Dr. Holger Franken


  • 06/2008 to 08/2012 research assistant at the Centre for Bioinformatics (ZBIT), University of Tübingen
  • 05/2008 diploma in Computer Science (Bioinformatics).
  • 10/2001-05/2008 Student of Bioinformatics at the University of Tübingen

Research Interests

  • Systems biology
  • Biomarker detection
  • Metabolic networks
  • Machine Learning Methods
  • Evolutionary Algorithms


Ph.D. Thesis


[1] Erhan Kenar, Holger Franken, Sara Forcisi, Kilian W6rmann, Hans-Ulrich H4ring, Rainer Lehmann, Philippe Schmitt-Kopplin, Andreas Zell, and Oliver Kohlbacher. Automated label-free quantification of metabolites from liquid chromatography-mass spectrometry data. Molecular & Cellular Proteomics, 13(1):348--359, 2014. [ DOI | arXiv | link ]
[2] Peiyuan Yin, Andreas Peter, Holger Franken, Xinjie Zhao, Sabine Sarah Neukamm, Lars Rosenbaum, Marianna Lucio, Andreas Zell, Hans-Ulrich Häring, Guowang Xu, and Rainer Lehmann. Pre-analytical aspects and sample quality assessment in metabolomics studies of human blood. Clinical Chemistry, 59(5):833--845, May 2013.
[3] R. Lehmann, H. Franken, S. Dammeier, L. Rosenbaum, K. Kantartzis, A. Peter, A. Zell, P. Adam, J. Li, G. Xu, A. Königsrainer, J. Machann, F. Schick, M. Hrabe de Angelis, M. Schwab, H. Staiger, E. Schleicher, A. Gastaldelli, A. Fritsche, H.-U. Häring, and N. Stefan. Circulating lyso-phosphatidylcholines are markers of ametabolically benign nonalcoholic fatty liver. Diabetes Care, 36(8):2331--2338, 2013.
[4] Holger Franken, Alexander Seitz, Rainer Lehmann, Hans-Ulrich Häring, Norbert Stefan, and Andreas Zell. Inferring disease-related metabolite dependencies with a bayesian optimization algorithm. In Mario Giacobini, Leonardo Vanneschi, and William Bush, editors, Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, volume 7246 of Lecture Notes in Computer Science, pages 62--73. Springer Berlin / Heidelberg, 2012. 10.1007/978-3-642-29066-4_6. [ link ]
[5] E. Kenar, H. Franken, L. Rosenbaum, R. Lehmann, S. Forcisi, K. Wörmann, M. Lucio, A. König, J. Rahnenfüher, P. Schmidt-Kopplin, H.-U. Häring, A. Zell, and O. Kohlbacher. Mit bioinformatik zu biomarkern. Medizinische Welt, 63(5):245--250, 2012.
[6] K. Wörmann, M. Lucio, S. Forcisi, S.S. Heinzmann, E. Kenar, H. Franken, L. Rosenbaum, P. Schmitt-Kopplin, O. Kohlbacher, A. Zell, H.-U. Häring, and R. Lehmann. Metabolomics in der Diabetesforschung. Der Diabetologe, pages 1--5, 2012. 10.1007/s11428-011-0778-9. [ link ]
[7] Holger Franken, Rainer Lehmann, Hans-Ulrich Häring, Andreas Fritsche, Norbert Stefan, and Andreas Zell. Wrapper- and ensemble-based feature subset selection methods for biomarker discovery in targeted metabolomics. In Marco Loog, Lodewyk Wessels, Marcel Reinders, and Dick de Ridder, editors, Pattern Recognition in Bioinformatics, volume 7036 of Lecture Notes in Computer Science, pages 121--132. Springer Berlin / Heidelberg, 2011. 10.1007/978-3-642-24855-9_11. [ link ]
[8] Miriam Hoene, Holger Franken, Louise Fritsche, Rainer Lehmann, Ann Kathrin Pohl, Hans-Ulrich Häring, Andreas Zell, Erwin D. Schleicher, and Cora Weigert. Activation of the mitogen-activated protein kinase (MAPK) signalling pathway in the liver of mice is related to plasma glucose levels after acute exercise. Diabetologia, 53(6):1131--1141, March 2010. [ DOI | link | pdf ]

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Metabolomic Feature Detection in LC-MS data - A probabilistic approach
E. Kenar, H. Franken, A. Fekete, S. Forcisi, K. Wörmann, Ph. Schmitt-Kopplin, R. Lehmann, H.U. Häring, A. Zell, and O. Kohlbacher
presented at 'Metabolomics & More' , March 10 - 12, 2010 - Freising-Weihenstephan, Germany

Address, Phone, Fax, Email

Eberhard-Karls-Universität Tübingen
Wilhelm-Schickard-Institut für Informatik
Lehrstuhl Kognitive Systeme
Sand 1
D - 72076 Tübingen

Tel: (+49/0) 7071 / 29 78970
Fax: (+49/0) 7071 / 29 5091
Email: uni at holgerfranken.de