Publications

• Pauling, Josch and Roettger, Richard and Tauch, Andreas and Azevedo, Vasco and Baumbach, Jan CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands In: Nucleic Acids Research, 2012
• Roettger, Richard; Rueckert, Ulrich; Taubert, Jan; Baumbach, Jan Towards the size of gene regulatory networks - How little to we actually know? In: Proceedings of the 10th Asian Pacific Bioinformatics Conference, 2012
• Alcaraz, Nicolas and Kucuk, Hande and Weile, Jochen and Wipat, Anil and Baumbach, Jan KeyPathwayMiner - Detecting case-specific biological pathways by using expression data In: Internet Mathematics, 2011
• Cerdeira, Louise Teixeira and Carneir, Aadriana Ribeiro and Ramos, Rommel Thiago Juca and de Almeida, Sintia Silva and D'Afonseca Vivian and Schneider, Maria Paula Cruz and Baumbach, Jan and Tauch, Andreas and McCulloch, John Anthony and Azevedo, Vasco Ariston Carvalho and Silva, Artur Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study In: Journal of Microbiological Methods, 2011
• Baumbach Jan Finding expressed key pathways. In: X-meeting,, 2011
• Krol, Elizaveta and Blom, Jochen and Winnebald, J\"orn and Berh\"orster, Alexander and Barnett, Melanie J. and Goesmann, Alexander and Baumbach, Jan and Becker, Anke RhizoRegNet - A database of rhizobial transcription factors and regulatory networks. In: Journal of Biotechnology, 2011
• Alcaraz Nicolas Milman and Kucuk Hande and Baumbach Jan KeyPathwayMiner - Detecting case-specific biological pathways by using expression data. In: Technology Track at 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 2011
• Morris, John H. and Apeltsin, Leonard and Newman, Aaron M. and Baumbach, Jan and Wittkop, Tobias and Su, Gang and Bader, Gary D. and Ferrin, Thomas E. clusterMaker: A Multi-algorithm Clustering Plugin for Cytoscape In: BMC Bioinformatics, 2011
• Ramos, Rommel T.J. and Carneiro, Adriana R. and Baumbach, Jan and Azevedo, Vasco and Schneider, Maria P.C. and Silva, Artur Analysis of quality raw data of second generation sequencers with Quality Assessment Software In: BMC Research Notes, 2011
• Ruiz, Jeronimo C.; D'Afonseca, Vivian; Silva, Artur; Ali, Amjad; Pinto, Anne C.; Santos, Anderson R.; Rocha, Aryanne A.M.C.; Lopes, Debora O.; Dorella, Fernanda A.; Pacheco, Luis G.C.; Costa, Marcilia P.; Turk, Meritxell Z.; Seyffert, Nubia; Moraes, Pablo M.R.O.; Soares, Siomar C.; Almeida, Sintia S.; Castro, Thiago L.P.; Abreu, Vinicius A.C.; Trost, Eva; Baumbach, Jan; Tauch, Andreas; Schneider, Maria Paula C.; McCulloch, John; Cerdeira, Louise T.; Ramos, Rommel T.J.; Zerlotini, Adhemar; Dominitini, Anderson; Resende, Daniela M.; Coser, Elisangela M.; Oliveira, Luciana M.; Pedrosa, Andre L.; Vieira, Carlos U.; Guimaraes, Claudia T.; Bartholomeu, Daniela C.; Oliveira, Diana M.; Santos, Fabricio R.; Rabelo, Elida Mara; Lobo, Francisco P.; Franco, Gloria R.; Costa, Ana Flavia; Castro, Ieso M.; Costa Dias, Silvia Regina; Ferro, Jesus A.; Ortega, Jose Miguel; Paiva, Luciano V.; Goulart, Luiz R.; Franco Almeida, Juliana; Ferro, Maria Ines; Carneiro, Newton P.; Falcao, Paula R.K.; Grynberg, Priscila; Teixeira, Santuza M.R.; Brommonschenkel, Sergio; Oliveira, Sergio C.; Meyer, Roberto; Moore, Robert J.; Miyoshi, Anderson; Oliveira, Guilherme C.; Azevedo, Vasco Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains In: PLoS One, 2011
• Santos, Anderson R and Santos, Marcos A and Baumbach, Jan and McCulloch, John A and Oliveira, Guilherme C and Silva, Artur and Miyoshi, Anderson and Azevedo, Vasco A singular value decomposition approach for improved taxonomy classification of biological sequences In: BMC Genomics, 2011
• Wittkop, Tobias and Emig, Dorothea and Truss, Anke and Albrecht, Mario and Boecker, Sebastian and Baumbach, Jan Comprehensive cluster analysis with Transitivity Clustering In: Nature Protocols, 2011
• Wittkop, Tobias and Rahmann, Sven and Roettger, Richard and Boecker, Sebastian and Baumbach, Jan Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis In: Internet Mathematics, 2011
• Dorothea Emig and Nathan Salomonis and Jan Baumbach and Thomas Lengauer and Bruce R. Conklin and Mario Albrecht AltAnalyze and DomainGraph: analyzing and visualizing exon expression data In: Nucleic Acids Research, 2010
• Tobias Wittkop and Sven Rahmann and Jan Baumbach Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0 In: J. Integrative Bioinformatics, 2010
• Baumbach, Jan On the power and limits of evolutionary conservation-unraveling bacterial gene regulatory networks. In: Nucleic Acids Res, Algorithms Group, International Computer Science Institute, Berkeley, USA. jbaumbac@mpi-inf.mpg.de,, 2010
• Wittkop Tobias, Lange Sita, Emig Dorothea, Rahmann Sven, Baumbach Jan Partitioning biological data with Transitivity Clustering. In: Technology Track at 9th European Conference on Computational Biology (ECCB), 2010
• Wittkop Tobias, Lange Sita, Rahmann Sven, Baumbach Jan Detection of functionally related proteins with Transitivity Clustering. In: Technology Track at 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB),, 2010
• Wittkop, Tobias and Emig, Dorothea and Lange, Sita and Rahmann, Sven and Albrecht, Mario and Morris, John H. and Boecker, Sebastian and Stoye, Jens and Baumbach, Jan Partitioning biological data with transitivity clustering. In: Nat Methods, 2010
• Jan Baumbach and Andreas Tauch and Sven Rahmann Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks In: Briefings in Bioinformatics, 2009
• Baumbach, Jan and Wittkop, Tobias and Kleindt, Christian Katja and Tauch, Andreas Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. In: Nat Protoc, Algorithms Group, International Computer Science Institute, Berkeley, California, USA. jbaumbac@icsi.berkeley.edu, 2009
• Keilwagen, Jens and Baumbach, Jan and Kohl, Thomas A. and Grosse, Ivo MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations. In: Genome Biol, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany. Jens.Keilwagen@ipk-gatersleben.de, 2009
• Krawczyk, Justina and Kohl, Thomas A. and Goesmann, Alexander and Kalinowski, J\"orn and Baumbach, Jan From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. In: Nucleic Acids Res, Computational Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany and International Computer Science Institute, Berkeley, CA, USA., 2009
• Jan Baumbach and Tobias Wittkop and Jochen Weile and Thomas Kohl and Sven Rahmann MoRAine - A web server for fast computational transcription factor binding motif re-annotation In: J. Integrative Bioinformatics, 2008
• Jan Baumbach CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks In: BMC Bioinformatics, 2007
• Tobias Wittkop and Jan Baumbach and Francisco P. Lobo and Sven Rahmann Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing In: BMC Bioinformatics, 2007
• Jan Baumbach and Alexander Bunkowski and Sita Lange and Timm Oberwahrenbrock and Nils Kleinbölting and Sven Rahmann and Jörg Ingo Baumbach IMS2 - An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath In: J. Integrative Bioinformatics, 2007
• Jacob Köhler and Jan Baumbach and Jan Taubert and Michael Specht and Andre Skusa and Alexander Rüegg and Christopher J. Rawlings and Paul Verrier and Stephan Philippi Graph-based analysis and visualization of experimental results with ONDEX In: Bioinformatics, 2006
• Jan Baumbach and Karina Brinkrolf and Tobias Wittkop and Andreas Tauch and Sven Rahmann CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes In: J. Integrative Bioinformatics, 2006