2000                Heinz Billing Award of the Max Planck Society

2005                bwCon Open Source Award

Selected Publications

Ziller MJ, Gu H, Müller F, Donaghey J, Kohlbacher O, Bernstein BE, Gnirke A, and Meissner A. Charting a dynamic DNA methylation landscape of the human genome. Nature 2013, 500:477-481.

Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J, Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O, and Jones AR.The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol Cell Prot 2013, 12(8):2332-40

Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O,Aebersold R, and Malmström L. An automated pipeline for high-throughput label-free quantitative proteomics. J Proteome Res 2013 (epub ahead of print, DOI: 10.1021/pr300992u)

Gifford, CA, Ziller, MJ, Gu, H, Trapnell, C, Donaghey, J, Tsankov, A, Shalek, AK, Shishkin, AA, Issner, R, Zhang, X, Fostel, JL, Holmes, L, Meldrim, J, Guttman, M, Epstein, C, Park, H, Kohlbacher O, Rinn, J, Gnirke, A, Lander, ES, Bernstein, BE, and Meissner, A. Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells. Cell, 2013, 153(5):1149-1163.

Nahnsen S, Bielow C, Reinert K, and Kohlbacher O. Tools for label-free peptide quantification. Mol Cell Prot, 2013,12(3):549-56.