Robert Küffner

E-Mail:	Robert.Kueffner * at * bio.ifi.lmu.de
Phone:	+49-89-2180-4045
Fax:	+49-89-2180-4054
Address:	Teaching and Research Unit Bioinformatics Institut für Informatik Ludwig-Maximilians-Universität München
	Amalienstr. 17, 80333 Munich, Germany
Office:	205, 2nd floor, front building

Research

Biochemical networks
Gene expression data analysis
Textmining

Teaching

WS 2008 / 2009	Vorlesung „Algorithmische Systembiologie“
SS 2008	Blockveranstaltung „Expressionsanalyse“
	Hauptseminar aktuelle Probleme der Bioinformatik
WS 2007 / 2008	Praktikum „Genomorientierte Bioinformatik“
	Programmierpraktikum Bioinformatik
SS 2007	Vorlesung „Algorithmische Systembiologie“
	Blockveranstaltung „Expressionsanalyse“
	Hauptseminar aktuelle Probleme der Bioinformatik
WS 2006 / 2007	Praktikum „Genomorientierte Bioinformatik“
	Programmierpraktikum Bioinformatik
SS 2006	Vorlesung „Algorithmische Systembiologie“
	Blockveranstaltung „Expressionsanalyse“
	Hauptseminar aktuelle Probleme der Bioinformatik
WS 2005 / 2006	Praktikum „Genomorientierte Bioinformatik“
	Programmierpraktikum Bioinformatik
SS 2005	Blockveranstaltung „Expressionsanalyse“
WS 2004 / 2005	Praktikum „Genomorientierte Bioinformatik“
	Programmierpraktikum Bioinformatik
SS 2004	Proseminar „Proteinanalyse“
WS 2003 / 2004	Praktikum „Genomorientierte Bioinformatik“
	Programmierpraktikum Bioinformatik
	Hauptseminar „Maschinelles Lernen“

Publications

Submitted

Books

Pegah Tavakkolkhah, Robert Küffner. Extending partially known networks. Verification of methods for gene network inference from Systems Genetics data, Springer, Submitted.

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

2014

Papers

Lukas Windhager, Jonas Zierer, Robert Küffner. Refining ensembles of predicted gene regulatory networks based on characteristic interaction sets. PLoS One, vol 9, no. 2, pp. e84596, 2014.

BibTex

Robert Küffner, N. Zach, R. Norel, Johann Hawe, D. Schoenfeld, G. Stolovitsky, M.L. Leitner, etal. Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression. Nature Biotechnology, no. Nov 2, 2014.

BibTex

2013

Papers

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

Robert Maier, Ralf Zimmer, Robert Küffner. A Turing test for artificial expression data. Bioinformatics, vol 29, no. 20, pp. 2603-2609, Aug 16 2013.

BibTex

Schrynemackers M, Robert Küffner, Geurts P. On protocols and measures for the validation of supervised methods for the inference of biological networks. Front Genet. , vol 4, pp. 262, Dec 3 2013.

BibTex

Sorg D, Danowski K, Korenkova V, Rusnakova V, Robert Küffner, Ralf Zimmer, Meyer HH, Kliem H. Microfluidic high-throughput RT-qPCR measurements of the immune response of primary bovine mammary epithelial cells cultured from milk to mastitis pathogens. Animal, vol 7, no. 5, pp. 799-805, May 2013.

BibTex

2012

Papers

Haroon Naeem, Ralf Zimmer, Pegah Tavakkolkhah, Robert Küffner. Rigorous assessment of gene set enrichment tests. Bioinformatics, vol bts164v1-bts164, pp. 7, April 2012.

BibTex

Robert Küffner, Tobias Petri, Pegah Tavakkolkhah, Lukas Windhager, Ralf Zimmer. Inferring Gene Regulatory Networks by ANOVA. Bioinformatics, vol 28, no. 10, pp. 1376-1382, March 2012.

BibTex

Daniel Marbach, James C. Costello, Robert Küffner, Nicole M. Vega, Robert J. Prill, Diogo M. Camacho, Kyle R. Allison, Manolis Kellis, James J. Collins, Gustavo Stolovitzky. Wisdom of crowds for robust gene network inference.. Nature methods, vol 9, pp. 796-804, 2012 2012.

BibTex

2011

Papers

Tobias Petri, Robert Küffner, Ralf Zimmer. Experiment Specific Expression Patterns. Vineet Bafna, Cenk S. Sahinalp (eds.): RECOMB 2011, Research in Computational Molecular Biology, LNBI 6577, vol 15, pp. 339-354, Springer, 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

Haroon Naeem, Robert Küffner, Gergely Csaba, Ralf Zimmer. miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature. BMC Bioinformatics, vol 11, pp. 135, 16 March 2010 2010.

BibTex

Software

ConceptMaker	ConceptMaker harnesses large scale measurements such as microarray experiments to automatically construct queries. The queries are then posed against the biomedical literature to retrieve functional relationships relevant for the experiment.
RelEx	RelEx uses semantic dependency trees to extract relations and relation types between named entities from the entire PubMed. Due to the dependency trees only few tree rules are required to harvest a wide range of complex relationship phrases.
ProSAS Database	ProSAS is a database for analyzing alternative splicing events in several mamalian genomes with respect to protein structure.
syngrep	syngrep is a fast named entity recognition tool that scans the entire PubMed for matches against multiple synonym lists in less than ten minutes.

Curriculum Vitae

Seit 2003	Group leader of the Practical Informatics and Bioinformatics Group (Prof. Dr. R. Zimmer), Ludwig-Maximilians-University, Munich
2000-2003	Head of the software development group PathDB, National Center for Genome Resources (NCGR), New Mexico, USA
1998-2000	Postdoc, Bioinformatics Group, University of Munich, (Prof. Dr. R. Zimmer, Prof. Dr. T. Lengauer) GMD, Sankt Augustin, Germany
1990-1999	Chemestry course, Heinrich-Heine-University Düsseldorf
22th July 1969	born in Leverkusen

Search

Links and Functions

Language Selection

User Menu

Breadcrumb Navigation

Main Navigation

Content

Service Menu

Footer