Welcome to my academic web site

Research interests, projects, and software

	To handle changing environmental surroundings and to manage unfavourable conditions, all microbial organisms have evolved complex transcriptional gene regulatory networks. My aim is to reconstruct and analyze these networks. Therefore, we developed two platforms: CoryneRegNet and MycoRegNet. Both provide comprehensive visualization capabilities and offer easy-to-use interfaces to execute computer analysis features to predict promising wet lab targets. CoryneRegNet is the reference database for corynebacteria, organisms of high impact in biotechnology (Corynebacterium glutamicum) and human medicine (C. diphtheriae and C. jeikeium). MycoRegNet concentrates on the human pathogen Mycobacterium tuberculosis. Tools - Selected Papers Krawczyk J, Kohl TA, Goesmann A, Kalinowski J, Baumbach J (2009) From Corynebacterium glutamicum to Mycobacterium tuberculosis - Towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. Nucleic Acids Res. 2009 Aug;37(14):e97. PubMed Baumbach J, Wittkop T, Kleindt CK, Tauch A (2009) Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. Nature Protocols. 2009 Jun;4(6):992-1005. PubMed Baumbach J, Rahmann S, Tauch A (2009) Towards the integrated analysis, visualization, and reconstruction of microbial gene regulatory networks. Brief Bioinform. 2009 Jan;10(1):75-83. PubMed Baumbach J (2007) CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks. BMC Bioinformatics 2007, 8:429. PubMed
	Partitioning data objects into groups, such that the objects in each group share common traits, is a long-standing challenge in computer science. We developed integrated biological data clustering frameworks: FORCE and TransClust. They are based on solving the NP-hard Weighted Transitive Graph Projection aka. Weighted Cluster Editing. While TransClust was developed very recently, FORCE finds frequent application in protein homology detection. Tools - Selected Papers Baumbach J, Rahmann S, Tauch A (2009) Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Syst Biol. 2009 Jan 15;3(1):8. PubMed 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 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
	A precise identification of transcription factor binding sites (TFBSs) is time-consuming and difficult. Often, TFBS annotations are extracted from the literature and stored routinely 5' → 3' relative to the target gene. Mixing the two possible orientations of a TFBS results in poor information content of subsequently computed models. Since these models are used to predict further TFBSs, we developed MoRAine and MotifAdjuster. They aim to re-adjust TFBS annotations automatically to improve subsequent classification performance. Note that this problem is very related to the so-called "Motif Discovery". Tools - MotifAdjuster Selected Papers 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. PDF Keilwagen J, Baumbach J, Kohl T, Grosse I (2009) MotifAdjuster: A tool for computational reassessment of transcription factor binding site annotations. Genome Biol 2009 May 1;10(5):R46. PubMed
	The introduction of high-throughput genome sequencing and post-genome analysis technologies has created the potential to unravel complex biological pathways on a large scale. To analyze and interpret this data in the context of experimental results, we developed tools that help to integrate and visualize all available pathway data together with wet lab data. ONDEX enables data from diverse biological data sets to be integrated and visualised. CoryneCenter is specialized for the analysis of corynebacterial gene regulatory interactions together with gene expression data. While ONDEX follows a so-called "Data Warehouse" strategy, CoryneCenter utilizes a SOAP-based Web Service communication scheme that integrates all contributing, independent platforms on demand. Tools - Selected Papers Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184. PubMed 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 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 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
	The genome-scale reconstruction of transcriptional gene regulatory networks is important for biotechnology and human medicine but cost-intensive, time-consuming, and impossible to perform for any species separately. By using bioinformatics methods one can partially transfer networks from model organisms to closely related species. Here, we developed bioinformatics workflows for CoryneRegNet and MycoRegNet that perform reliable network transfers from C. glutamicum to other corynebacteria, e.g. C. diphtheriae, and to M. tuberculosis. The main idea behind the prediction pipeline is illustrated here. Tools - Selected Papers Baumbach J, Rahmann S, Tauch A (2009) Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Syst Biol. 2009 Jan 15;3(1):8. PubMed Krawczyk J, Kohl TA, Goesmann A, Kalinowski J, Baumbach J (2009) From Corynebacterium glutamicum to Mycobacterium tuberculosis - Towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. Nucleic Acids Res. 2009 Aug;37(14):e97. PubMed Baumbach J, Wittkop T, Kleindt CK, Tauch A (2009) Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. Nature Protocols. 2009 Jun;4(6):992-1005. PubMed Baumbach J, Rahmann S, Tauch A (2009) Towards the integrated analysis, visualization, and reconstruction of microbial gene regulatory networks. Brief Bioinform. 2009 Jan;10(1):75-83. PubMed