Scientific Interest

• Computational proteomics (CPX), data analysis in quantitative mass spectrometry
• Statistical learning theory, pattern recognition, design of experiments
• CPX software development

Affiliations

• Steen & Steen Lab, Proteomics Center, Departments of Pathology, Harvard Medical School and Children's Hospital Boston, Boston, MA, USA

Collaborations

• Computational Proteomics (CPX) Group, Multidimensional Image Processing Group, Interdisciplinary Center for Scientific Computing, University of Heidelberg, Germany.
• Mayer Lab, Zentrum für Molekulare Biologie, University of Heidelberg, Heidelberg, Germany.
• Lehmann Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany.
• Heeren Lab, FOM-Institute for Atomic and Molecular Physics, Amsterdam, The Netherlands.

Publications

• Kirchner M, Timm W, Fong P, Wangemann P, Steen H (2010). Nonlinear Classification for On-The-Fly Fractional Mass Filtering and Targeted Precursor Fragmentation in Mass Spectrometry Experiments. Bioinformatics, in press.
• Kirchner M*, Renard BY*, Koethe U, Pappin DJ, Hamprecht FA, Steen H*, Steen JAJ* (2010). Computational Protein Profile Similarity Screening for Quantitative Mass Spectrometry Experiments Bioinformatics Advance Access [10.1093/bioinformatics/btp607 | in press pdf | MATLAB toolbox]
• Yang W, Vizio DD, Kirchner M, Steen H, Freeman MR (2009). Proteome-scale characterization of human s-acylated proteins in lipid raft-enriched and non-raft membranes. Molecular & Cellular Proteomics, in press [10.1074/mcp.M800448-MCP200 | in press pdf]
• Renard BY, Kirchner M, Monigatti F, Ivanov AR, Rappsilber J, Winter D, Steen JAJ, Hamprecht FA, Steen H (2009). When Less Can Yield More - Computational Preprocessing of MS/MS Spectra for Peptide Identification. PROTEOMICS, in press [10.1002/pmic.200900326 | Software]
• Hanselmann M, Koethe U, Kirchner M, Renard BY, Amstalden ER, Glunde K, Heeren RMA, Hamprecht FA (2009). Toward Digital Staining using Imaging Mass Spectrometry and Random Forests. Journal of Proteome Research, 8(7), 3558-3567 [10.1021/pr900253y]
• Kirchner M*, Renard BY*, Steen H, Steen JAJ, Hamprecht FA (2008). NITPICK: Peak Identification for Mass Spectrometry Data, BMC Bioinformatics 2008, 9:355 [10.1186/1471-2105-9-355 | pdf | R package]
• Hanselmann M, Kirchner M*, Renard BY*, Amstalden ER, Glunde K, Heeren RMA, Hamprecht FA (2008). Concise Representation of Mass Spectrometry Images by Probabilistic Latent Semantic Analysis, Analytical Chemistry, ASAP Article. [10.1021/ac801303x]
• Steen JAJ, Steen H, Georgi A, Parker K, Springer M, Kirchner M, Hamprecht FA, Kirschner MW (2008). Different phosphorylation states of the anaphase promoting complex in response to antimitotic drugs: A quantitative proteomic analysis, Proceedings of the National Academy of Sciences (PNAS), 105(16), pp. 6069-6074 . [10.1073/pnas.0709807104 | pdf]
• Koenig T, Menze BH, Kirchner M*, Monigatti F*, Parker KC*, Patterson T, Steen JAJ, Hamprecht FA, Steen H (2008). Robust Prediction of the MASCOT Score for an Improved Quality Assessment in Mass Spectrometric Proteomics, Journal of Proteome Research 7 (9), 3708-3717, 2008. [10.1021/pr700859x]
• Kirchner M, Saussen B, Steen H, Steen JAJ, Hamprecht FA. (2007) "amsrpm: Robust Point Matching for Retention Time Alignment of LC/MS Data with R", Journal of Statistical Software, Special Issue on Spectroscopy and Chemometrics in R, 18(4) [pdf]

• Kirchner M*, Renard BY*, Koethe U, Steen JAJ, Steen H, Hamprecht, FA. (2009). Automatic Computational Protein Co-Regulation Screening for Quantitative Mass Spectrometry Experiments. Conference of the American Society for Mass Spectrometry (ASMS) 2009.
• Kreshuk A, Kirchner M*, Renard BY, Winter D, Steen H, Steen JAJ, Lehmann WD, Hamprecht FA. (2009). Automatic Quantification of 16/18O-Labeled LC/MS Data. Conference of the American Society for Mass Spectrometry (ASMS) 2009.
• Voss BM, Renard BY, Kreshuk A, Hanselmann M, Koethe U, Steen H, Steen JAJ, Kirchner M, Hamprecht FA. (2009). Simultaneous Multiple Alignment for LC/MS Peak Lists. Conference of the American Society for Mass Spectrometry (ASMS) 2009.
• Lou X, Kirchner M*, Renard BY*, Koethe U, Graf C, Steen JAJ, Steen H, Mayer MP, Hamprecht FA. (2009). HeXicon++: Automating HDX Data Analysis. Conference of the American Society for Mass Spectrometry (ASMS) 2009.
• Renard BY, Monigatti F, Kirchner M, Ivanov AR, Rappsilber J, Steen JAJ, Hamprecht FA, Steen H. (2009). Computational MS/MS Spectra Preprocessing - a Free Lunch. Conference of the American Society for Mass Spectrometry (ASMS) 2009.
• Hanselmann M, Koethe U, Kirchner M*, Renard BY*, Amstalden ER, Glunde K, Heeren RMA, Hamprecht FA. (2009). Automated Classification and Grading of Tumors in Mass Spectrometric Images using postprocessed Random Forests. Conference of the American Society for Mass Spectrometry (ASMS) 2009.
• Lou X, Kirchner M*, Renard BY*, Graf C, Steen JAJ, Steen H, Mayer MP, Hamprecht FA. (2008). HeXion: Automatic Information Extraction for HX-MS Data, HX interest group meeting, Conference of the American Society for Mass Spectrometry (ASMS) 2008.
• Kirchner M*, Renard BY*, Monigatti F, Hamprecht FA, Steen JAJ, Steen H. (2008). Optimal Significane Determination in iTRAQ experiments, Conference of the American Society for Mass Spectroemtry (ASMS) 2008.
• Kirchner M*, Renard BY*, Steen JAJ, Steen H, Hamprecht FA. (2008). STRAP2: Reliable, Hierarchical Feature Extraction from Multicomponent Mass Spectra, Conference of the American Society for Mass Spectroemtry (ASMS) 2008.
• Hanselmann M, Kirchner M, Renard BY, Kharchenko A, Klerk L, Koethe U, Heeren RMA, Hamprecht FA. (2008) Concise representation of MS Images by Probabilistic Latent Semantic Analysis, Conference of the American Society for Mass Spectroemtry (ASMS) 2008.
• Boppel S, Kirchner M*, Renard BY*, Steen H, Koethe U, Hamprecht FA. (2008). Sparse Profile Reconstruction for LC/MS Feature Extraction, Conference of the American Society for Mass Spectroemtry (ASMS) 2008.
• Lou X, Kirchner M*, Renard BY*, Koethe U, Steen H, Mayer MA, Hamprecht FA. (2008). Fully Automated HX-MS Data Analysis with Complete Deuteration Distribution Estimation, Conference of the American Society for Mass Spectroemtry (ASMS) 2008.
• Renard BY, Kirchner M, Steen JAJ, Steen H, Hamprecht FA (2007). Extended Fractional Averagine for Improved Peak Identification in Mass Spectrometry Data, European Conference on Computational Biology (ISMB/ECCB) 2007
• Kirchner M, Renard BY, Goerlitz L, Steen H, Steen JAJ, Hamprecht FA (2007). A sparsity-promoting non-negative regression approach for deconvolution, deisotoping, and quantification of mixture mass spectra, American Society for Mass Spectrometry, Annual Conference, ASMS 2007
• Renard BY, Kirchner M, Steen JAJ, Steen H, Hamprecht FA (2007). Fractional Averagine: Improved Modeling Of Isotope Distributions For Peak Picking. American Society for Mass Spectrometry, Annual Conference, ASMS 2007.
• Koenig T, Menze BH, Kirchner M, Steen H, Steen JAJ, Monigatti F, Parker KC, Patterson T, Hamprecht FA (2007). A Quality Score for Product Ion Spectra in Proteomics: How to Teach an Expert System with Minimal Manual Input, American Society for Mass Spectrometry, Annual Conference, ASMS 2007
• Steen H, Steen JAJ, Parker K, Georgi A, Ross P, Kirchner M, Hamprecht FA, Pappin D, Kirschner MW. (2006) Deciphering the Cell Cycle Through Quantitative Proteomics, 17th International Mass Spectrometry Conference (IMSC) 2006
• Bonowski F, Kirchner M, Steen H, Steen JAJ, Hamprecht FA. (2006) "ProteoPeak" - a modular framework for intelligent peak picking in biopolymer samples using adaptive templates, 17th International Mass Spectrometry Conference (IMSC) 2006
• Saussen B, Kirchner M, Steen JAJ, Steen H, Hamprecht FA. (2006) The rpm package: aligning LC/MS mass spectra with R, useR!2006.
• Waldon ZO, Kirchner M, Bonowski F, Hamprecht FA, Steen H, Jebanathirajah J. (2006) Discriminatrix: A System for Discovering Microbial Biomarkers, American Society for Mass Spectrometry, Annual Conference, ASMS 2006.
• Kirchner M, Krafft C, and Hamprecht, FA. (2005) Extending SMCR: spatial smoothnes constraints in Alternating Least Squares estimation. 12th International Conference on Near Infrared Spectroscopy, Auckland, New Zealand.