Research Interests

In our research we mainly focus on the analyzis of biological networks and large-scale biomedical datasets. We aim to use existing information as efficently as possible and extract knowledge of the plythora of available biological data. Only the efficeint combination of several types of biological datasets allows for a deeper understanding on how organisms manage cell responses, reproduction and adaption to changing environmental conditions.

Among others, we developed TransClust, an efficient, state-of-the-art clustering tool and web-platforms for the in depths analysis of gene regulatory networks. Please find more information about our current projects by following the links:

List of Publications

Peer Reviewed Publications

  • Richard Röttger Clustering of Biological Datasets in the Era of Big DataJournal of Integrative Bioinformatics (2016): 13 (1), 300, DOI:10.2390/biecoll-jib-2016-300
  • Christian Wiwie, Richard Röttger. On the power and limits of sequence similarity based clustering of proteins into families.Pacific Symposium on Biocomputing (2016): 22, 39.
  • Diogo Almeida, Ida Skov, Artur Silva, Fabio Vandin, Qihua Tan, Richard Röttger, Jan Baumbach. Efficient detection of differentially methylated regions using DiMmeRBioinformatics (2016): btw657, DOI:10.1093/bioinformatics/btw657
  • Edson Luiz Folador, Paulo Vinícius Sanches Daltro de Carvalho, Wanderson Marques Silva, Rafaela Salgado Ferreira, Artur Silva, Michael Gromiha, Preetam Ghosh, Debmalya Barh, Vasco Azevedo, Richard Röttger. In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networksBMC Systems Biology (2016): 10.1 103, DOI:10.1186/s12918-016-0346-4
  • Mubo Chen, Jan Baumbach, Fabio Vandin, Richard Röttger, Eudes Barbosa, Mingchui Dong, Morten Frost, Lene Christiansen, Qihua Tan. Differentially Methylated Genomic Regions in Birth‐Weight Discordant Twin Pairs. Annals of human genetics 80.2 (2016): 81-87, DOI:10.1111/ahg.12146
  • Christian Wiwie, Jan Baumbach, Richard Röttger. Comparing the performance of biomedical clustering methods. Nature methods 12.11 (2015): 1033-1038, DOI:10.1038/nmeth.3583
  • Vinicius AC Abreu, Sintia Almeida, Sandeep Tiwari, Syed S Hassan, Diego Mariano, Artur Silva, Jan Baumbach, Vasco Azevedo, Richard Röttger. CMRegNet–An interspecies reference database for corynebacterial and mycobacterial regulatory networks. BMC genomics (2015) 16 (1), 452, DOI:10.1186/s12864-015-1631-0.
  • Jan Baumbach, Richard Röttger. Computational Integrative Biology–on the joint analysis of diverse biological data sets. Integrative Biology 6.11 (2014): 1008-1009, DOI:10.1039/C4IB90037E
  • Eudes Barbosa, Richard Röttger, Anne-Christin Hauschild, Vasco Azevedo, Jan Baumbach. On the limits of computational functional genomics for bacterial lifestyle prediction. Briefings in Functional Genomics (2014), 13 (5): 398-408, DOI:10.1093/bfgp/elu014
  • Goksel Misirli, Jennifer Hallinan, Richard Röttger, Jan Baumbach, Anil Wipat. BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species. Integrative Bioinformatics (2014), 11 (2), 244, DOI:10.2390/biecoll-jib-2014-244
  • Peng Sun, Nora K Speicher, Richard Röttger, Jiong Guo, Jan Baumbach. Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering. Nucleic Acids Research (2014), DOI: 10.1093/nar/gku201
  • Anderson R Santos, Vanessa Bastos Pereira, Eudes Barbosa, Jan Baumbach, Josch Pauling, Richard Röttger, Meritxell Zurita Turk, Artur Silva, Anderson Miyoshi, Vasco Azevedo. Mature Epitope Density - A strategy for target selection based on immunoinformatics and exported prokaryotic proteins. BMC Genomics (2013), 14 (Suppl 6), S4
  • Richard Röttger, Prabhav Kalaghatgi, Peng Sun, Siomar de Castro Soares, Vasco Azevedo, Tobias Wittkop, Jan Baumbach. Density parameter estimation for nding clusters of homologous proteins - tracing actinobacterial pathogenicity lifestyles. Bioinformatics (2013), 29 (2), 215-222, DOI:10.1093/bioinformatics/bts653
  • Richard Röttger, Jan Baumbach. How Little DoWe Actually Know? - On the Size of Gene Regulatory Networks. Shortened form for the highlight track of the German Conference on Bioinformatics 2012 (original publication appeared IEEE/ACM transactions on computational biology and bioinformatics)
  • Duong Vu, Szaniszlo Szöke, Christian Wiwie, Jan Baumbach, Gianluigi Cardinali, Richard Röttger, Vincent Robert. Massive fungal biodiversity data re-annotation with multi-level clustering. Scientific reports 4 (2013): 6837-6837, DOI:10.1038/srep06837.
  • Richard Röttger, Christoph Kreutzer, Thuy Duong Vu, Tobias Wittkop, Jan Baumbach. Online Transitivity Clustering of Biological Data with Missing Values. German Conference on Bioinformatics 2012, 57-68, ISBN: 978-3-939897-44-6, DOI: 10.4230/OASIcs.GCB.2012.57
  • Richard Röttger, Ulrich Rückert, Jan Taubert, Jan Baumbach. How Little Do We Actually Know? - On the Size of Gene Regulatory Networks. IEEE/ACM transactions on computational biology and bioinformatics (2012), 9(5), 1293-1300, DOI: 10.1109/TCBB.2012.71
  • Richard Röttger*, Josch Pauling*, Andreas Neuner, Heladia Salgado, Julio Collado-Vides, Andreas Tauch, Alfred Puehler, Jan Baumbach. On the trail of EHEC/EAEC - Unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria. Integr. Biol. (2012), 4, 728-733, DOI:10.1039/C2IB00132B. (*joint rst authors)
  • Josch Pauling, Richard Röttger, Andreas Tauch, Vasco Azevedo, Jan Baumbach. 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
  • Tobias Wittkop, Sven Rahmann, Richard Röttger, Sebastian Böcker, Jan Baumbach. Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis. Int Math. (2011), 7:4, 255-273
  • Fabian Kneißl, Richard Röttger, Uwe Sandner, Helmut Krcmar. All-I-Touch as Combination of NFC and Lifestyle. 1st International Workshop on Near Field Communication 2009, pp.51-55, DOI:10.1109/NFC.2009.19

Conference Talks

  • Richard Röttger, Christoph Kreutzer, Thuy Duong Vu, Tobias Wittkop, Jan Baumbach. Online Transitivity Clustering of Biological Data with Missing Values, GCB, Jena (Germany), 2012
  • Richard Röttger, Jan Baumbach, How little do we know? – On the Size and Completeness of Gene Regulatory Networks, APBC, Melbourne (Australia), 2012
  • Richard Röttger, Jan Baumbach, Estimating the Size and Completeness of Gene Regulatory Networks, BCATS, Stanford (CA, USA), 2009
  • Fabian Kneißl, Richard Röttger, Uwe Sandner, Helmut Krcmar. All-I-Touch as Combination of NFC and Lifestyle, 1st International IEEE Workshop on Near Field Communication, Hagenberg (Austria), 2009

CV

Education

  • 12/10 - 05/14 Max Planck Institute for Informatics, Saarbrücken, Germany
    PhD in Computer Science
  • 11/11 Newcastle University, Newcastle Upon Tyne, UK
    Research Visit
  • 10/04 - 10/10 Technische Universität München, Munich, Germany
    Diploma in Computer Science, Minor Math
  • 08/09 - 12/09 International Computer Science Institute, UC Berkeley, CA, USA
    Research Fellow, DAAD Scholarship
  • 03/07 - 09/09 Center for Digital Technology and Management, Munich, Germany
    Honours degree in Technology Management, GPA: 1.4
  • 08/08 - 01/09 School of Information, UC Berkeley, CA, USA
    Research Fellow, Lothar und Sigrid Rohde-Stiftung scholarship

Awards

  • 2012 Research Highlight German Conference on Bioinformatics, Jena, Germany
    Richard Röttger, Jan Baumbach, How little do we know? – On the Size and Completeness of Gene Regulatory Networks
  • 2010 Siemens Award
  • 2009 TheoPrax Award
  • 2008 Theseus Talente Award (Ministry of Economics and Technology, 4th rank)