University of Munich
2011-2016	PhD (DFG International Research Training Group 1563/1 RECESS)
2004-2010	Dipl.-Bioinf. (M.Sc. Equiv.), Passed with High Distinction, Study of Bioinformatics, University of Munich, Germany
1995-2003	Abitur (A-levels Equiv.), Wilhelm-Ostwald-Gymnasium, Leipzig, Germany
Diploma Thesis
title	Mapping of Gene Expression Data onto Networks of Biochemical Processes
supervisors	Prof. Nicola Mulder (University of Cape Town, South Africa) Prof. Ralf Zimmer (University of Munich, Germany)
description	Apr–Oct 2010 Institute of Infectious Disease and Molecular Medicine University of Cape Town, South Africa
Experience
Oct 2015	Research visit, Scientific exchange and project discussions, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), São Paulo, Brazil
Jul 2013	Workshop Computational Biology @ Bayer, Bayer Life Sciences, Leverkusen, Germany
Jul 2011	Research visit, Scientific exchange and project discussions within RECESS, Research and Training Center on Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
Apr-Jul 2009	Student Scientist, Research on the Evolution of the Phosphoproteome, Shanghai Center for Bioinformation Technology, Shanghai, China
2006-2010	Student Assistant, Analysis of High-Throughput Genomic Chip Data, Institute of Genetic Epidemiology, National Research Center for Environment and Health, Helmholtz Center Munich, Germany
2008	Student Assistant, LaTeX and Sweave Support for Scripts and Lectures, Institute of Biostatistics, Technical University, Munich, Germany
2003-2004	Civilian Service
Awards
Sep 2011	Research Highlight Talk at the German Conference on Bioinformatics 2011
Jun 2011	Best Diploma Thesis in Bioinformatics 2010/2011, TU & LMU Munich
Jan 2011	DFG Grant 1563/1 RECESS
Sep 2010	”Paula und Richard von Hertwig”-Award 2010 for Interdisciplinary Cooperation

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