Richard Röttger, Associate Professor, Dr. rer. nat.

I am an Associate Professor for Bioinformatics at the University of Southern Denmark (SDU) at the Department for Mathematics and Computer Science (IMADA) and head of the Computational Biology Group. I started at SDU in Summer 2014 as Assistant Professor (promotion to Associate Professor in November 2017) and have since been actively researching in various kinds of machine learning of biomedical data. I furthermore spent 5 month on a Sabbatical leave at the University of Cambridge at the Medical Research Council Laboratory of Molecular Biology (MRC-LMB) in the group of Prof. Madan Babu. Before I joined SDU, I received my PhD (Dr. rer. nat.) from the Max-Planck-Institute for Informatics, in Saarbrücken for my work on Active Transitivity Clustering. I was awarded an International Max Planck Research School (IMPRS) PhD fellowship for my research at the Max Planck Institute. Before my PhD studies, I studied computer science at the Technical University of Munich (TUM) and Technology Management at the Center for Digital Technology and Management (CDTM). During my studies I had two research visits at the University of California at Berkeley at the School of Information as well as at the International Computer Science Institute where my diploma thesis originated. My thesis on the completeness of gene regulatory networks was awarded with the prestigious Siemens price.

Research Interests

The main research interest of my lab lies in the development and establishment of next-generation machine learning and artificial intelligence technology for analyzing big biomedical data and algorithms for systems-medical research.

We are particularly well known for our research on unsupervised learning. One example is ClustEval, a fully automated ensemble clustering platform for massive-scale biomedical data. It is the first bioinformatics tool for de novo predicting the most accurate unsupervised data analysis model and parameter range given a previously unseen data set. Further, we are the core developers of Transitivity Clustering and develop active clustering methods

We also host reference databases of bacterial gene regulatory networks (GRNs) and researched their statistical properties and completeness.

Further, my lab has a history of successful collaborations across faculties. For instance, in collaboration with the Department for Molecular Biology at SDU, we developed techniques to cluster biomolecular networks conjointly with high-dimensional OMICS data. We termed this novel approach “human augmented clustering” and coupled it to time-series network enrichment to identify subnetworks of enriched temporal cross-talk. The software (TiCoNE, very recently published in Systems Medicine) was downloaded already >13,000x times from the Cytoscape app store alone. We further developed tools for de novo discovery of differentially methylated regions in birth-weight discordant monozygotic twins in a collaboration with the Faculty of Health and the Odense University Hospital.

List of Publications

Journal & Conference Publications

  1. C. Wiwie, I. Kuznetsova, A. Mostafa, A. Rauch, A. Haakonsson, I. Barrio-Hernandez, B. Blagoev, S. Mandrup, H.H.H.W. Schmidt, S. Pleschka, R. Röttger, J. Baumbach. Time-resolved systems medicine reveals viral infection-modulating host targets. (2019), Systems Medicine, in press.
  2. A. Rauch, AK. Haakonsson, JG. Madsen, M. Larsen, MR. Madsen, EL. Van Hauwaert, R. Nielsen, BD. Larsen, C. Wiwie, R. Röttger, J. Baumbach, M. Kassem, S. Mandrup. Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis. (2019), Nature Genetics, 1546-1718. doi:10.1038/s41588-019-0359-1
  3. S. Larsen, R. Röttger, H. Schmidt, J. Baumbach. E. coli gene regulatory networks are inconsistent with gene expression data. (2018) Nucleic Acids Research, 47 (1), 85-92. doi:10.1093/nar/gky1176
  4. C. Wiwie, J. Baumbach, R. Röttger. Guiding biomedical clustering with ClustEval. (2018) Nature Protocols, 13 (6), 1429 2018. doi:10.1038/nprot.2018.038
  5. T. Frisch, J. Gøttcke, R. Röttger, Q. Tan, J. Baumbach. DiMmer: Discovery of Differentially Methylated Regions in Epigenome-Wide Association Study (EWAS) Data. (2018) Data Mining for Systems Biology, 51-62. doi:10.1007/978-1-4939-8561-6_5
  6. S. Hassan, S. Jamal, L. Radusky, S. Tiwari, A. Ullah, J. Ali, P. Carvalho, R. Shams, S. Khan, H. Figueiredo, D. Barh, P. Ghosh, A. Silva, J. Baumbach, R. Röttger, A. Gustavo, V. Azevedo. The Druggable Pocketome of Corynebacterium diphtheriae: A new approach for in-silico putative druggable targets. (2018) Frontiers in Genetics, 9, 44. doi:10.3389/fgene.2018.00044
  7. C. Wiwie, A. Rauch, A. Haakonsson, I. Barrio-Hernandez, B. Blagoev, S. Mandrup, R. Röttger, J. Baumbach. Elucidation of time-dependent systems biology cell response patterns with time course network enrichment. (2017) arXiv preprint, arXiv:1710.10262.
  8. S. Jamal, S. Hassan, S. Tiwari, M. Viana, L. Benevides, A. Ullah, A. Turjanski, D. Barh, P. Ghosh, D. Costa, A. Silva, R. Röttger, J. Baumbach, V. Azevedo. An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. (2017) PloS ONE, 12(10), e0186401. doi:10.1371/journal.pone.0186401
  9. E. Barbosa, R. Röttger, A.-C. Hauschild, S. Soares, S. Böcker, V. Azevedo, J. Baumbach. LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. (2017) Journal of Integrative Bioinformatics, doi:10.1515/jib-2017-0010
  10. C. Wiwie, R. Röttger. On the power and limits of sequence similarity based clustering of proteins into families. (2017) Pacific Symposium on Biocomputing, Pacific Symposium on Biocomputing 22, 39-50. doi:10.1142/9789813207813_0005
  11. E. Folador, P. de Carvalho, W. Silva, R. Ferreira, A. Silva, M. Gromiha, P. Ghosh, D. Barh, V. Azevedo, R. Röttger. In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks. (2016) BMC Systems Biology, 10 (1), 103. doi:10.1186/s12918-016-0346-4
  12. D. Almeida, I. Skov, A. Silva, F. Vandin, Q. Tan, R. Röttger, J. Baumbach. Efficient detection of differentially methylated regions using DiMmeR. (2016) Bioinformatics, btw657. doi:10.1093/bioinformatics/btw657
  13. D. Almeida, I. Skov, J. Lund, A. Mohammadnejad, A. Silva, F. Vandin, Q. Tan, J. Baumbach, R. Röttger. Jllumina - A comprehensive Java-based API for statistical Illumina Innium HumanMethylation450 and Innium MethylationEPIC BeadChip data processing. (2016) Journal of Integrative Bioinformatics, 13.4: 24-32. doi:10.1515/jib-2016-294
  14. R. Röttger. Clustering of Biological Datasets in the Era of Big Data. (2016) Journal of Integrative Bioinformatics, 13 (1), 300. doi:10.1515/jib-2016-300
  15. M. Chen, J. Baumbach, F. Vandin, R. Röttger, E. Barbosa, M. Dong, M. Frost, L. Christiansen, Q. Tan. Differentially Methylated Genomic Regions in Birth-Weight Discordant Twin Pairs. (2016) Annals of Human Genetics, 80 (2), 81-87, doi:10.1111/ahg.12146
  16. V. A. Abreu, S. Almeida, S. Tiwari, S. Hassan, D. Mariano, A. Silva, J. Baumbach, V. Azevedo, R. Röttger. CMRegNetAn interspecies reference database for corynebacterial and mycobacterial regulatory networks. (2015) BMC genomics, 16(1), 452. doi:10.1186/s12864-015-1631-0
  17. C. Wiwie, J. Baumbach, R. Röttger. Comparing the performance of biomedical clustering methods. (2015) Nature Methods, 12 (11), 1033-1038, doi:10.1038/nmeth.3583
  18. D. Vu, S. Szöke, C. Wiwie, J. Baumbach, G. Cardinali, R. Röttger, V. Robert. Massive fungal biodiversity data re-annotation with multi-level clustering. (2014) Scientific Reports, 4. doi:10.1038/srep06837
  19. G. Misirli, J. Hallinan, R. Röttger, J. Baumbach, A. Wipat. BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species. (2014) Journal of Integrative Bioinformatics, 11(2), 244. doi:10.2390/biecoll-jib-2014-244
  20. E. Barbosa, R. Röttger, A. Hauschild, V. Azevedo, J. Baumbach. On the limits of computational functional genomics for bacterial lifestyle prediction. (2014) Briefings in Functional Genomics, 13 (5): 398-408. doi:10.1093/bfgp/elu014
  21. P. Sun, N. Speicher, R. Röttger, J. Guo, J. Baumbach. Bi-Force - Large-scale bicluster editing and its application to gene expression data biclustering. (2014) Nucleic Acids Research, 42 (9): e78. doi:10.1093/nar/gku201
  22. J. Baumbach, R. Röttger. Computational Integrative Biology - on the joint analysis of diverse biological data sets. (2014) Integrative Biology, 6(11), 1008-1009. doi:10.1039/C4IB90037E
  23. A. Santos, V. Pereira, E. Barbosa, J. Baumbach, J. Pauling, R. Röttger, M.Turk, A. Silva, A. Miyoshi, V. Azevedo. Mature Epitope Density-A strategy for target selection based on immunoinformatics and exported prokaryotic proteins. (2014) BMC Genomics, 14 (Suppl 6), S4. doi:10.1186/1471-2164-14-S6-S4
  24. R. Röttger, P. Kalaghatgi, P. Sun, S. Soares, V. Azevedo, T. Wittkop, J. Baumbach. Density parameter estimation for finding clusters of homologous proteins  tracing actinobacterial pathogenicity lifestyles. (2013) Bioinformatics, 29 (2), 215-222. doi:10.1093/bioinformatics/bts653
  25. R. Röttger, C. Kreutzer, T. Vu, T. Wittkop, J. Baumbach. Online Transitivity Clustering of Biological Data with Missing Values. (2012) German Conference on Bioinformatics, 57-68, ISBN: 978-3-939897-44-6. doi:10.4230/OASIcs.GCB.2012.57
  26. R. Röttger*, J. Pauling*, A. Neuner, H. Salgado, J. Collado-Vides, A. Tauch, A. Puehler, J. Baumbach. On the trail of EHEC/EAEC - Unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria. (2012) Integrative Biology, 4, 728-733. doi:10.1039/C2IB00132B
    *joint first authors
  27. R. Röttger, U. Rückert, J. Taubert, J. Baumbach. How Little Do We Actually Know?  On the Size of Gene Regulatory Networks. (2012) IEEE/ACM Transactions on Computational Biology and Bioinformatics IEEE, ACM, 9(5), 1293-1300. doi:10.1109/TCBB.2012.71
  28. T. Wittkop, S. Rahmann, R. Röttger, S. Böcker, J. Baumbach. Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis. (2011) Int Math., 7:4, 255-273. doi:10.1080/15427951.2011.604559
  29. J. Pauling, R. Röttger, A. Tauch, V. Azevedo, J. Baumbach. CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Research, Jan;40(1):D610-4. doi:10.1093/nar/gkr883
  30. F. Kneissl, R. Röttger, U. Sandner, H. 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.

Book Chapters

  1. N. Pržulj, Analyzing Network Data in Biology and Medicine: An Interdisciplinary Textbook for Biological, Medical and Computational Scientists. (2019) Cambridge University Press. ISBN:9781108377706.
    Sole Author of the Chapter “Unsupervised Learning: Cluster Analysis”.
  2. P. Nepper, N. Konrad. The Future of Social Commerce. Trend Report 2007/2008. Center for Digital Technology & Management (CDTM), München, 2009. ISBN: 9783981220315
    Co-Author of two chapters.

Curriculum Vitae

Current Position

  • since 11/17 University of Southern Denmark, Odense, Denmark
    Associate Professor
    Head of the Computational Biology Lab.
    Coordinator of the Computational BioMedicine undergraduate education program.
    Research interests: big data, machine learning, clustering, data integration.

Education

  • 04/17 - 08/17 MRC-LMB, University of Cambridge, United Kingdom
    Sabbatical
    Visiting researcher at the Structural Studies Division. Large scale study of the evolutionary conservation of genomic regions in different ethnicities.
  • 06/14 - 11/17 University of Southern Denmark, Odense, Denmark
    Assistant Professor
    Head of the Practical Computer Science in BioMedicine Lab.
  • 12/10 - 05/14 Max Planck Institute for Informatics, Saarbrücken, Germany
    PhD Student
    Member of the Computational System Biology group.
  • 10/04 - 10/10 Technical University of Munich, Germany
    Computer Science, Minor Math
    Diploma GPA: 1.0. Thesis Written in Berkeley, awarded with the Siemens Award.
  • 08/09 - 12/09 International Computer Science Institute, UC Berkeley, CA, USA
    Research Fellow
    Thesis: Estimating the Size and Completeness of Gene Regulatory Networks.
  • 03/07 - 09/09 Center for Digital Technology and Management, Munich, Germany
    Technology Management
    Honours degree in Technology Management, GPA: 1.4.
  • 08/08 - 01/09 School of Information, UC Berkeley, CA, USA
    Research Fellow
    Development of a simulator for user behavior on social network sites.

Funding & Fellowships

  • since 01/19 H2020 RIA Grant, FeatureCloud, Grant Agreement No. 826078
    Co-PI, Workpackage Leader
    Awarded 4.5 million EUR total, my share: 500k EUR.
  • 12/10 - 05/14 PhD scholarship, International Max Planck Research School
    Funding for three years, approx. 55k EUR.
  • 08/09 - 12/09 Diploma scholarship, German Academic Exchange Service
  • 08/08 - 01/09 Diploma scholarship, Lothar und Sigrid Rohde-Stiftung

Teaching and Supervision

  • Completed the Lecturer Training Program of SDU in 2016
  • Lecturer for Deep Learning, spring 2018-2019
  • Lecturer for Deep Learning summer school, summer 2018
  • Lecturer for Introduction to Bioinformatics, fall 2016, fall 2018
  • Lecturer for Unsupervised Learning, spring 2015-2017
  • Lecturer for Computer Architecture, fall 2014-2016
  • Guest teaching position at Reutlingen University for the course Principal Component Analysis, winter 2016
  • Supervision:
    • PhD students (main supervisor): 3 students
    • PhD students (co-supervisor): 5 students
    • BSc and MSc theses: 20+ students
    • Individual study activities and research assistants: 15+ students

Other Professional Activities

  • since 11/2017 Study Program Co-Coordinator, Computational BioMedicine, SDU
  • since 11/2017 Executive Board, eScience Center, SDU
  • since 09/2016 Coordinator for international student intake and outreach at IMADA
  • since 12/2018 Founding Co-Director of the International Association for Systems Medicine
  • since 09/18 COST Action Management Committee Member CA15120 - OpenMultiMed
  • Editorial Board Memberships
    • Systems Medicine
    • Nature Scientific Reports
    • Journal of Integrative Bioinformatics
    • Metabolites
  • Grant Reviewing
    • Luxembourg National Research Fund (FNR)
    • Israel Science Foundation (ISF)
    • German Academic Exchange Council (DAAD)
  • Program Committees
    • International Symposium on Integrative Bioinformatics 2017
    • ISMB/ECCB 2017, Network Biology Track
    • International Joint Conference on Artificial Intelligence 2016

Awards & Honors

  • 2018 Keynote speaker
    North and Northeast Symposium of Bioinformatics (III SNNB)
  • 2017 Keynote speaker
    International Symposium on Integrative Bioinformatics (IB’17)
  • 2016 Keynote speaker
    Brazilian Bioinformatics Conference (x-meeting’16)
  • 2016 Invited speaker
    European Conference on Computational Biology (ECCB’16)
  • 2016 Highlight track talk
    Great Lakes Bioinformatics Conference (GLBIO’16)
  • 2010 Siemens Award
    (1000 EUR)
  • 2009 TheoPrax Award
    (600 EUR)
  • 2008 Theseus Talente Award
    (Ministry of Economics and Technology, 4th rank, 5000 EUR)