GROUP: Computational Oncology

We are adapting methods from machine learning to various data types from molecular genetics. We are developing new methods for their analysis, in particular with applications to oncology.


  • Batra R, Harder N, Gogolin S, Diessl N, Soons Z, Jäger-Schmidt C,Lawerenz C, Eils R, Rohr K, Westermann F, König R. Time-lapse imaging of neuroblastoma cells to determine cell fate upon gene knockdown, PLoS ONE (2012, in press).
  • Goglin S, Batra R, Harder N, Ehemann V, Paffhausen T , Diessl N, Gade S, Nolte I, Rohr K, König R, Westermann F. MYCN-mediated overexpression of mitotic spindle regulatory genes and loss of p53-p21 function jointly support the survival of tetraploid neuroblastoma cells, Cancer Letters (2012, accepted)
  • Bauer, T., R. Eils, and R. Konig. 2011. “RIP: The Regulatory Interaction Predictor - a Machine Learning Based Approach for Predicting Target Genes of Transcription Factors.” Bioinformatics 27 (16) (June 20): 2239–47. DOI: http://dx.doi.org/10.1093/bioinformatics/btr366
  • Kranz, Anna-Lena, Roland Eils, and Rainer König. 2011. “Enhancers Regulate Progression of Development in Mammalian Cells.” Nucleic Acids Research (July 23). DOI: http://dx.doi.org/10.1093/nar/gkr602
  • Lewis, Nathan E, Kim K Hixson, Tom M Conrad, Joshua A Lerman, Pep Charusanti, Ashoka D Polpitiya, Joshua N Adkins, et al. 2010. “Omic Data from Evolved E. Coli Are Consistent with Computed Optimal Growth from Genome-scale Models.” Molecular Systems Biology 6 (July): 390. DOI: http://dx.doi.org/10.1038/msb.2010.47
  • Lewis, Nathan E, Gunnar Schramm, Aarash Bordbar, Jan Schellenberger, Michael P Andersen, Jeffrey K Cheng, Nilam Patel, et al. 2010. “Large-scale in Silico Modeling of Metabolic Interactions Between Cell Types in the Human Brain.” Nature Biotechnology 28 (12) (November 21): 1279–85. DOI: http://dx.doi.org/10.1038/nbt.1711
  • Plaimas, Kitiporn, Roland Eils, and Rainer König. 2010. “Identifying Essential Genes in Bacterial Metabolic Networks with Machine Learning Methods.” BMC Systems Biology 4 (January): 56. DOI: http://dx.doi.org/10.1186/1752-0509-4-56
  • Schramm, Gunnar, Nandakumar Kannabiran, and Rainer König. 2010. “Regulation Patterns in Signaling Networks of Cancer.” BMC Systems Biology 4 (January): 162. DOI: http://dx.doi.org/10.1186/1752-0509-4-162
  • Schramm, Gunnar, Eva-Maria Surmann, Stefan Wiesberg, Marcus Oswald, Gerhard Reinelt, Roland Eils, and Rainer König. 2010. “Analyzing the Regulation of Metabolic Pathways in Human Breast Cancer.” BMC Medical Genomics 3 (January): 39. DOI: http://dx.doi.org/10.1186/1755-8794-3-39
  • Schramm, Gunnar, Stefan Wiesberg, Nicolle Diessl, Anna-Lena Kranz, Vitalia Sagulenko, Marcus Oswald, Gerhard Reinelt, Frank Westermann, Roland Eils, and Rainer König. 2010. “PathWave: Discovering Patterns of Differentially Regulated Enzymes in Metabolic Pathways.” Bioinformatics (Oxford, England) 26 (9) (May 1): 1225–31. DOI: http://dx.doi.org/10.1093/bioinformatics/btq113
  • Suratanee, Apichat, Ilka Rebhan, Petr Matula, Anil Kumar, Lars Kaderali, Karl Rohr, Ralf Bartenschlager, Roland Eils, and Rainer König. 2010. “Detecting Host Factors Involved in Virus Infection by Observing the Clustering of Infected Cells in siRNA Screening Images.” Bioinformatics (Oxford, England) 26 (18) (September 15): i653–8. DOI: http://dx.doi.org/10.1093/bioinformatics/btq398