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  • B. Bischl, G. Casalicchio, M. Feurer, F. Hutter, M. Lang, R. G. Mantovani, J. N. van Rijn and J. Vanschoren. OpenML Benchmarking Suites and the OpenML100. ArXiv e-prints, August 2017.
  • Giuseppe Casalicchio, Jakob Bossek, Michel Lang, Dominik Kirchhoff, Pascal Kerschke, Benjamin Hofner, Heidi Seibold, Joaquin Vanschoren and Bernd Bischl. OpenML: An R package to connect to the machine learning platform OpenML. Computational Statistics, Jun 2017. [DOI]
  • Anne-Sophie Heimes, Katrin Madjar, Karolina Edlund, Marco J. Battista, Katrin Almstedt, Tania Elger, Slavomir Krajnak, Jörg Rahnenführer, Walburgis Brenner, Annette Hasenburg, Jan G. Hengstler and Marcus Schmidt. Subtype-specific prognostic impact of different immune signatures in node-negative breast cancer. Breast Cancer Research and Treatment, Jun 2017. [DOI]
  • S. Kuhnast, J. Schiffner Rohe, J. Rahnenführer and F. Leverkus. Evaluation of Adjusted and Unadjusted Indirect Comparison Methods in Benefit Assessment. A Simulation Study for Time-to-event Endpoints. Methods Inf Med, vol. 56 no. 3, pages 261-267, May 2017.
  • G. Pallocca, J. Nyffeler, X. Dolde, M. Grinberg, G. Gstraunthaler, T. Waldmann, J. Rahnenführer, A. Sachinidis and M. Leist. Impairment of human neural crest cell migration by prolonged exposure to interferon-beta. Arch. Toxicol., Apr 2017.
  • Julia Serong, Lars Koppers, Edith Luschmann, Alejandro Molina Ramirez, Kristian Kersting, Jörg Rahnenführer and Holger Wormer. Öffentlichkeitsorientierung von Wissenschaftsinstitutionen und Wissenschaftsdisziplinen. Publizistik, pages 1-26, April 2017. [DOI]
  • B. Bischl, J. Richter, J. Bossek, D. Horn, J. Thomas and M. Lang. mlrMBO: A Modular Framework for Model-Based Optimization of Expensive Black-Box Functions. ArXiv e-prints, March 2017.
  • M. Grinberg, D. Djureinovic, H. R. Brunnstrom, J. S. Mattsson, K. Edlund, J. G. Hengstler, L. La Fleur, S. Ekman, H. Koyi, E. Branden, E. Stahle, K. Jirstrom, D. K. Tracy, F. Ponten, J. Botling, J. Rahnenführer and P. Micke. Reaching the limits of prognostication in non-small cell lung cancer: an optimized biomarker panel fails to outperform clinical parameters. Mod. Pathol., Mar 2017.
  • V. Rieder, B. Blank Landeshammer, M. Stuhr, T. Schell, K. Biss, L. Kollipara, A. Meyer, M. Pfenninger, H. Westphal, A. Sickmann and J. Rahnenführer. DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs. BMC Bioinformatics, vol. 18 no. 1, page 148, Mar 2017.
  • Andrea Bommert, Jörg Rahnenfürer and Michel Lang. A Multicriteria Approach to Find Predictive and Sparse Models with Stable Feature Selection for High-Dimensional Data. Computational and Mathematical Methods in Medicine, 2017. [DOI]
  • Mikheil Gogiashvili, Salome Horsch, Rosemarie Marchan, Kathrin Gianmoena, Cristina Cadenas, Berno Tanner, Sabrina Naumann, Diana Ersova, Frank Lippek, Jörg Rahnenführer, Jan T. Andersson, Roland Hergenröder, Jörg Lambert, Jan G. Hengstler and Karolina Edlund. Impact of intratumoral heterogeneity of breast cancer tissue on quantitative metabolomics using high -resolution magic angle spinning (1) H NMR spectroscopy. NMR in Biomedicine, page e3862, 2017. PMID: 29206323. [DOI]
  • Anne-Sophie Heimes, Katrin Madjar, Karolina Edlund, Marco J. Battista, Katrin Almstedt, Susanne Gebhard, Sebastian Foersch, Jörg Rahnenführer, Walburgis Brenner, Annette Hasenburg, Jan G. Hengstler and Marcus Schmidt. Prognostic significance of interferon regulating factor 4 (IRF4) in node-negative breast cancer. Journal of Cancer Research and Clinical Oncology, pages 1-9, 2017. [DOI]
  • Salome Horsch, Dominik Kopczynski, Elias Kuthe, Jörg Ingo Baumbach, Sven Rahmann and Jörg Rahnenführer. A detailed comparison of analysis processes for MCC-IMS data in disease classification—Automated methods can replace manual peak annotations. PLOS ONE, vol. 12 no. 9, page e0184321, 2017. [DOI]
  • Verena Jabs, Karolina Edlund, Helena König, Marianna Grinberg, Katrin Madjar, Jörg Rahnenführer, Simon Ekman, Michael Bergkvist, Lars Holmberg, Katja Ickstadt, Johan Botling, Jan G. Hengstler and Patrick Micke. Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer. PLOS ONE, vol. 12 no. 11, pages 1-23, 11 2017. [DOI]
  • Helena Kotthaus, Jakob Richter, Andreas Lang, Janek Thomas, Bernd Bischl, Peter Marwedel, Jörg Rahnenführer and Michel Lang. RAMBO: Resource-Aware Model-Based Optimization with Scheduling for Heterogeneous Runtimes and a Comparison with Asynchronous Model-Based Optimization. In Proceedings of the 11th International Conference: Learning and Intelligent Optimization (LION 11) (accepted for publication).. Lecture Notes in Computer Science, Springer, 2017.
  • Michel Lang. Efficient R Programming. Journal of Statistical Software, Book Reviews, vol. 80 no. 3, pages 1-4, 2017. [DOI]
  • Michel Lang. checkmate: Fast Argument Checks for Defensive R Programming. The R Journal, vol. 9 no. 1, pages 437-445, 2017.
  • Michel Lang, Bernd Bischl and Dirk Surmann. batchtools: Tools for R to work on batch systems. The Journal of Open Source Software, vol. 2 no. 10, 2017. [DOI]
  • Rosemarie Marchan, Bettina Büttner, Jörg Lambert, Karolina Edlund, Iris Glaeser, Meinolf Blaszkewicz, Gregor Leonhardt, Lisa Marienhoff, Darius Kaszta, Moritz Anft, Carsten Watzl, Katrin Madjar, Marianna Grinberg, Eugen Rempel, Roland Hergenröder, Silvia Selinski, Jörg Rahnenführer, Michaela S Lesjak, Joanna D Stewart, Cristina Cadenas and Jan G. Hengstler. Glycerol-3-phosphate acyltransferase 1 promotes tumor cell migration and poor survival in ovarian carcinoma. Cancer Research, 2017. [DOI]
  • Vera Rieder, Bernhard Blank Landeshammer, Marleen Stuhr, Tilman Schell, Karsten Biß, Laxmikanth Kollipara, Achim Meyer, Markus Pfenninger, Hildegard Westphal, Albert Sickmann and Jörg Rahnenführer. DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs. BMC Bioinformatics, vol. 18 no. 1, page 148, 2017. [DOI]
  • Vera Rieder, Karin U. Schork, Laura Kerschke, Bernhard Blank Landeshammer, Albert Sickmann and Jörg Rahnenführer. Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra. Journal of Proteome Research, vol. 16 no. 11, pages 4035-4044, 2017. PMID: 28959885. [DOI]
  • Marleen Stuhr, Claire E. Reymond, Vera Rieder, Pamela Hallock, Jörg Rahnenführer, Hildegard Westphal and Michal Kucera. Reef calcifiers are adapted to episodic heat stress but vulnerable to sustained warming. PLOS ONE, vol. 12 no. 7, pages 1-20, 07 2017. [DOI]


  • Birte Hellwig, Katrin Madjar, Karolina Edlund, Rosemarie Marchan, Cristina Cadenas, Anne-Sophie Heimes, Katrin Almstedt, Antje Lebrecht, Isabel Sicking, Marco J. Battista, Patrick Micke, Marcus Schmidt, Jan G. Hengstler and Jörg Rahnenführer. Epsin Family Member 3 and Ribosome-Related Genes Are Associated with Late Metastasis in Estrogen Receptor-Positive Breast Cancer and Long-Term Survival in Non-Small Cell Lung Cancer Using a Genome-Wide Identification and Validation Strategy. PLOS ONE, vol. 11 no. 12, page e0167585, December 2016. [DOI]
  • V. Shinde, S. Perumal Srinivasan, M. Henry, T. Rotshteyn, J. Hescheler, J. Rahnenführer, M. Grinberg, J. Meisig, N. Bluthgen, T. Waldmann, M. Leist, J. G. Hengstler and A. Sachinidis. Comparison of a teratogenic transcriptome-based predictive test based on human embryonic versus inducible pluripotent stem cells. Stem Cell Res Ther, vol. 7 no. 1, page 190, Dec 2016.
  • Lars Koppers, Holger Wormer and Katja Ickstadt. Towards a Systematic Screening Tool for Quality Assurance and Semiautomatic Fraud Detection for Images in the Life Sciences. Science and Engineering Ethics, pages 1-16, November 2016. [DOI]
  • M. Schwaiger, M. Grinberg, D. Moser, J. C. Zang, M. Heinrichs, J. G. Hengstler, J. Rahnenführer, S. Cole and R. Kumsta. Altered Stress-Induced Regulation of Genes in Monocytes in Adults with a History of Childhood Adversity. Neuropsychopharmacology, vol. 41 no. 10, pages 2530-2540, Sep 2016.
  • Dijana Djureinovic, Björn M. Hallström, Masafumi Horie, Johanna Sofia Margareta Mattsson, Linnea La Fleur, Linn Fagerberg, Hans Brunnström, Cecilia Lindskog, Katrin Madjar, Jörg Rahnenführer, Simon Ekman, Elisabeth Ståhle, Hirsh Koyi, Eva Brandén, Karolina Edlund, Jan G. Hengstler, Mats Lambe, Akira Saito, Johan Botling, Fredrik Pontén, Mathias Uhlén and Patrick Micke. Profiling cancer testis antigens in non–small-cell lung cancer. JCI Insight, vol. 1 no. 10, July 2016. [DOI]
  • Elena Erdmann, Karin Boczek, Lars Koppers, Gerret von Nordheim, Christian Pölitz, Alejandro Molina, Katharina Morik, Henrik Müller, Jörg Rahnenführer and Kristian Kersting. Machine Learning meets Data-Driven Journalism: Boosting International Understanding and Transparency in News Coverage. arXiv:1606.05110 [cs, stat], jun 2016. arXiv: 1606.05110.
  • Jakob Richter, Helena Kotthaus, Bernd Bischl, Peter Marwedel, Jörg Rahnenführer and Michel Lang. Faster Model-Based Optimization Through Resource-Aware Scheduling Strategies. In Learning and Intelligent Optimization, pages 267-273. Springer, Cham, May 2016. [DOI]
  • V. Shinde, L. Hoelting, S. P. Srinivasan, J. Meisig, K. Meganathan, S. Jagtap, M. Grinberg, J. Liebing, N. Bluethgen, J. Rahnenführer, E. Rempel, R. Stoeber, S. Schildknecht, S. Forster, P. Godoy, C. van Thriel, J. A. Gaspar, J. Hescheler, T. Waldmann, J. G. Hengstler, M. Leist and A. Sachinidis. Definition of transcriptome-based indices for quantitative characterization of chemically disturbed stem cell development: introduction of the STOP-Toxukn and STOP-Toxukk tests. Archives of Toxicology, pages 1-26, May 2016.
  • L. Hoelting, S. Klima, C. Karreman, M. Grinberg, J. Meisig, M. Henry, T. Rotshteyn, J. Rahnenführer, N. Blüthgen, A. Sachinidis, T. Waldmann and M. Leist. Stem Cell-Derived Immature Human Dorsal Root Ganglia Neurons to Identify Peripheral Neurotoxicants. Stem Cells Transl Med, vol. 5 no. 4, pages 476-487, Apr 2016.
  • M. D. Arbo, S. Melega, R. Stober, M. Schug, E. Rempel, J. Rahnenführer, P. Godoy, R. Reif, C. Cadenas, M. de Lourdes Bastos, H. Carmo and J. G. Hengstler. Hepatotoxicity of piperazine designer drugs: up-regulation of key enzymes of cholesterol and lipid biosynthesis. Archives of Toxicology, Jan 2016.
  • G. Pallocca, M. Grinberg, M. Henry, T. Frickey, J. G. Hengstler, T. Waldmann, A. Sachinidis, J. Rahnenführer and M. Leist. Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration. Archives of Toxicology, vol. 90 no. 1, pages 159-180, Jan 2016.
  • Bernd Bischl, Michel Lang, Lars Kotthoff, Julia Schiffner, Jakob Richter, Erich Studerus, Giuseppe Casalicchio and Zachary M. Jones. Mlr: Machine Learning in R. Journal of Machine Learning Research, vol. 17 no. 170, pages 1-5, 2016.
  • Mikheil Gogiashvili, Karolina Edlund, Kathrin Gianmoena, Rosemarie Marchan, Alexander Brik, Jan T. Andersson, Jörg Lambert, Katrin Madjar, Birte Hellwig, Jörg Rahnenführer, Jan G. Hengstler, Roland Hergenröder and Cristina Cadenas. Metabolic profiling of ob/ob mouse fatty liver using HR-MAS 1H-NMR combined with gene expression analysis reveals alterations in betaine metabolism and the transsulfuration pathway. Analytical and Bioanalytical Chemistry, pages 1-16, 2016. [DOI]


  • Miriam Lohr, Birte Hellwig, Karolina Edlund, Johanna S.M. Mattsson, Johan Botling, Marcus Schmidt, Jan G. Hengstler, Patrick Micke and Jörg Rahnenführer. Identification of sample annotation errors in gene expression datasets. Archives of Toxicology, vol. 89 no. 12, pages 2265-2272, Dec 2015.
  • Sarah Kühnast, Julia Schiffner Rohe, Jörg Rahnenführer and Friedhelm Leverkus. Indirect Comparisons in Benefit Assessment. Value Health, vol. 18 no. 7, page A721, Nov 2015.
  • Anna-Maria Stock, Franziska Klee, Karolina Edlund, Marianna Grinberg, Seddik Hammad, Rosemarie Marchan, Cristina Cadenas, Bernd Niggemann, Kurt S Zänker, Jörg Rahnenführer, Marcus Schmidt, Jan G Hengstler and Frank Entschladen. Gelsolin Is Associated with Longer Metastasis-free Survival and Reduced Cell Migration in Estrogen Receptor-positive Breast Cancer. Anticancer Res., vol. 35 no. 10, pages 5277-5285, Oct 2015.
  • Eugen Rempel, Lisa Hoelting, Tanja Waldmann, Nina V. Balmer, Stefan Schildknecht, Marianna Grinberg, John Antony Das Gaspar, Vaibhab Shinde, Regina Stober, Rosemarie Marchan, Christoph van Thriel, Julia Liebing, Johannes Meisig, Nils Blüthgen, Agapios Sachinidis, Jörg Rahnenführer, Jan G. Hengstler and Marcel Leist. A transcriptome-based classifier to identify developmental toxicants by stem cell testing: design, validation and optimization for histone deacetylase inhibitors. Arch. Toxicol., vol. 89 no. 9, pages 1599-1618, Sep 2015.
  • Simona Constantinescu, Ewa Szczurek, Pejman Mohammadi, Jörg Rahnenführer and Niko Beerenwinkel. TiMEx: a waiting time model for mutually exclusive cancer alterations. Bioinformatics, Jul 2015.
  • Jörg Rahnenführer and Marcel Leist. From smoking guns to footprints: mining for critical events of toxicity pathways in transcriptome data. Arch. Toxicol., vol. 89 no. 5, pages 813-817, May 2015.
  • Johanna S.M. Mattsson, Bengt Bergman, Marianna Grinberg, Karolina Edlund, Millaray Marincevic, Karin Jirström, Fredrik Pontén, Jan G. Hengstler, Jörg Rahnenführer, Mats G. Karlsson, Christina Karlsson, Gisela Helenius, Johan Botling, Patrick Micke and Miklos Gulyas. Prognostic impact of COX-2 in non-small cell lung cancer: a comprehensive compartment-specific evaluation of tumor and stromal cell expression. Cancer Lett., vol. 356 no. 2 Pt B, pages 837-845, Jan 2015.
  • Maike Ahrens​, Michael Turewicz, Katrin Marcus, Helmut E. Meyer, Caroline May, Martin Eisenacher and Jörg Rahnenführer. FSOL - a workflow for the detection of patient subgroups and affected molecular features in high-throughput omics data. PeerJ PrePrints, vol. 3, page e1604, 2015.
  • Bernd Bischl, Michel Lang, Olaf Mersmann, Jörg Rahnenführer and Claus Weihs. BatchJobs and BatchExperiments: Abstraction Mechanisms for Using R in Batch Environments. Journal of Statistical Software, vol. 64 no. 11, pages 1-235, 2015.
  • Salome Horsch, Dominik Kopczynski, Jörg Ingo Baumbach, Jörg Rahnenführer and Sven Rahmann. From raw ion mobility measurements to disease classification: a comparison of analysis processes. PeerJ PrePrints, vol. 3, page e1591, 2015.
  • Michel Lang. Automatische Modellselektion in der Überlebenszeitanalyse. Dissertation, TU Dortmund, Dortmund, 2015.
  • V. Shinde, S. Klima, P. S. Sureshkumar, K. Meganathan, S. Jagtap, E. Rempel, J. Rahnenführer, J. G. Hengstler, T. Waldmann, J. Hescheler, M. Leist and A. Sachinidis. Human Pluripotent Stem Cell Based Developmental Toxicity Assays for Chemical Safety Screening and Systems Biology Data Generation. J Vis Exp, page e52333, 2015.


  • M. Grinberg, R. M. Stober, K. Edlund, E. Rempel, P. Godoy, R. Reif, A. Widera, K. Madjar, W. Schmidt Heck, R. Marchan, A. Sachinidis, D. Spitkovsky, J. Hescheler, H. Carmo, M. D. Arbo, B. van de Water, S. Wink, M. Vinken, V. Rogiers, S. Escher, B. Hardy, D. Mitic, G. Myatt, T. Waldmann, A. Mardinoglu, G. Damm, D. Seehofer, A. Nussler, T. S. Weiss, A. Oberemm, A. Lampen, M. M. Schaap, M. Luijten, H. van Steeg, W. E. Thasler, J. C. Kleinjans, R. H. Stierum, M. Leist, J. Rahnenführer and J. G. Hengstler. Toxicogenomics directory of chemically exposed human hepatocytes. Arch. Toxicol., vol. 88 no. 12, pages 2261-2287, Dec 2014.
  • Patrick Micke, Johanna Sofia Margareta Mattsson, Karolina Edlund, Miriam Lohr, Karin Jirström, Anders Berglund, Johan Botling, Jörg Rahnenfuehrer, Millaray Marincevic, Fredrik Pontén, Simon Ekman, Jan Hengstler, Stefan Wöll, Ugur Sahin and Özlem Türeci. Aberrantly activated claudin 6 and 18.2 as potential therapy targets in non-small-cell lung cancer. International Journal of Cancer, vol. 135 no. 9, pages 2206-2214, November 2014. [DOI]
  • D. M. Waldera Lupa, F. Kalfalah, A. M. Florea, S. Sass, F. Kruse, V. Rieder, J. Tigges, E. Fritsche, J. Krutmann, H. Busch, M. Boerries, H. E. Meyer, F. Boege, F. Theis, G. Reifenberger and K. Stuhler. Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts. Aging (Albany NY), vol. 6 no. 10, pages 856-878, Oct 2014.
  • Daniel M. Waldera Lupa, Faiza Kalfalah, Ana-Maria Florea, Steffen Sass, Fabian Kruse, Vera Rieder, Julia Tigges, Ellen Fritsche, Jean Krutmann, Hauke Busch, Melanie Boerries, Helmut E. Meyer, Fritz Boege, Fabian Theis, Guido Reifenberger and Kai Stühler. Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts. Aging, vol. 6 no. 10, pages 856-878, October 2014. [DOI]
  • Cecilia Lindskog, Linn Fagerberg, Björn Hallström, Karolina Edlund, Birte Hellwig, Jörg Rahnenführer, Caroline Kampf, Mathias Uhlén, Fredrik Pontén and Patrick Micke. The lung-specific proteome defined by integration of transcriptomics and antibody-based profiling. The FASEB Journal, pages fj.14-254862, August 2014. [DOI]
  • Nina V. Balmer, Stefanie Klima, Eugen Rempel, Violeta N. Ivanova, Raivo Kolde, Matthias K. Weng, Kesavan Meganathan, Margit Henry, Agapios Sachinidis, Michael R. Berthold, Jan G. Hengstler, Jörg Rahnenführer, Tanja Waldmann and Marcel Leist. From transient transcriptome responses to disturbed neurodevelopment: role of histone acetylation and methylation as epigenetic switch between reversible and irreversible drug effects. Archives of Toxicology, vol. 88 no. 7, pages 1451-1468, July 2014. [DOI]
  • Patricio Godoy, Cristina Cadenas, Birte Hellwig, Rosemarie Marchan, Joanna Stewart, Raymond Reif, Miriam Lohr, Matthias Gehrmann, Jörg Rahnenführer, Markus Schmidt and Jan G. Hengstler. Interferon-inducible guanylate binding protein (GBP2) is associated with better prognosis in breast cancer and indicates an efficient T cell response. Breast Cancer, vol. 21 no. 4, pages 491-499, July 2014. [DOI]
  • Helena Kotthaus, Ingo Korb, Michel Lang, Bernd Bischl, Jörg Rahnenführer and Peter Marwedel. Runtime and memory consumption analyses for machine learning R programs. Journal of Statistical Computation and Simulation, vol. 85 no. 1, pages 14-29, June 2014. [DOI]
  • Michel Lang, Helena Kotthaus, Peter Marwedel, Claus Weihs, Jörg Rahnenführer and Bernd Bischl. Automatic model selection for high-dimensional survival analysis. Journal of Statistical Computation and Simulation, vol. 85 no. 1, pages 62-76, June 2014. [DOI]
  • Stefan Linsler, Dennis Kraemer, Christina Driess, Joachim Oertel, Kai Kammers, Jörg Rahnenführer, Ralf Ketter and Steffi Urbschat. Molecular Biological Determinations of Meningioma Progression and Recurrence. PLoS ONE, vol. 9 no. 4, page e94987, April 2014. [DOI]
  • Tanja Waldmann, Eugen Rempel, Nina V. Balmer, André König, Raivo Kolde, John Antonydas Gaspar, Margit Henry, Jürgen Hescheler, Agapios Sachinidis, Jörg Rahnenführer, Jan G. Hengstler and Marcel Leist. Design Principles of Concentration-Dependent Transcriptome Deviations in Drug-Exposed Differentiating Stem Cells. Chemical Research in Toxicology, vol. 27 no. 3, pages 408-420, March 2014. [DOI]
  • Satoshi Noguchi, Akira Saito, Masafumi Horie, Yu Mikami, Hiroshi I. Suzuki, Yasuyuki Morishita, Mitsuhiro Ohshima, Yoshimitsu Abiko, Johanna Sofia Margareta Mattsson, Helena König, Miriam Lohr, Karolina Edlund, Johan Botling, Patrick Micke and Takahide Nagase. An Integrative Analysis of the Tumorigenic Role of TAZ in Human NonCell Lung Cancer. Clinical Cancer Research, vol. 20 no. 17, pages 4660-4672, January 2014. [DOI]
  • Cristina Cadenas, Leonie van de Sandt, Karolina Edlund, Miriam Lohr, Birte Hellwig, Rosemarie Marchan, Marcus Schmidt, Jörg Rahnenführer, Henrik Oster and Jan G. Hengstler. Loss of circadian clock gene expression is associated with tumor progression in breast cancer. Cell Cycle, vol. 13 no. 20, pages 3282-3291, 2014.
  • S. Lee, J. Rahnenführer, M. Lang, K. De Preter, P. Mestdagh, J. Koster, R. Versteeg, R. L. Stallings, L. Varesio, S. Asgharzadeh, J. H. Schulte, K. Fielitz, M. Schwermer, K. Morik and A. Schramm. Robust selection of cancer survival signatures from high-throughput genomic data using two-fold subsampling. PLoS ONE, vol. 9 no. 10, page e108818, 2014.
  • Michaela S. Lesjak, Rosemarie Marchan, Joanna D. Stewart, Eugen Rempel, Jörg Rahnenführer and Jan G. Hengstler. EDI3 links choline metabolism to integrin expression, cell adhesion and spreading. Cell Adh Migr, vol. 8 no. 5, pages 499-508, 2014.
  • Alexander Muck, Christian Langesberg, Michael Mugler, Jörg Rahnenführer, Bernd Wullich and Wolfgang Schafhauser. Clinical Outcome of Patients with Lymph Node-Positive Prostate Cancer following Radical Prostatectomy and Extended Sentinel Lymph Node Dissection. Urologia Internationalis, 2014. [DOI]
  • I. Sicking, K. Edlund, E. Wesbuer, V. Weyer, M. J. Battista, A. Lebrecht, C. Solbach, M. Grinberg, J. Lotz, G. Hoffmann, J. Rahnenführer, J. G. Hengstler and M. Schmidt. Prognostic influence of pre-operative C-reactive protein in node-negative breast cancer patients. PLoS ONE, vol. 9 no. 10, page e111306, 2014.


  • Marcel Leist, Annette Ringwald, Raivo Kolde, Susanne Bremer, Christoph van Thriel, Karl-Heinz Krause, Jörg Rahnenführer, Agapios Sachinidis, Jürgen Hescheler and Jan G. Hengstler. Test systems of developmental toxicity: state-of-the art and future perspectives. Archives of Toxicology, vol. 87 no. 12, pages 2037-2042, December 2013. [DOI]
  • Miriam Lohr, Karolina Edlund, Johan Botling, Seddik Hammad, Birte Hellwig, Amnah Othman, Anders Berglund, Mats Lambe, Lars Holmberg, Simon Ekman, Michael Bergqvist, Fredrik Pontén, Cristina Cadenas, Rosemarie Marchan, Jan G. Hengstler, Jörg Rahnenführer and Patrick Micke. The prognostic relevance of tumour-infiltrating plasma cells and immunoglobulin kappa C indicates an important role of the humoral immune response in non-small cell lung cancer. Cancer Letters, vol. 333 no. 2, pages 222-228, June 2013. [DOI]
  • Marc Vaudel, Daniela Breiter, Florian Beck, Jörg Rahnenführer, Lennart Martens and René P. Zahedi. D-score: A search engine independent MD-score. PROTEOMICS, vol. 13 no. 6, pages 1036-1041, March 2013. [DOI]
  • Johan Botling, Karolina Edlund, Miriam Lohr, Birte Hellwig, Lars Holmberg, Mats Lambe, Anders Berglund, Simon Ekman, Michael Bergqvist, Fredrik Pontén, André König, Oswaldo Fernandes, Mats Karlsson, Gisela Helenius, Christina Karlsson, Jörg Rahnenführer, Jan G. Hengstler and Patrick Micke. Biomarker Discovery in NonCell Lung Cancer: Integrating Gene Expression Profiling, Meta-analysis, and Tissue Microarray Validation. Clinical Cancer Research, vol. 19 no. 1, pages 194-204, January 2013. [DOI]
  • Anne K. Krug, Raivo Kolde, John A. Gaspar, Eugen Rempel, Nina V. Balmer, Kesavan Meganathan, Kinga Vojnits, Mathurin Baquié, Tanja Waldmann, Roberto Ensenat Waser, Smita Jagtap, Richard M. Evans, Stephanie Julien, Hedi Peterson, Dimitra Zagoura, Suzanne Kadereit, Daniel Gerhard, Isaia Sotiriadou, Michael Heke, Karthick Natarajan, Margit Henry, Johannes Winkler, Rosemarie Marchan, Luc Stoppini, Sieto Bosgra, Joost Westerhout, Miriam Verwei, Jaak Vilo, Andreas Kortenkamp, Jürgen Hescheler, Ludwig Hothorn, Susanne Bremer, Christoph van Thriel, Karl-Heinz Krause, Jan G. Hengstler, Jörg Rahnenführer, Marcel Leist and Agapios Sachinidis. Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Archives of Toxicology, vol. 87 no. 1, pages 123-143, January 2013. [DOI]
  • Maike Ahrens, Michael Turewicz, Swaantje Casjens, Caroline May, Beate Pesch, Christian Stephan, Dirk Woitalla, Ralf Gold, Thomas Brüning, Helmut E. Meyer, Jörg Rahnenführer and Martin Eisenacher. Detection of Patient Subgroups with Differential Expression in Omics Data: A Comprehensive Comparison of Univariate Measures. PLoS ONE, vol. 8 no. 11, page e79380, 11 2013. [DOI]


  • Wulf Siggelkow, Daniel Boehm, Susanne Gebhard, Marco Battista, Isabel Sicking, Antje Lebrecht, Christine Solbach, Birte Hellwig, Jörg Rahnenführer, Heinz Koelbl, Mathias Gehrmann, Rosemarie Marchan, Cristina Cadenas, Jan G. Hengstler and Marcus Schmidt. Expression of aurora kinase A is associated with metastasis-free survival in node-negative breast cancer patients. BMC Cancer, vol. 12 no. 1, page 562, November 2012. [DOI]
  • Cristina Cadenas, Sonja Vosbeck, Eva-Maria Hein, Birte Hellwig, Alice Langer, Heiko Hayen, Dennis Franckenstein, Bettina Büttner, Seddik Hammad, Rosemarie Marchan, Matthias Hermes, Silvia Selinski, Jörg Rahnenführer, Begüm Peksel, Zsolt Török, László Vıgh and Jan G. Hengstler. Glycerophospholipid profile in oncogene-induced senescence.. Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids, vol. 1821 no. 9, pages 1256-68, September 2012. [DOI]
  • Marcus Schmidt, Birte Hellwig, Seddik Hammad, Amnah Othman, Miriam Lohr, Zonglin Chen, Daniel Boehm, Susanne Gebhard, Ilka Petry, Antje Lebrecht, Cristina Cadenas, Rosemarie Marchan, Joanna D. Stewart, Christine Solbach, Lars Holmberg, Karolina Edlund, Hanna Göransson Kultima, Achim Rody, Anders Berglund, Mats Lambe, Anders Isaksson, Johan Botling, Thomas Karn, Volkmar Müller, Aslihan Gerhold Ay, Christina Cotarelo, Martin Sebastian, Ralf Kronenwett, Hans Bojar, Hans-Anton Lehr, Ugur Sahin, Heinz Koelbl, Mathias Gehrmann, Patrick Micke, Jörg Rahnenführer and Jan G. Hengstler. A comprehensive analysis of human gene expression profiles identifies stromal immunoglobulin $C as a compatible prognostic marker in human solid tumors.. Clinical Cancer Research, vol. 18 no. 9, pages 2695-703, May 2012. [DOI]
  • Tanja Heise, Markus Schug, Dorothe Storm, Heidrun Ellinger Ziegelbauer, Hans-Jürgen Ahr, Birte Hellwig, Jörg Rahnenführer, Ahmed Ghallab, Georgia Guenther, Julia Sisnaiske, Raymond Reif, Patricio Godoy, Hans Mielke, Ursula Gundert Remy, Alfonso Lampen, Axel Oberemm and Jan G. Hengstler. In Vitro - In Vivo Correlation of Gene Expression Alterations Induced by Liver Carcinogens. Current Medicinal Chemistry, vol. 19 no. 11, pages 1721-1730, April 2012.
  • Marco Grzegorczyk and Dirk Husmeier. A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology.. Statistical Applications in Genetics and Molecular Biology, vol. 11 no. 4, January 2012. [DOI]
  • Miriam Lohr, Claudia Köllmann, Evgenia Freis, Birte Hellwig, Jan G. Hengstler, Katja Ickstadt and Jörg Rahnenführer. Optimal strategies for sequential validation of significant features from high-dimensional genomic data.. Journal of Toxicology and Environmental Health-Part A-Current Issues, vol. 75 no. 8-10, pages 447-60, January 2012. [DOI]
  • Bernd Bischl, Michel Lang, Olaf Mersmann, Jörg Rahnenführer and Claus Weihs. Computing on high performance clusters with R: Packages BatchJobs and BatchExperiments. Technical Report 1/2012, TU Dortmund, Department of Statistics, 2012.
  • Sebastian Briesemeister, Jörg Rahnenführer and Oliver Kohlbacher. No Longer Confidential: Estimating the Confidence of Individual Regression Predictions. PLoS ONE, vol. 7 no. 11, page e48723, 11 2012. [DOI]
  • Katrin Hainke, Jörg Rahnenführer and Roland Fried. Cumulative disease progression models for cross-sectional data: A review and comparison. Biometrical Journal, vol. 54 no. 5, pages 617-640, 2012. [DOI]
  • Erhan Kenar, Holger Franken, Lars Rosenbaum, Rainer Lehmann, Sara Forcisi, Kilian Wörmann, Marianna Lucio, André König, Jörg Rahnenführer, Philippe Schmitt Kopplin, Hans-Ulrich Häring, Andreas Zell and Oliver Kohlbacher. Mit Bioinformatik zu Biomarkern: Rechnergestützte Analyse massenspektrometrischer Metabolomikdaten. Die Medizinische Welt - aus der Wissenschaft in die Praxis, vol. 63 no. 5, pages 245-250, 2012.
  • Christian Netzer and Jörg Rahnenführer. Sample Size Estimation for Cancer Progression Models. International Journal of Computational Bioscience, vol. 1 no. 1, 2012. [DOI]


  • Sven Nahnsen, Andreas Bertsch, Jörg Rahnenführer, Alfred Nordheim and Oliver Kohlbacher. Probabilistic consensus scoring improves tandem mass spectrometry peptide identification.. Journal of Proteome Research, vol. 10 no. 8, pages 3332-43, August 2011. [DOI]
  • Marco Grzegorczyk, Dirk Husmeier and Jörg Rahnenführer. Modelling non-stationary dynamic gene regulatory processes with the BGM model. Computational Statistics, vol. 26 no. 2, pages 199-218, June 2011. [DOI]
  • Marco Grzegorczyk and Dirk Husmeier. Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes.. Bioinformatics (Oxford, England), vol. 27 no. 5, pages 693-9, March 2011. [DOI]
  • Marco Grzegorczyk and Dirk Husmeier. Non-homogeneous dynamic Bayesian networks for continuous data. Machine Learning, vol. 83 no. 3, pages 355-419, February 2011. [DOI]
  • Marcus Schmidt, Ilka B. Petry, Daniel Böhm, Antje Lebrecht, Christian von Törne, Susanne Gebhard, Aslihan Gerhold Ay, Cristina Cotarelo, Marco Battista, Wiebke Schormann, Evgenia Freis, Silvia Selinski, Katja Ickstadt, Jörg Rahnenführer, Martin Sebastian, Martin Schuler, Heinz Koelbl, Mathias Gehrmann and Jan G. Hengstler. Ep-CAM RNA expression predicts metastasis-free survival in three cohorts of untreated node-negative breast cancer.. Breast cancer research and treatment, vol. 125 no. 3, pages 637-46, February 2011. [DOI]
  • Kai Kammers, Michel Lang, Jan G Hengstler, Marcus Schmidt and Jörg Rahnenführer. Survival models with preclustered gene groups as covariates.. BMC Bioinformatics, vol. 12 no. 478, January 2011. [DOI]
  • Ruth-Jessica Karlowatz, Jürgen Scharhag, Jörg Rahnenführer, Ulrich Schneider, Ernst Jakob, Wilfried Kindermann and Klaus Dieter Zang. Polymorphisms in the IGF1 signalling pathway including the myostatin gene are associated with left ventricular mass in male athletes.. British Journal of Sports Medicine, vol. 45 no. 1, pages 36-41, January 2011. [DOI]
  • Steffi Urbschat, Jörg Rahnenführer, Worlfram Henn, Wolfgang Feiden, Silke Wemmert, Stefan Linsler, Klaus D. Zang, Joachim Oertel and Ralf Ketter. Clonal cytogenetic progression within intratumorally heterogeneous meningiomas predicts tumor recurrence. International Journal of Oncology, vol. 39 no. 6, pages 1601-1608, January 2011. [DOI]
  • Frank Dondelinger, Andrej Aderhold, Sophie Lèbre, Marco Grzegorczyk and Dirk Husmeier. A Bayesian regression and multiple changepoint model for systems biology. In ForteAnabelLopéz-QuilezAntonio Conesa, David and Facundo Mu\ noz, editors, Proceedings of the 26th International Workshop on Statistical Modelling, pages 189-194, Valencia, Spain, 2011. Copiformes S.L..
  • Dirk Husmeier, Adriano V. Werhli and Marco Grzegorczyk. Advanced Applications of Bayesian Networks in Systems Biology. In Michael P. H. Stumpf, David J. Balding and rk Girolami, editors, Handbook of Statistical Systems Biology, pages 270-289. John Wiley & Sons, Ltd, 2011.
  • Christiane Matuschek, Michael Rudoy, M Peiper, Peter A. Gerber, Norman-Philipp Hoff, Bettina A. Buhren, Bertram Flehmig, Wilfried Budach, Wolfram T. Knoefel, Hans Bojar, Hans-Bernd Prisack, Gerald Steinbach, Vershalee Shukla, Andreas Schwarz, Kai Kammers, A Erhardt, Almut Scherer, Edwin Bölke and Matthias Schauer. Do insulin-like growth factor associated proteins qualify as a tumor marker? results of a prospective study in 163 cancer patients*. European Journal of Medical Research, vol. 16 no. 10, page 451, 2011. [DOI]


  • Stefan Linsler, Silke Wemmert, Jörg Rahnenführer, Wolf-Ingo Steudel, Steffi Urbschat and Ralf Ketter. A Predictive genetic marker for tumor recurrence in meningiomas. Neuro-Oncology, vol. 12 no. Suppl 3, page 54, September 2010.
  • Wolfgang A. Schulz, Marc Ingenwerth, Carolle E. Djuidje, Christiane Hader, Jörg Rahnenführer and Rainer Engers. Changes in cortical cytoskeletal and extracellular matrix gene expression in prostate cancer are related to oncogenic ERG deregulation. BMC Cancer, vol. 10 no. 505, September 2010. [DOI]
  • Sebastian Briesemeister, Jörg Rahnenführer and Oliver Kohlbacher. YLoc-an interpretable web server for predicting subcellular localization. Nucleic Acids Research, vol. 38 no. Suppl 2, pages W497-W502, July 2010. [DOI]
  • Marco Grzegorczyk, Dirk Husmeier and Jörg Rahnenführer. Modelling non-stationary dynamic gene regulatory processes with the BGM model. Computational Statistics, vol. 26 no. 2, pages 199-218, June 2010. [DOI]
  • Jan C. Brase, Marcus Schmidt, Thomas Fischbach, Holger Sültmann, Hans Bojar, Heinz Kölbl, Birte Hellwig, Jörg Rahnenführer, Jan G. Hengstler and Mathias C. Gehrmann. ERBB2 and TOP2A in Breast Cancer: A Comprehensive Analysis of Gene Amplification, RNA Levels, and Protein Expression and Their Influence on Prognosis and Prediction. Clinical Cancer Research, vol. 16 no. 8, pages 2391-2401, April 2010. [DOI]
  • Katharina Podwojski, Martin Eisenacher, Michael Kohl, Michael Turewicz, Helmut E. Meyer, Jörg Rahnenführer and Christian Stephan. Peek a peak: a glance at statistics for quantitative label-free proteomics. Expert Review of Proteomics, vol. 7 no. 2, pages 249-261, April 2010. [DOI]
  • Cristina Cadenas, Dennis Franckenstein, Marcus Schmidt, Mathias Gehrmann, Matthias Hermes, Bettina Geppert, Wiebke Schormann, Lindsey J. Maccoux, Markus Schug, Anika Schumann, Christian Wilhelm, Evgenia Freis, Katja Ickstadt, Jörg Rahnenführer, Jörg I Baumbach, Albert Sickmann and Jan G. Hengstler. Role of thioredoxin reductase 1 and thioredoxin interacting protein in prognosis of breast cancer.. Breast cancer research, vol. 12 no. 3, page R44, January 2010. [DOI]
  • Martin Peifer, Jonathan Weiss, Martin L. Sos, Mirjam Koker, Stefanie Heynck, Christian Netzer, Stefanie Fischer, Haridas Rode, Daniel Rauh, Jörg Rahnenführer and Roman K. Thomas. Analysis of compound synergy in high-throughput cellular screens by population-based lifetime modeling.. PloS one, vol. 5 no. 1, page e8919, January 2010. [DOI]
  • Ilka Brigitte Petry, Esther Fieber, Marcus Schmidt, Mathias Gehrmann, Susanne Gebhard, Matthias Hermes, Wiebke Schormann, Silvia Selinski, Evgenia Freis, Holger Schwender, Marc Brulport, Katja Ickstadt, Jörg Rahnenführer, Lindsey Maccoux, Jonathan West, Heinz Kölbl, Martin Schuler and Jan Georg Hengstler. ERBB2 induces an antiapoptotic expression pattern of Bcl-2 family members in node-negative breast cancer.. Clinical cancer research, vol. 16 no. 2, pages 451-60, January 2010. [DOI]
  • Sebastian Briesemeister, Jörg Rahnenführer and Oliver Kohlbacher. Going from where to why-interpretable prediction of protein subcellular localization. Bioinformatics, vol. 26 no. 9, pages 1232-1238, 2010. [DOI]
  • Birte Hellwig, Jan G Hengstler, Marcus Schmidt, Mathias C. Gehrmann, Wiebke Schormann and Jörg Rahnenführer. Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes. BMC Bioinformatics, vol. 11, 2010. [DOI]
  • Kai Kammers. Improved Interpretability of Survival Models with Gene Groups as Covariates. Technical Report 2/2010, TU Dortmund, Department of Statistics, 2010.
  • Miriam Lohr, Patricio Godoy, Jan G Hengstler, Jörg Rahnenführer and Marco Grzegorczyk. Extracting differential regulatory sub-networks from genome-wide microarray expression data. In Proceedings of the Seventh International Workshop on Computational Systems Biology (WCSB 2010), pages 63-66, Luxembourg, 2010.
  • Samuel E. Wuest, Kitty Vijverberg, Anja Schmidt, Manuel Weiss, Jacqueline Gheyselinck, Miriam Lohr, Frank Wellmer, Jörg Rahnenführer, Christian von Mering and Ueli Grossniklaus. Arabidopsis Female Gametophyte Gene Expression Map Reveals Similarities between Plant and Animal Gametes. Current Biology, vol. 20 no. 6, pages 506-512, 2010. [DOI]


  • Martin L Sos, Kathrin Michel, Thomas Zander, Jonathan Weiss, Peter Frommolt, Martin Peifer, Danan Li, Roland Ullrich, Mirjam Koker, Florian Fischer, Takeshi Shimamura, Daniel Rauh, Craig Mermel, Stefanie Fischer, Isabel Stückrath, Stefanie Heynck, Rameen Beroukhim, William Lin, Wendy Winckler, Kinjal Shah, Thomas LaFramboise, Whei F Moriarty, Megan Hanna, Laura Tolosi, Jörg Rahnenführer, Roel Verhaak, Derek Chiang, Gad Getz, Martin Hellmich, Jürgen Wolf, Luc Girard, Michael Peyton, Barbara A Weir, Tzu-Hsiu Chen, Heidi Greulich, Jordi Barretina, Geoffrey I. Shapiro, Levi A. Garraway, Adi F. Gazdar, John D Minna, Matthew Meyerson, Kwok-Kin Wong and Roman K. Thomas. Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. Journal of Clinical Investigation, vol. 119 no. 6, pages 1727-1740, June 2009. [DOI]
  • Silke Wemmert, Ralf Ketter, Jörg Rahnenführer, Kai Kammers, Wolf-Ingo Steudel and Steffi Urbschat. MGMT and p15 promotor methylation-prognostic parameters for glioblastoma patients?. Chromosome Research, vol. 17 no. 1, pages 172-173, June 2009.
  • Marco Grzegorczyk and Dirk Husmeier. Avoiding Spurious Feedback Loops in the Reconstruction of Gene Regulatory Networks with Dynamic Bayesian Networks. In Visakan Kadirkamanathan, Guido Sanguinetti, Mark Girolami, Mahesan Niranjan and Josselin Noirel, editors, Pattern Recognition in Bioinformatics, number 5780 in Lecture Notes in Computer Science, pages 113-124. Springer Berlin Heidelberg, January 2009.
  • Evgenia Freis, Silvia Selinski, Birte Weibert, Ulrike Krahn, Marcus Schmidt, Mathias Gehrmann, Matthias Hermes, Lindsey Maccoux, Jonathan West, Holger Schwender, Jörg Rahnenführer, Jan G. Hengstler and Katja Ickstadt. Effects of metagene calculation on survival: An integrative approach using cluster and promoter analysis. In Proceedings of the Sixth International Workshop on Computational Systems Biology (WCSB 2009), pages 47-50, Aarhus, 2009.
  • Marco Grzegorczyk and Dirk Husmeier. Modelling non-stationary gene regulatory processes with a non-homogeneous dynamic Bayesian network and the change point process. In Proceedings of the 6th International Workshop on Computational Systems Biology, volume 48, pages 51-54, 2009.
  • Marco Grzegorczyk and Dirk Husmeier. Non-stationary continuous dynamic Bayesian networks. In Yoshua Bengio, Dale Schuurmans, John D. Lafferty, Chris K. I. Williams and Aron Culotta, editors, Advances in Neural Information Processing Systems 22, pages 682-690. Curran Associates, Inc., 2009.
  • Katharina Podwojski, Arno Fritsch, Daniel C. Chamrad, Wolfgang Paul, Barbara Sitek, Kai Stuehler, Petra Mutzel, Christian Stephan, Helmut E. Meyer, Wolfgang Urfer, Katja Ickstadt and Jörg Rahnenführer. Retention time alignment algorithms for LC/MS data must consider non-linear shifts. Bioinformatics, vol. 25 no. 6, pages 758-764, 2009. [DOI]
  • Silke Wemmert, Marc Bettscheider, Simone Alt, Ralf Ketter, Kai Kammers, Wolfgang Feiden, Wolf-Ingo Steudel, Jörg Rahnenführer and Steffi Urbschat. p15 promoter methylation - A novel prognostic marker in glioblastoma patients. International Journal of Oncology, vol. 34 no. 6, pages 1743-1748, 2009.


  • Ralf Ketter, Jörg Rahnenführer, Wolfram Henn, Yoo-Jin Kim, Wolfgang Feiden, Wolf-Ingo Steudel, Klaus D Zang and Steffi Urbschat. Correspondence of tumor localization with tumor recurrence and cytogenetic progression in meningiomas. Neurosurgery, vol. 62 no. 1, pages 61-70, January 2008. [DOI]
  • Jasmina Bogojeska, Adrian Alexa, Andre Altmann, Thomas Lengauer and Jörg Rahnenführer. Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores. Bioinformatics, vol. 24 no. 20, pages 2391-2392, 2008. [DOI]
  • Jasmina Bogojeska, Thomas Lengauer and Jörg Rahnenführer. Stability analysis of mixtures of mutagenetic trees. BMC Bioinformatics, vol. 9 no. 165, 2008. [DOI]
  • Max Hornstein, Michèle J. Hoffmann, Adrian Alexa, Masanori Yamanaka, Mirko Müller, Volker Jung, Jörg Rahnenführer and Wolfgang A. Schulz. Protein phosphatase and TRAIL receptor genes as new candidate tumor genes on chromosome 8p in prostate cancer. Cancer Genomics Proteomics, vol. 5 no. 2, pages 123-136, 2008.
  • Ralf Ketter, Jörg Rahnenführer, Wolfram Henn, Wolfgang Feiden, Wolf-Ingo Steudel, Silke Wemmert and Steffi Urbschat. Prognostic implication of cytogenetic features in meningiomas. Neuro-Oncology, vol. 10 no. 6, page 1132, 2008.
  • Katharina Podwojski, Arno Fritsch, Daniel C. Chamrad, Wolfgang Paul, Petra Mutzel, Katja Ickstadt and Jörg Rahnenführer. A retention-time alignment algorithm for LC/MS data. In Miika Ahdesmäki, Korbinian Strimmer, Nicole Radde, Jörg Rahnenführer, Konstantin Klemm, Harri Lähdesmäki and Olli Yli Harja, editors, Proceedings of the Fifth International Workshop on Computational Systems Biology (WCSB 2008) Leipzig, June 11-13, volume 41 of TISCP, pages 129-132, 2008.
  • Holger Schwender, Katja Ickstadt and Jörg Rahnenführer. Classification with High-Dimensional Genetic Data: Assigning Patients and Genetic Features to Known Classes. Biometrical Journal, vol. 50 no. 6, pages 911-926, 2008. [DOI]
  • Silke Wemmert, Ralf Ketter, Marc Bettscheider, Simone Alt, Kai Kammers, Jörg Rahnenführer, Wolf-Ingo Steudel and Steffi Urbschat. MGMT and P15 promotor methylation-prognostic parameters for temozolomide treatment?. Neuro-Oncology, vol. 10 no. 6, page 1128, 2008.


  • Francisco S Domingues, Jörg Rahnenführer and Thomas Lengauer. Conformational analysis of alternative protein structures.. Bioinformatics, vol. 23 no. 23, pages 3131-3138, December 2007. [DOI]
  • Ralf Ketter, Steffi Urbschat, Wolfram Henn, Wolfgang Feiden, Niko Beerenwinkel, Thomas Lengauer, Wolf-Ingo Steudel, Klaus D Zang and Jörg Rahnenführer. Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas.. International Journal of Cancer, vol. 121 no. 7, pages 1473-1480, October 2007. [DOI]
  • Ralf Ketter, Yoo-Jin Kim, Simone Storck, Jörg Rahnenführer, Bernd F M Romeike, Wolf-Ingo Steudel, Klaus D Zang and Wolfram Henn. Hyperdiploidy defines a distinct cytogenetic entity of meningiomas.. Journal of Neuro-Oncology, vol. 83 no. 2, pages 213-221, June 2007. [DOI]
  • Jörn Kamradt, Volker Jung, Kerstin Wahrheit, Laura Tolosi, Jörg Rahnenführer, Martin Schilling, Robert Walker, Sean Davis, Michael Stöckle, Paul Meltzer and Bernd Wullich. Detection of Novel Amplicons in Prostate Cancer by Comprehensive Genomic Profiling of Prostate Cancer Cell Lines Using Oligonucleotide-Based ArrayCGH. PLoS ONE, vol. 2(8), page e769, 2007.
  • Andreas Schlicker, Jörg Rahnenführer, Mario Albrecht, Thomas Lengauer and Francisco S Domingues. GOTax: investigating biological processes and biochemical activities along the taxonomic tree.. Genome Biol, vol. 8 no. 3, page R33, 2007. [DOI]
  • Wolfgang A Schulz, Adrian Alexa, Volker Jung, Christiane Hader, Michèle J Hoffmann, Masanori Yamanaka, Sandy Fritzsche, Agnes Wlazlinski, Mirko Müller, Thomas Lengauer, Rainer Engers, Andrea R Florl, Bernd Wullich and Jörg Rahnenführer. Factor interaction analysis for chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer.. Molecular Cancer, vol. 6 no. 14, 2007. [DOI]


  • Ralf Ketter, Jörg Rahnenführer, Wolfram Henn, Silke Wemmert, Yoo-Jin Kim, Thomas Lengauer, Klaus D Zang, Wolf-Ingo Steudel and Steffi Urbschat. Intratumoral patterns of clonal evolution in meningiomas. EJC Supplements, vol. 4 no. 6, pages 39-40, June 2006. [DOI]
  • Adrian Alexa, Jörg Rahnenführer and Thomas Lengauer. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics, vol. 22 no. 13, pages 1600-1607, 2006. [DOI]
  • Ralf Ketter, Jörg Rahnenführer, Wolfram Henn, Silke Wemmert, Yoo-Jin Kim, Thomas Lengauer, Klaus D Zang, Wolf-Ingo Steudel and Steffi Urbschat. Intertumoral patterns in meningiomas: A genetic model of meningioma progression. Neuro-Oncology, vol. 8 no. 4, pages 343-344, 2006.
  • Andreas Schlicker, Francisco S Domingues, Jörg Rahnenführer and Thomas Lengauer. A new measure for functional similarity of gene products based on Gene Ontology.. BMC Bioinformatics, vol. 7 no. 302, 2006. [DOI]
  • Adriano V Werhli, Marco Grzegorczyk and Dirk Husmeier. Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks. Bioinformatics, vol. 22 no. 20, pages 2523-2531, 2006. [DOI]
  • Junming Yin, Niko Beerenwinkel, Jörg Rahnenführer and Thomas Lengauer. Model selection for mixtures of mutagenetic trees.. Statistical Applications in Genetics and Molecular Biology, vol. 5 no. 1, 2006. [DOI]


  • Niko Beerenwinkel, Tobias Sing, Thomas Lengauer, Jörg Rahnenführer, Kirsten Roomp, Igor Savenkov, Roman Fischer, Daniel Hoffmann, Joachim Selbig, Klaus Korn, Hauke Walter, Thomas Berg, Patrick Braun, Gerd Fätkenheuer, Mark Oette, Jürgen Rockstroh, Bernd Kupfer, Rolf Kaiser and Martin Däumer. Computational methods for the design of effective therapies against drug resistant HIV strains.. Bioinformatics, vol. 21 no. 21, pages 3943-3950, November 2005. [DOI]
  • Nadine Kutzner, Ingrid Hoffmann, Christina Linke, Thomas Thienel, Marco Grzegorczyk, Wolfgang Urfer, Dirk Martin, Günther Winde, Thilo Traska, Gerd Hohlbach, Klaus-Michael Müller, Cornelius Kuhnen and Oliver Müller. Non-invasive detection of colorectal tumours by the combined application of molecular diagnosis and the faecal occult blood test. Cancer Letters, vol. 229 no. 1, pages 33-41, November 2005. [DOI]
  • Silke Wemmert, Ralf Ketter, Jörg Rahnenführer, Niko Beerenwinkel, Martin Strowitzki, Wolfgang Feiden, Christian Hartmann, Thomas Lengauer, Florian Stockhammer, Klaus D Zang, Eckart Meese, Wolf-Ingo Steudel, Andreas von Deimling and Steffi Urbschat. Patients with high-grade gliomas harboring deletions of chromosomes 9p and 10q benefit from temozolomide treatment.. Neoplasia, vol. 7 no. 10, pages 883-893, October 2005.
  • Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig and Thomas Lengauer. Learning Multiple Evolutionary Pathways from Cross-Sectional Data. Journal of Computational Biology, vol. 12 no. 6, pages 584-598, July 2005. [DOI]
  • Niko Beerenwinkel, Martin Däumer, Tobias Sing, Jörg Rahnenführer, Thomas Lengauer, Joachim Selbig, Daniel Hoffmann and Rolf Kaiser. Estimating HIV evolutionary pathways and the genetic barrier to drug resistance. Journal of Infectious Diseases, vol. 191 no. 11, pages 1953-1960, June 2005. [DOI]
  • Ani V. Das, Jackson James, Jörg Rahnenführer, Wallace B. Thoresona, Sumitra Bhattacharyaa, Xing Zhaoa and Iqbal Ahmada. Retinal properties and potential of the adult mammalian ciliary epithelium stem cells. Vision Research, vol. 45 no. 13, pages 1653-1666, June 2005. [DOI]
  • Niko Beerenwinkel, Jörg Rahnenführer, Rolf Kaiser, Daniel Hoffmann, Joachim Selbig and Thomas Lengauer. Mtreemix: a software package for learning and using mixture models of mutagenetic trees.. Bioinformatics, vol. 21 no. 9, pages 2106-2107, May 2005. [DOI]
  • Andreas Hahn, Jörg Rahnenführer, Priti Talwar and Thomas Lengauer. Confirmation of human protein interaction data by human expression data.. BMC Bioinformatics, vol. 6 no. 112, 2005. [DOI]


  • Jackson James, Ani V Das, Jörg Rahnenführer and Iqbal Ahmad. Cellular and molecular characterization of early and late retinal stem cells/progenitors: differential regulation of proliferation and context dependent role of Notch signaling.. Journal of Neurobiology, vol. 61 no. 3, pages 359-376, December 2004. [DOI]
  • Ani V. Das, Jackson James, Xing Zhao, Jörg Rahnenführer and Iqbal Ahmad. Identification of c-Kit receptor as a regulator of adult neural stem cells in the mammalian eye: interactions with Notch signaling.. Developmental Biology, vol. 273 no. 1, pages 87-105, September 2004. [DOI]
  • Francisco S Domingues, Jörg Rahnenführer and Thomas Lengauer. Automated clustering of ensembles of alternative models in protein structure databases.. Protein Engineering, Design and Selection, vol. 17 no. 6, pages 537-543, June 2004. [DOI]
  • Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig and Thomas Lengauer. Learning multiple evolutionary pathways from cross-sectional data.. In Philip E. Bourne and Dan Gusfield, editors, RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology, volume 12, pages 36-44, New York, March 27-31 2004. ACM. [DOI]
  • Ingolf Sommer, Jörg Rahnenführer, Francisco S. Domingues, Ulrik de Lichtenberg and Thomas Lengauer. Predicting protein structure classes from function predictions.. Bioinformatics, vol. 20 no. 5, pages 770-776, March 2004. [DOI]


  • Niko Beerenwinkel, Rolf Kaiser, Jörg Rahnenführer, Martin P. Däumer, Daniel C. Hoffmann, Joachim Selbig and Thomas Lengauer. Tree models for the evolution of drug resistance. Antiviral Therapy, vol. 8 no. 3, pages U95-U96, June 2003.
  • Jackson James, Ani V. Das, Jörg Rahnenführer, Frank A. Soto Leon and Iqbal Ahmad. Identification of rat brahma (rBRM), a subunit of SWI/SNF chromatin remodeling complex: Involvement in the differentiation of retinal stem cells/progenitors. Investigative Ophthalmology & Visual Science, vol. 44 no. 1, page U391, 2003.


  • Daniel Bozinov and Jörg Rahnenführer. Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering. Bioinformatics, vol. 18 no. 5, pages 747-756, May 2002.
  • Daniel Bozinov, Jörg Rahnenführer, CM Burson and Ofer Spiegelstein. Automated grid alignment for high-throughput Analysis of Microarray Images. In H.R. Arabnia and Y. Mun, editors, Proc 2002 Int Conf on łdots. CSREA Press, 2002.
  • Arnold Janssen and Jörg Rahnenführer. A hazard based approach to dependence tests for bivariate censored models. Mathematical Methods of Statistics, vol. 11 no. 3, pages 297-322, 2002.

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