Bernhard Y. Renard

About me

• I am a group leader of an independent bioinformatics research group ( NG 4) at Robert Koch-Institute in Berlin, Germany.
• Previously, I was a research scientist with the Computational Medicine Unit at TRON, the Institute for Translational Oncology and Immunology, Mainz.
• Even earlier, I got my PhD at HCI, University of Heidelberg, and was a long term visitor with the Steen & Steen lab at Children's Hospital Boston/Harvard Medical School and the Seminar for Statistics at ETH Zurich.
• Before that, I studied Information Engineering, Statistics, and Applied Cultural Sciences in Karlsruhe, Columbus and Heidelberg and obtained a BSc and Diplom (MSc) degree from the University of Karlsruhe and as a Fulbright-scholar a MSc degree from The Ohio State University.
• Email: renardB AT rki.de, Mail: Nordufer 20, 13353 Berlin, Germany, Phone: +49 30 18754 2561

Scientific Interests

• Robust algorithms, statistical methods, and software tools for the analysis of biomedical data and bioinformatics
• High dimensional genomics and proteomics data from next generation sequencing and mass spectrometry platforms
• Integration of biomedical experiments and data sets
• Statistical learning and computational statistics

Teaching

• I regularly teach classes at the department of mathematics and computer science at Freie Universität Berlin and at the School of Process Sciences at Technische Universität Berlin.
• In the summer term 2013, I teach a statistics for bioinformatics class at Freie Universität.

Recent Journal Articles

• SH Giese, F Zickmann, BY Renard (2013). Specificity Control for Read Alignments Using an Artificial Reference Genome Guided False Discovery Rate. Bioinformatics (in press) [10.1093/bioinformatics/btt225][Software]
• MS Lindner, M Kollock, F Zickmann, BY Renard (2013). Analyzing Genome Coverage Profiles with Applications to Quality Control in Metagenomics. Bioinformatics (in press) [10.1093/bioinformatics/btt147][Software]
• M Hanselmann, J Roeder, U Koethe, BY Renard, RMA Heeren, FA Hamprecht (2013). Active Learning for Convenient Annotation and Classification of Mass Spectrometry Images. Analytical Chemistry, 2013, 85(1):147-155 [10.1021/ac3023313][Software]
• MS Lindner, BY Renard (2013). Metagenomic Abundance Estimation and Diagnostic Testing on Species Level. Nucleic Acids Research, 2013, 41(1):e10. [10.1093/nar/gks803][Software]
• H Filbert, S Attig, N Bidmon, BY Renard, S Janetzki, U Sahin, MJP Welters, C Ottensmeier, SH van der Burg, C Gouttefangeas and CM Britten (2012). Serum-free freezing-media support high cell quality and excellent ELISPOT assay performance across a wide variety of different assay protocols. Cancer Immunology, Immuntherapy [10.1007/s00262-012-1359-5]
• M Kuhring, BY Renard (2012). iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations. PLoS ONE 2012, 7(12):e50246[10.1371/journal.pone.0050246][Software]
• M Loewer*, BY Renard*, J de Graaf, M Wagner, C Paret, C Kneip, O Tuereci, M Diken, C Britten, S Kreiter, M Koslowski, JC Castle, U Sahin (2012). Framework for confidence-based somatic mutation detection. PLoS Computational Biology, 2012, 8(9): e1002714. [10.1371/journal.pcbi.1002714][Software]
• BY Renard, B Xu, M Kirchner, F Zickmann, D Winter, S Korten, NW Brattig, A Tzur, H Steen, FA Hamprecht (2012). Overcoming Species Boundaries in Peptide Identification with BICEPS. Molecular & Cellular Proteomics, 2012, 11:M111.014167. [10.1074/mcp.M111.014167][Software]
• H Soblik, AE Younis, M Mitreva, BY Renard, M Kirchner, F Geisinger, H Steen, NW Brattig (2011). Life cycle stage-resolved proteomic analysis of the excretome secretome from Strongyloides ratti - Identification of stage-specific protease. Molecular & Cellular Proteomics, 2011, 10(12):M111.010157. [10.1074/mcp.M111.010157]
• BY Renard*, M Loewer*, Y Kuehne, U Reimer, A Rothermel, O Tuereci, JC Castle, U Sahin (2011). rapmad: Robust Analysis of Peptide Microarray Data. BMC Bioinformatics, 2011. 12:324 [10.1186/1471-2105-12-324][Software]
• BM Voss, M Hanselmann, BY Renard, MS Lindner, U Koethe, M Kirchner, FA Hamprecht (2011). SIMA: Simultaneous Alignment of LC/MS Peak Lists. Bioinformatics, 2011: 27 (7): 987-993. [10.1093/bioinformatics/btr051][Software]
• BY Renard, W Timm, M Kirchner, FA Hamprecht, H Steen. (2010). Estimating the Confidence of Peptide Identifications without Decoy Databases. Analytical Chemistry, 2010, 82(11):4314-4318. [10.1021/ac902892j][Software]
• X Lou, BY Renard*, M Kirchner*, U Koethe, C Graf, C-T Lee, JAJ Steen, H Steen, MP Mayer, FA Hamprecht (2010). Deuteration Distribution Estimation with Improved Sequence Coverage for HDX/MS Experiments. Bioinformatics, 2010, 26(12):1535-1541.[10.1093/bioinformatics/btq165][Software]
• BY Renard*, M Kirchner*, U Koethe, DJ Pappin, FA Hamprecht, H Steen, JJ Steen (2010). Computational Protein Profile Similarity Screening for Quantitative Mass Spectrometry Experiments. Bioinformatics, 2010, 26(1):77-83. [10.1093/bioinformatics/btp607][Software]
• N Ozlu, F Monigatti, BY Renard, CM Field, H Steen, TJ Mitchison, JJ Steen (2010). Binding partner switching on microtubules and aurora-B in the mitosis to cytokinesis transition. Molecular & Cellular Proteomics, 2010, 9(2):336-350. [10.1074/mcp.M900308-MCP200]
• BY Renard, M Kirchner, F Monigatti, AR Ivanov, J Rappsilber, D Winter, JAJ Steen, FA Hamprecht, H Steen (2009). When Less Can Yield More - Computational Preprocessing of MS/MS Spectra for Peptide Identification. PROTEOMICS, 2009, 9(21):4978-4984. [10.1002/pmic.200900326][Software]
• M Hanselmann, U Koethe, M Kirchner, BY Renard, ER Amstalden, K Glunde, RMA Heeren, FA Hamprecht (2009). Toward Digital Staining using Imaging Mass Spectrometry and Random Forests. Journal of Proteome Research, 8(7), 3558-3567. [10.1021/pr900253y]
• BY Renard*, M Kirchner*, H Steen, JAJ Steen, FA Hamprecht (2008). NITPICK: Peak Identification for Mass Spectrometry Data. BMC Bioinformatics 2008, 9:355 [10.1186/1471-2105-9-355][Software]
• M Hanselmann, M Kirchner*, BY Renard*, ER Amstalden, K Glunde, RMA Heeren, FA Hamprecht (2008). Concise Representation of Mass Spectrometry Images by Probabilistic Latent Semantic Analysis. Analytical Chemistry, 80(24):9649-9658. [10.1021/ac801303x][Software]