MPI-INF D3 Publications

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  1. Current breathomics – A review on data pre-processing techniques and machine learning in metabolomics breath analysis
    Agnieszka Smolinska, Anne-Christin Hauschild, Rianne Fijten, Jan Dallinga, Jan Baumbach, and Frederik van Schooten

  2. MIMA - A software for analyte identification in MCC/IMS chromatograms by mapping accompanying GC/MS measurements
    Felix Maurer, Anne-Christin Hauschild, Kathrin Eisinger, Jan Baumbach, Arno Mayor, and Jörg Ingo Baumbach
    International Journal for Ion Mobility Spectrometry , 2014
  3. On the importance of statistics in breath analysis - Hope or curse?
    Sandrah Eckel, Jan Baumbach, and Anne-Christin Hauschild
    . Note: comment and reply to Journal of Breath Research
  4. An Integrative Clinical Database and Diagnostics Platform for Biomarker Identification and Analysis in Ion Mobility Spectra of Human Exhaled Air
    Till Schneider, Anne-Christin Hauschild, Joerg Ingo Baumbach, and Jan Baumbach
    Journal of Integrative Bioinformatics 10 (2), 2013
  5. Density Parameter Estimation for Finding Clusters of Homologous Proteins - Tracing Actinobacterial Pathogenicity Life Styles
    Richard Röttger, Prabhav Kalaghatgi, Peng Sun, Siomar de Castro Soares, Vasco Azevedo, Tobias Wittkop, and Jan Baumbach
    Bioinformatics 29 (2): 215-222, 2013
  6. Paving the Way for Automated Clinical Breath Analysis and Biomarker Detection
    Anne-Christin Hauschild, Joerg Ingo Baumbach, and Jan Baumbach
    GCB Highlight track

  7. Peak Detection Method Evaluation for Ion Mobility Spectrometry by using Machine Learning Approaches
    Anne-Christin Hauschild, Dominik Kopczynski, Marianna D'Addario, Joerg Ingo Baumbach, Sven Rahmann, and Jan Baumbach
    Metabolites 3 (2): 277-293, 2013
  8. Computational Methods for Metabolomic Data Analysis of Ion Mobility Spectrometry Data - Reviewing the State of the Art
    Anne-Christin Hauschild, Till Schneider, Josch Pauling, Kathrin Rupp, Mi Jang, Jörg Ingo Baumbach, and Jan Baumbach
    Metabolites 2: 733-755, 2012
    [PDF: Download: metabolites-02-00733.pdf]
  9. CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands
    Josch Pauling, Richard Röttger, Andreas Tauch, Vasco Azevedo, and Jan Baumbach
    Nucleic Acids Research 40 (Database issue): D610-D614, 2012
  10. How Little Do We Actually Know? - On the Size of Gene Regulatory Networks.
    Richard Röttger, Ulrich Rueckert, Jan Taubert, and Jan Baumbach
    IEEE/ACM transactions on computational biology and bioinformatics 9 (5): 1293-1300, 2012
  11. Integrated statistical learning of metabolic ion mobility spectrometry profiles for pulmonary disease identification
    Anne-Christin Hauschild, Jörg Ingo Baumbach, and Jan Baumbach
    Genetics and Molecular Research 11 (3): 2733-2744, 2012

  12. Integrative computational biology
    Jan Baumbach
    Integrative Biology 4 (7): 713-714, 2012
  13. KeyPathwayMiner - Detecting case-specific biological pathways by using expression data
    Nicolas Alcaraz, Hande Kucuk, Jochen Weile, Anil Wipat, and Jan Baumbach
    Internet Mathematics 7 (4): 299-313, 2012
  14. On the trail of EHEC/EAEC - unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria
    Josch Pauling, Richard Röttger, Andreas Neuner, Heladia Salgado, Julio Collado-Vides, Prabhav Kalaghatgi, Vasco Azevedo, Andreas Tauch, Alfred Pühler, and Jan Baumbach
    Integrative Biology 4: 728-733, 2012
  15. Online Transitivity Clustering of Biological Data with Missing Values
    Richard Röttger, Christoph Kreutzer, Thuy Duong Vu, Tobias Wittkop, and Jan Baumbach
    In: German Conference on Bioinformatics 2012 (GCB 2012), Jena, Germany, 2012, 57-68
  16. PIPS: Pathogenicity Island Prediction Software
    Siomar C. Soares, Vinícius A. C. Abreu, Rommel T. J. Ramos, Louise Cerdeira, Artur Silva, Jan Baumbach, Eva Trost, Andreas Tauch, Raphael Hirata, Ana L. Mattos-Guaraldi, Anderson Miyoshi, and Vasco Azevedo
    PLoS One 7 (2): e30848,1-e30848,10, 2012
  17. A singular value decomposition approach for improved taxonomy classification of biological sequences
    Anderson R Santos, Marcos A Santos, Jan Baumbach, John A McCulloch, Guilherme C Oliveira, Artur Silva, Anderson Miyoshi, and Vasco Azevedo
    BMC Genomics 12 (Suppl. 4): S11,1-S11,15, 2011
  18. Analysis of quality raw data of second generation sequencers with Quality Assessment Software
    Rommel T.J. Ramos, Adriana R. Carneiro, Jan Baumbach, Vasco Azevedo, Maria P.C. Schneider, and Artur Silva
    BMC Research Notes 4 (1): 130,1-130,6, 2011
  19. clusterMaker: A Multi-algorithm Clustering Plugin for Cytoscape
    John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, and Thomas E. Ferrin
    BMC Bioinformatics 12 (1): 436,1-436,14, 2011
  20. Comprehensive cluster analysis with Transitivity Clustering
    Tobias Wittkop, Dorothea Emig, Anke Truss, Mario Albrecht, Sebastian Böcker, and Jan Baumbach
    Nature Protocols 6 (3): 285-295, 2011
  21. Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
    Jeronimo C. Ruiz, Vivian D'Afonseca, Artur Silva, Amjad Ali, Anne C. Pinto, Anderson R. Santos, Aryanne A. M. C. Rocha, Debora O. Lopes, Fernanda A. Dorella, Luis G. C. Pacheco, Marcilia P. Costa, Meritxell Z. Turk, Nubia Seyffert, Pablo M. R. O. Moraes, Siomar C. Soares, Sintia S. Almeida, Thiago L. P. Castro, Vinicius A. C. Abreu, Eva Trost, Jan Baumbach, Andreas Tauch, Maria P. C. Schneider, John McCulloch, Louise T. Cerdeira, Rommel T. J. Ramos, Adhemar Zerlotini, Anderson Dominitini, Daniela M. Resende, Elisangela M. Coser, Luciana M. Oliveira, Andre L. Pedrosa, Carlos U. Vieira, Claudia T. Guimaraes, Daniela C. Bartholomeu, Diana M. Oliveira, Fabricio R. Santos, Elida Mara Rabelo, Francisco P. Lobo, Gloria R. Franco, Ana Flavia Costa, Ieso M. Castro, Silvia Regina Dias, Jesus A. Ferro, Jose Miguel Ortega, Luciano V. Paiva, Luiz R. Goulart, Juliana Franco Almeida, Maria Ines Ferro, Newton P. Carneiro, Paula R. K. Falcao, Priscila Grynberg, Santuza M. R. Teixeira, Sergio Brommonschenkel, Sergio C. Oliveira, Roberto Meyer, Robert J. Moore, Anderson Miyoshi, Guilherme C. Oliveira, and Vaco Azevedo
    PLoS One 6 (4): e18551 p., 2011
  22. Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis
    Tobias Wittkop, Sven Rahmann, Richard Roettger, Sebastian Boecker, and Jan Baumbach
    Internet Mathematics 7 (4): 255-273, 2011
  23. Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study
    Louise Teixeira Cerdeira, Aadriana Ribeiro Carneir, Rommel Thiago Juca Ramos, Sintia Silva de Almeida, Vivian D'Afonseca, Maria Paula Cruz Schneider, Jan Baumbach, Andreas Tauch, John Anthony McCulloch, Vasco Ariston Carvalho Azevedo, and Aartur Silva
    Journal of Microbiological Methods 86 (2): 218-223, 2011
  24. RhizoRegNet - A database of rhizobial transcription factors and regulatory networks.
    Elizaveta Krol, Jochen Blom, Jörn Winnebald, Alexander Berhörster, Melanie J. Barnett, Alexander Goesmann, Jan Baumbach, and Anke Becker
    Journal of Biotechnology 155 (1): 127-134, 2011
  25. Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0
    Tobias Wittkop, Sven Rahmann, and Jan Baumbach
    In: Special Issue: 6th International Symposium on Integrative Bioinformatics, Cambridge, UK, 2010, 117,1-117,11, paper no. 117.
  26. On the power and limits of evolutionary conservation - unraveling bacterial gene regulatory networks
    Jan Baumbach
    Nucleic Acids Research 38 (22): 7877-7884, 2010. Note: in press
  27. Partitioning biological data with transitivity clustering
    Tobias Wittkop, Dorothea Emig, Sita Lange, Sven Rahmann, Mario Albrecht, John H. Morris, Sebastian Böcker, Jens Stoye, and Jan Baumbach
    Nature Methods 7 (6): 419-420, 2010
  28. AltAnalyze and DomainGraph: analyzing and visualizing exon expression data
    Dorothea Emig, Nathan Salomonis, Jan Baumbach, Thomas Lengauer, Bruce R. Conklin, and Mario Albrecht
    Nucleic Acids Research 38 (Suppl. 2): W755-W762, 2010