My fields of interest include computational proteomics, quantitative data analysis in mass spectrometry, statistical learning theory, pattern recognition and design of experiments. A significant amount of my time is devoted to designing algorithms tailored to mass spectrometry data analysis and pushing algorithmic developments into application.

Journal
Publications

23. Renard BY, Xu B, Kirchner M, Tzur A, Korten S, Brattig NQ, Steen H, Hamprecht FA (2011). Overcoming Species Boundaries in Peptide Identification with BICEPS. Submitted.
22. Ozlü N, Kirchner M, Steen JJ (2012). Measuring phosphorylation-specific changes in response to kinase inhibitors in mammalian cells using quantitative proteomics. Methods in Molecular Biology 795:217-31.
21. Soblik H, Younis AE, Mitreva M, Renard BY, Kirchner M, Geisinger F, Steen H, Brattig NW (2011). Life cycle stage-resolved proteomic analysis of the excretome secretome from Strongyloides ratti identification of stage-specific protease. Molecular and Cellular Proteomics. Accepted.
20. Singh S, Kirchner M, Steen JA, Steen H (2011). A Practical Guide to the FLEXIQuant Method. Methods in Molecular Biology. Submitted.
19. Wilhelm M*, Kirchner M*, Steen JA, Steen H (2011). mz5: Space- and Time-Efficient Storage of Mass Spectrometry Data Sets. Molecular and Cellular Proteomics. Accepted. [software]
18. Anderson DS, Kirchner M, Kellogg M, Kalish L, Vanasse G, Berliner N, Fleming MD, Steen H (2011). Design and validation of a novel high-throughput Matrix-Assisted Laser Desorption Ionization mass spectrometry method for quantification of hepcidin in human plasma. Analytical Chemistry. Accepted.
17. Kirchner M*, Xu B*, Steen H, Steen JA (2011). libfbi: A C++ Implementation for Fast Box Intersection and Application to Sparse Mass Spectrometry Data. Bioinformatics 27(8), 1166-1167 [doi | preprint | supplementary | software]
16. Voss B*, Hanselmann M*, Renard BY, Lindner M, Koethe U, Kirchner M, Hamprecht FA (2011). SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists. Bioinformatics Advance Access. [doi | preprint | software]
15. Kreshuk A, Stankiewicz M, Lou X, Kirchner M, Hamprecht FA, Mayer MP (2010). Automated detection and analysis of bimodal isotope peak distributions in H/D exchange mass spectrometry using HeXicon International Journal of Mass Spectrometry (in press). [doi]
14. Renard BY, Timm W, Kirchner M, Steen JAJ, Hamprecht FA, Steen H (2010). Estimating the Confidence of Peptide Identifications without Decoy Databases. Analytical Chemistry 82(11):4314-4318 [doi | R package]
13. Lou X, Kirchner M, Renard BY, Koethe U, Boppel S, Graf C, Lee C, Steen JAJ, Steen H, Mayer M, Hamprecht FA (2010). Deuteration Distribution Estimation with Improved Sequence Coverage for HX/MS Experiments. Bioinformatics 26(12):1535-1541 [PubMed]
12. Kirchner M, Steen JAJ, Hamprecht FA, Steen H (2010). MGFp: An open Mascot Generic Format parser library implementation. Journal of Proteome Research 9(5):2762-2763. [doi | Sourceforge project]
11. 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 26(6):791-797 [PubMed | R scripts]
10. 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 26(1):77-83 [PubMed | MATLAB toolbox]
9. 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 9(1):54-70 [doi]
8. 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 9(21):4978-4984 [doi | Software]
7. 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 [doi]
6. Hanselmann M, Koethe U, Renard BY, Kirchner M, Heeren RMA, Hamprecht, FA (2009). Multivariate Watershed Segmentation of Compositional Data. Proceedings of DGCI 2009:180-192
5. Kirchner M*, Renard BY*, Steen H, Steen JAJ, Hamprecht FA (2008). NITPICK: Peak Identification for Mass Spectrometry Data, BMC Bioinformatics 2008, 9:355 [doi | pdf | R package]
4. 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 80(24):9649-5 . [doi]
3. 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):6069-6074 . [doi | pdf]
2. 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. [doi]
1. 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]

Conference
Contributions

32. Singh S, Winter D, Kirchner M, Tzur A, Kirschner MW, Steen JA, Steen H (2012). Multiple Quantitative Proteomics Strategies Identify Targets and Mechanisms of Degradation by the Anaphase Promoting Complex. Submitted to USHUPO 2012.
31. Singh S*, Winter D*, Kirchner M*, Tzur A, Kirschner MW, Steen H, Steen JA (2012). A Quantitative Proteomic Analysis of the Mammalian Cell Cycle Identifies Motors as APC Targets. Protein Degradation Pathways in Health and Diseases 2012.
30. Kirchner M*, Winter D*, Steen JA, Steen H (2011). Changing the Rules of the Game: Next Generation Quantification (NGQ) Enables Complete Isotopic Multiplexing for Quantitative Functional and Dynamic Proteomics. Conference of the American Society for Mass Spectrometry (ASMS) 2011.
29. Winter D*, Singh S*, Kirchner M*, Steen H, Steen JA (2011). Large Scale Identification of Co-Regulated Mitotic Proteins. Conference of the American Society for Mass Spectrometry (ASMS) 2011.
28. Kirchner M*, Winter D*, Ashrafi G, Schwarz T, Steen JA, Steen H (2011). Next Generation Quantification (NGQ): studying the mitotic microtubule interactome using a novel metabolic 5-plex quantification method. Conference of the American Society for Mass Spectrometry (ASMS) 2011.
27. Winter D, Kirchner M, Belin S, Steen H, Steen JA (2011). Deciphering the ribosome composition during cell cycle by 16/18O labelling. Conference of the American Society for Mass Spectrometry (ASMS) 2011.
26. Kirchner M*, Xu B*, Steen JA, Steen H (2011). Boxing and stabbing: fast, error-tolerant subset queries for sparse LC/MS data sets. RECOMB Satellite Conference on Computational Proteomics 2011.
25. Timm W, Winter D, Kirchner M, Steen JAJ, Steen H. (2010) Increasing the number of TMT-quantifyable proteins by missing value imputation. Conference of the American Society for Mass Spectrometry (ASMS) 2010.
24. Kreshuk A, Kirchner M, Renard BY, Winter D, Kausler BX, Lou X, Hanselmann M, Steen JAJ, Steen H, Lehmann WD, Hamprecht FA (2010). Automatic Relative Quantification for High-Resolution LC/MS 16/18O Labeling Experiments. Conference of the American Society for Mass Spectrometry (ASMS) 2010.
23. 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. Conference of the American Society for Mass Spectrometry (ASMS) 2010.
22. Kausler BX, Kirchner M, Kreshuk A, Renard BY, Hahne H, Kuster B, Steen H, Hamprecht FA Resolution as a function of m/z for TOF, FT-ICR, and Orbitrap: predicted and confirmed. Conference of the American Society for Mass Spectrometry (ASMS) 2010.
21. 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.
20. 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.
19. 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.
18. 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.
17. 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.
16. 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.
15. 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.
14. 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.
13. 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.
12. 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.
11. 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.
10. 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.
9. 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
8. 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
7. 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.
6. 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
5. 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
4. 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
3. Saussen B, Kirchner M, Steen JAJ, Steen H, Hamprecht FA. (2006) The rpm package: aligning LC/MS mass spectra with R, useR!2006.
2. 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.
1. Kirchner M, Krafft C, and Hamprecht, FA. (2005) Extending SMCR: spatial smoothness constraints in Alternating Least Squares estimation. 12th International Conference on Near Infrared Spectroscopy, Auckland, New Zealand.