Dr. Jan Baumbach

Member of the Algorithms group

I'm a member of the Algorithms group at the International Computer Science Institute at University of California, Berkeley. Previously, I was a member of the Center for Biotechnology (CeBiTec), Bielefeld, Germany.

Contact Research Publications Projects Theses CV

Contact

Dr. Jan Baumbach	Office:	612
International Computer Science Institute	Phone:	+1 510 666-2976
University of California, Berkeley	Fax:	+1 510 666-2956
1947 Center Street. Suite 612	email:	jbaumbac\|at\|icsi.berkeley.edu
Berkeley, CA 94704	www:	www.icsi.berkeley.edu/~jbaumbac

Office hours: by email!

Research Interests

Reverse engineering of gene regulatory networks
Graph based analysis and modeling of biological networks
Graph modification problems
Large-scale protein homology detection
Data mining in biomedical data
Automatic transcription factor binding site reassessment

Publications

Peer-reviewed journal publications

Baumbach J, Rahmann S, Tauch A (2008) Towards the integrated analysis, visualization, and reconstruction of microbial gene regulatory networks. Briefings in Bioinformatics (accepted for publication).
Kohl T, Baumbach J, Jungwirth B, Puehler A, Tauch A (2008) The GlxR regulon of the amino acid producer Corynebacterium glutamicum: in silico and in vitro detection of DNA binding sites of a global transcription regulator. J Biotechnol. 31;135(4):340-350. PubMed (download from Science Direct)
Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184. PubMed (download from BMC)
Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Hueser AT, Kalinowski J, Oehm S, Puehler A, Rahmann S, Weile J, Goesmann A (2007) CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Syst Biol 1(1):55. PubMed (download from BMC)
Baumbach J (2007) CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks. BMC Bioinformatics 2007, 8:429. PubMed (download from BMC)
Wittkop T, Baumbach J, Lobo FP, Rahmann S (2007) Large scale clustering of protein sequences with FORCE -- A layout based heuristic for weighted cluster editing. BMC Bioinformatics 2007, 8:396. PubMed (download from BMC)
Baumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A (2006) CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli. J Biotechnol., 2007 Apr 30;129(2):279-289. PubMed (download from ScienceDirect)
Baumbach J, Brinkrolf K, Czaja LF, Rahmann S, Tauch A (2006) CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics. 2006 Feb 14;7(1):24. PubMed (download)
Koehler J, Baumbach J, Taubert J, Specht M, Skusa A, Rueegg A, Rawlings C, Verrier P, Philippi S (2006) Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics. 2006 Mar 13;22(11):1383-1390. PubMed (download from Oxford Journals)

Peer-reviewed conference publications

Baumbach J, Wittkop T, Weile J, Kohl T, Rahmann S, (2008) MoRAine - A web server for fast computational transcription factor binding motif re-annotation. Journal of Integrative Bioinformatics, 5(2):91, 2008. (download)
Baumbach J, Bunkowski A, Lange S, Oberwahrenbrock T, Kleinboelting N, Rahmann S, Baumbach JI (2007) IMS2 – An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath. Journal of Integrative Bioinformatics, 4(3): 75, 2007. (download)
Rahmann S, Wittkop T, Baumbach J, Martin M, Truss A, Boecker S (2007) Exact and Heuristic Algorithms for Weighted Cluster Editing. In Proc. 6th CSB, volume 6 of Computational Systems Bioinformatics. Imperial College Press, 2007. PubMed (download from Life Sciences Society)
Baumbach J, Brinkrolf K, Wittkop T, Tauch A, Rahmann S (2006) CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes. Journal of Integrative Bioinformatics, 3(2):24, 2006. (download)

Peer-reviewed conference talks

Tobias Wittkop, Jan Baumbach (2007) FORCE- A heuristic, force based cluster editing algorithm. BREW Bioinformatics Research and Education Workshop, May 2-5 2007, Bergen (Norway).
Baumbach JI, Vautz W, Westhoff M, Litterst P, Freitag L, Rahmann S, Bunkowski A, Baumbach J (2007) Metabolic Profiling of Human Breath Using Ion Mobility Spectrometry. 3rd Annual Advances in Metabolic Profiling Conference. Nov. 13-14, 2007, Boston (MA, USA). (conference web site)
Baumbach JI, Vautz W, Westhoff M, Litterst P, Freitag L, Baumbach J, Bunkowski A, Rahmann S (2007) Early lung cancer detection using ion mobility spectrometry data of human breath. Breath Analysis Summit 2007: Clinical Applications of Breath Testing. Nov. 1-3, 2007, Ohio (Cleveland, USA). (conference web site)
Baumbach JI, Vautz W, Bader S, Litterst P, Freitag L, Baumbach J, Bunkowski A, Rahmann S, Westhoff M (2007) Ion Mobility Spectrometry for Metabolic Profiling of Human Breath. Breath Analysis Summit 2007: Clinical Applications of Breath Testing. Nov. 1-3, 2007, Ohio (Cleveland, USA). (conference web site)
Baumbach JI, Bader S, Vautz W, Litterst P, Freitag L, Baumbach J, Bunkowski A, Rahmann S, Westhoff M (2007) Metabolites in Human Breath. Breath Analysis Summit 2007: Clinical Applications of Breath Testing. Nov. 1-3, 2007, Ohio (Cleveland, USA). (conference web site)
Taubert J, Hindle M, Hoekman B, Winnenburg R, Weile J, Sieren K P, Baumbach J, Ernst S, Elsner S, Hassani-Pak K, Lysenko A, Philippi S, Yates T, Verrier P, Rawlings C, Koehler J (2007) The ONDEX data integration framework. Bioinformatics Open Source Conference (BOSC 2007), as SIG meeting in conjunction with the ECCB/ISMB 2007 in Vienna (Austria). (conference web site)
Baumbach J, Rahmann S, Tauch A (2007) CoryneRegNet: An Integrative Bioinformatics Platform for the Analysis of Transcription Factors and Regulatory Networks. Software Demonstration at European Conference on Computational Biology 2006, Eilat (Israel). (conference web site)

PhD thesis

Baumbach J (2008) CoryneRegNet - A reference database and analysis platform for corynebacterial gene regulatory networks. (download)

Current and Recent Projects + Software

CoryneRegNet is a database of corynebacterial transcription factors and regulatory elements.
FORCE is a FORce based Cluster Editing heuristic for the efficient large-scale identification of protein clusters.
MoRAine is an online tool for sequence logo painting and the reannotation of transcription factor binding motifs.
CoryneCenter is an online resource for the integrated analysis of corynebacterial genome and transcriptome data..
ONDEX (ONtological INDEXing) is a data integration and analysis framework that helps to integrate data of many heterogeneous biolocal data sources into one data repository and to apply graph based analyses methods in context of experimental results.

Theses (Bachelor, Master, Diploma)

Oberwahrenbrock, Timm (Master): Clustering of nucleotide and amino acid sequences by means of Ant Colony Optimization (ACO)
Kleinboelting, Nils (Master): An extended heuristic approach for Weighted Cluster Editing -- Ant Colony Clustering (ACC) coupled to force based heuristics
Pauling, Josch (Diploma): An integrated machine learning and evaluation environment for metabolic fingerprinting of mass spectra (in cooperation with the Institute for Analytical Sciences, Dortmund, Metabolomics Department)
Bunkowski, Alexander (Diploma): An integrated medical software framework providing lung cancer detection using GC/IMS spectra (in cooperation with the Institute for Analytical Sciences, Dortmund, Metabolomics Department)
Ernst, Sonja (Diploma): A web based framework providing methods for the analysis and visualisation of integrated biological data sources (in cooperation with Rothamsted Research, Harpenden (UK), Bioinformatics Group)
Elsner, Sebastian (Diploma): Development of analytical methods based on the fusion of the ontological data warehouse systems ONDEX and CoryneRegNet (in cooperation with Rothamsted Research, Harpenden (UK), Bioinformatics Group)
Moussa, Roland (Bachelor): Graph-basierte Analyse von genregulatorischen Netzwerken im Kontext von Microarray-Daten
Rademacher, Katrin (Bachelor): Statistische Analyse und Visualisierung von Transkriptionsfaktorbindestellen
Schneider, Jessica (Bachelor): Evaluierung von Tools zur Vorhersage von Operon-Zugehörigkeiten und deren Integration in die Genregulations-Datenbank CoryneRegNet
Weile, Jochen (Bachelor): Development of algorithms for graph based analysis of molecular biological networks (in cooperation with Rothamsted Research, Harpenden (UK), Bioinformatics Group)

CV

Education

09/08 - Current	PostDoc studies at International Computer Science Institute, University of California, Berkeley
07/05 - 05/08	PhD studies: CoryneRegNet - A reference database and analysis platform for corynebacterial gene regulatory networks, Bielefeld University, Computational Methods for Emerging Technologies (COMET) Group, International Graduate School in Bioinformatics and Genome Research (final grade: very good with distinction, summa cum laude)
10/04 - 06/05	Diploma thesis: Graph based analysis of biological networks in the context of experimental results, Rothamsted Research, Harpenden (UK), Bioinformatics Group (download)
10/00 - 06/05	Degree program: Applied Computer Science in the Natural Sciences (Diploma), Bielefeld University (final grade: very good with distinction)

Miscellanies

03/06 - 02/08

Member of the executive board of the Center for Biotechnology (CeBiTec), Bielefeld University

Scholarships

09/08 - Current	PostDoc Scholarship, DAAD, International Computer Science Institute, University of California, Berkeley
07/05 - 07/08	PhD Scholarship, International NRW Graduate School in Bioinformatics and Genome Research, Bielefeld University
08/04 - 01/05	Diploma Scholarship, DAAD, Rothamsted Research, Harpenden (UK)

Fellowships and awards

08/08	Travelling fellowship, Invitation as lecturer, Bioinformatics workgroup at TU Brunswick
02/08 - 05/08	Visiting fellowship, Boehringer Ingelheim Fonds, University of California, San Francisco, Resource on Biocomputing, Visualization and Informatics, San Francisco (CA, USA)
12/07	Travelling fellowship, Invitation as lecturer, Bergen Center for Computational Science, University of Bergen
11/07	ScienceFair junior research award, ScienceFair, Perspektive 2007
10/07	Travelling fellowship, Invitation as lecturer, IPK Gatersleben
09/07	Travelling fellowship, Integrative Bioinformatics Workshop 2007 (IB07) in Ghent, Belgium
03/07 - 12/07	Bielefeld University supplementary project grant
03/07	Travelling fellowship, Shanghai Spring School of genome-based systems biology of biotechnologically relevant prokaryotes, CAS-MPG Partner Institute for Computational Biology
01/07	Travelling fellowship, Invitation as lecturer, Waterman Seminar Series on Bioinformatics, IPK Gatersleben
04/06	Travelling fellowship, Invitation as lecturer, ISAS Dortmund
03/06 - 12/06	Bielefeld University supplementary project grant