Max-Planck-Institut für Informatik
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informatik
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Publications


Peer-reviewed journal publications

  1. Hauschild AD, Baumbach JI, Baumbach J (2012) Integrated Statistical Learning of Metabolic Ion Mobility Spectrometry Profiles for Pulmonary Disease Identification. Genet Mol Res. (accepted).

  2. Roettger R, Rueckert R Taubert J, Baumbach J (2012) Towards the size of gene regulatory networks - How little to we actually know? IEEE/ACM Transactions on Computational Biology and Bioinformatics (in press) (previously appeared in shorter form in the proceedings of the APBC 2012).

  3. Cumeras R, Schneider T, Favrod P, Figueras E, Gracia I, Maddula S, Baumbach JI (2012) Stability and alignment of MCC/IMS devices. Int. J. Ion Mobil. Spec. 2012 Jan 25;15(1):41-46. (download from Springer)

  4. Alcaraz N, Friedrich T, Koetzing T, Krohmer A, Mueller J, Pauling J, Baumbach J (2012) Efficient key pathway mining - Combining networks and OMICS data. Integr Biol. 2012 (in press). DOI: 10.1039/C2IB00133K.

  5. Soares SC, Abreu V, McCulloch J, D'Afonseca V, Ramos RTJ, Silva AL, Ruiz JC, Baumbach J, Trost E, Tauch A, Hirata R, Mattos-Guaraldi AL, Miyoshi A, Azevedo V (2012) PIPS - Pathogenicity Island Prediction Software. PLoS ONE 7(2): e30848. (download from PLoS)

  6. Pauling J, Roettger R, Neuner A, Salgado H, Collado-Vides J, Tauch A, Puehler A, Baumbach J (2012) On the trail of EHEC/EAEC - Unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria. Integr Biol. 2012 (in press). DOI: 10.1039/C2IB00132B.

  7. Pauling J, Roettger R, Tauch A, Azevedo V, Baumbach J (2012) CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Res. 2012 Jan;40(1):D610-4.. PubMed (download from Oxford Press)

  8. Kumar V, Sun P, Vamathevan J, Li Y, Ingraham K, Palmer L, Huang J, Brown JR (2011) Comparative Genomics of Klebsiella pneumoniae Strains with Different Antibiotic Resistance Profiles. Antimicrob Agents Chemother. 2011 Sep;55(9):4267-76. PubMed (download from American Society for Microbiology)

  9. Wittkop T, Rahmann S, Roettger R, Boecker S, Baumbach J (2011) Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis. Int Math. 2011, 7:4, 255-273. (download from Tayler and Francis Online)

  10. Santos AR, Santos MA, McCulloch JA, Baumbach J, Oliveira GC, Silva AJ, Miyoshi A, Azevedo V (2011) A singular value decomposition approach for improved taxonomy classification of biological sequences. BMC Genomics 2011, 12(Suppl 4):S11. (download from BMC)

  11. Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE (2011) clusterMaker: A Multi-algorithm Clustering Plugin for Cytoscape. BMC Bioinformatics 2011 Nov 9;12(1):436. PubMed (download from BMC)

  12. Alcaraz NM, Kucuk H, Weile J, Wipat A, Baumbach J (2011) KeyPathwayMiner - Detecting case-specific biological pathways by using expression data. Int Math. 2011, 7:4, 299-313. (download from Tayler and Francis Online)

  13. Wittkop T, Emig D, Truss A, Albrecht M, Boecker S, Baumbach J (2011) Comprehensive cluster analysis with Transitivity Clustering. Nature Protocols 2011 Feb;6(3):285-95. PubMed (download from Nature Publishing Group)

  14. Cerdeira LT, Carneir AR, Ramos RTJ, de Almeida SS, D'Afonseca V, Schneider MPC, Baumbach J, Andreas Tauch A, McCulloch JA, Azevedo VA, Silva A (2011) Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. J Microbiol Methods. 2011 Aug;86(2):218-23. PubMed (download from Science Direct)

  15. Ramos TRTJ, Carneiro AR, Baumbach J, Azevedo V, Schneider MPC, Silva A (2011) Analysis of quality raw data of second generation sequencers with Quality Assessment Software. BMC Res Notes. 2011 Apr 18;4(1):130. PubMed (download from BMC)

  16. Ruiz JC, D'Afonseca V, Silva A, Ali A, Pinto AC, Santos AR, Rocha AA, Lopes DO, Dorella FA, Pacheco LG, Costa MP, Turk MZ, Seyffert N, Moraes PM, Soares SC, Almeida SS, Castro TL, Abreu VA, Trost E, Baumbach J, Tauch A, Schneider MP, McCulloch J, Cerdeira LT, Ramos RT, Zerlotini A, Dominitini A, Resende DM, Coser EM, Oliveira LM, Pedrosa AL, Vieira CU, Guimaraes CT, Bartholomeu DC, Oliveira DM, Santos FR, Rabelo EM, Lobo FP, Franco GR, Costa AF, Castro IM, Dias SR, Ferro JA, Ortega JM, Paiva LV, Goulart LR, Almeida JF, Ferro MI, Carneiro NP, Falcao PR, Grynberg P, Teixeira SM, Brommonschenkel S, Oliveira SC, Meyer R, Moore RJ, Miyoshi A, Oliveira GC, Azevedo V (2011) Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains. PLoS One. 2011 Apr 18;6(4):e18551. PubMed (download from PLoS)

  17. Krol E, Blom J, Winnebald J, Berhorster A, Barnett MJ, Goesmann A ,Baumbach J, Becker A (2011) RhizoRegNet-A database of rhizobial transcription factors and regulatory networks. J Biotechnol. 2011 Aug 20;155(1):127-34. PubMed (download from ScienceDirect)

  18. Baumbach J (2010) On the power and limits of evolutionary conservation - unraveling bacterial gene regulatory networks. Nucleic Acids Res. 2010 Dec 1;38(22):7877-84. PubMed (download from Oxford Journals)

  19. Wittkop T, Emig D, Lange SJ, Rahmann S, Albrecht M, Morris JH, Boecker S, Stoye J, Baumbach J (2010) Partitioning biological data with Transitivity Clustering. Nature Methods 2010 Jun;7(6):419-20. PubMed (download from Nature Publishing Group)

  20. Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M (2010) AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res. 2010 Jul 1;38 Suppl:W755-62. PubMed (download from Oxford Journals)

  21. 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 (download from Oxford Journals)

  22. 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 (download from Nature Publishing Group)

  23. Lin M, Hu B, Chen L, Sun P, Fan Y, Wu P, Chen X (2009) Computational identification of potential molecular interactions in Arabidopsis. Plant Physiol. 2009 Sep;151(1):34-46. PubMed (download from Plant Physiology)

  24. 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 (download from Genome Biology)

  25. 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 (download from BMC)

  26. 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 (download from Oxford Journals)

  27. 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)

  28. 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)

  29. 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)

  30. Baumbach J (2007) CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks. BMC Bioinformatics 2007, 8:429. PubMed (download from BMC)

  31. 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)

  32. 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)

  33. 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)

  34. 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

  1. Baumbach J, Friedrich T, Koetzing T, Kromer A, Mueller J, Pauling J (2012) Efficient algorithms for extracting biological key pathways with global constraints. Proceedings of the Genetic and Evolutionary Computation Conference, GECCO 2012, (in press).

  2. Sun P, Guo J, Baumbach J (2012) Integrated simultaneous analysis of different biomedical data types with exact weighted bi-cluster editing. J Integr Bioinform, (in press).

  3. Roettger R, Rueckert R Taubert J, Baumbach J (2012) Towards the size of gene regulatory networks -- How little to we actually know? Proceedings of the 10th Asian Pacific Bioinformatics Conference, Jan 2012, Melbourne, Australia (in press).

  4. Khodaee M, Hashemi V, Aminisharifabad M (2011) A Simple Algorithm for Solving the All-Pairs Minimum Value Cut Problem Using DNA Computing. Proceedings of the Bioinformatics and Computational Biology (BICoB) 2011: 201-204, New Orleans, Louisiana, USA (to appear).

  5. Wittkop T, Rahmann S, Baumbach J (2010) Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0. J Integr Bioinform, 2008 Aug 25;5(2). PubMed (download from JIB)

  6. Baumbach J, Wittkop T, Weile J, Kohl T, Rahmann S, (2008) MoRAine - A web server for fast computational transcription factor binding motif re-annotation. J Integr Bioinform, 5(2):91, 2008. PubMed (download from JIB)

  7. 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. J Integr Bioinform, 4(3): 75, 2007. (download from JIB)

  8. 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)

  9. 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. J Integr Bioinform, 3(2):24, 2006. (download from JIB)

Reviewed conference talks

  1. Baumbach J (2011) Finding expressed key pathways. X-meeting, October 12-15 2011, Florianopolis (Brazil). conference web site

  2. Alcaraz NM, Kucuk H, Baumbach J (2011) KeyPathwayMiner - Detecting case-specific biological pathways by using expression data. Technology Track at 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), July 17-19 2011, Vienna (Au). conference web site

  3. Wittkop T, Lange S, Emig D, Rahmann S, Baumbach J (2010) Partitioning biological data with Transitivity Clustering. Technology Track at 9th European Conference on Computational Biology (ECCB), Sept 26-29 2010, Ghent (Belgium). conference web site

  4. Wittkop T, Lange S, Rahmann S, Baumbach J (2010) Detection of functionally related proteins with Transitivity Clustering. Technology Track at 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), July 11-13 2010, Boston (MA, USA). conference web site

  5. Roettger R, Baumbach J (2009) Estimating the size and completeness of gene regulatory networks. BCATS, Stanford (CA, USA). conference web site

  6. Wittkop J, Baumbach J (2007) FORCE- A heuristic, force based cluster editing algorithm. BREW Bioinformatics Research and Education Workshop, May 2-5 2007, Bergen (Norway).

  7. 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)

  8. 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)

  9. 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)

  10. 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)

  11. 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)

  12. 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)

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