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Conference Paper

Hanselmann, M, Köthe, U, Renard, B Y, Kirchner, M, Heeren, R M A and Hamprecht, F A (2009). Multivariate Watershed Segmentation of Compositional Data. Proceedings of the 15th International Conference on Discrete Geometry for Computer Imagery (DGCI), in press. Springer. 5810 180-192

Technical Report (1.25 MB)

Journal Article

Kirchner, M, Saussen, B, Steen, H, Steen, J A J and Hamprecht, F A (2007). amsrpm: Robust Point Matching in Retention Time Alignment of LC/MS Data with R. Journal of Statistical Software. 18 1-12. http://www.jstatsoft.org/v18/i04/paper

Kreshuk, A, Stankiewicz, M, Lou, X, Kirchner, M, Hamprecht, F A and Mayer, M P (2010). Automated detection and analysis of bimodal isotope peak distribution in H/D exchange mass spectrometry using HeXicon. International Journal of Mass Spectrometry. 302 125-131

Technical Report (3.22 MB)

Kirchner, M, Renard, B Y, Köthe, U, Pappin, D J, Hamprecht, F A, Steen, J A J and Steen, H (2010). Computational Protein Profile Similarity Screening for Quantitative Mass Spectrometry Experiments. Bioinformatics. 26 (1) 77-83

Technical Report (380.19 KB)

Hanselmann, M, Kirchner, M, Renard, B Y, Amstalden, E R, Glunde, K, Heeren, R M A and Hamprecht, F A (2008). Concise Representation of MS Images by Probabilistic Latent Semantic Analysis. Analytical Chemistry. 80 9649-9658

Technical Report (3.91 MB)

Lou, X, Kirchner, M, Renard, B Y, Köthe, U, Graf, C, Lee, C, Steen, J A J, Steen, H, Mayer, M P and Hamprecht, F A (2010). Deuteration Distribution Estimation with Improved Sequence Coverage for HX/MS Experiments. Bioinformatics. 26(12) 1535-1541

Technical Report (518.01 KB)

Steen, J A J, Steen, H, Georgi, A, Parker, K C, Springer, M, Kirchner, M, Hamprecht, F A and Kirschner, M W (2008). Different Phosphorylation States of the Anaphase Promoting Complex in Response to Anti-Mitotic Drugs: A Quantitative Proteomic Analysis. Proceedings of the National Academy of Sciences. 105 6069-6074

Technical Report (173.02 KB)

Renard, B Y, Timm, W, Kirchner, M, Steen, J A J, Hamprecht, F A and Steen, H (2010). Estimating the Confidence of Peptide Identifications without Decoy Databases. Analytical Chemistry. 4314-4318

Technical Report (619.11 KB)

Kirchner, M, Steen, J A J, Hamprecht, F A and Steen, H (2010). MGFp: An Open Mascot Generic Format Parser Library Implementation. Journal of Proteome Research. 9 (5) 27622763

Technical Report (125.18 KB)

Renard, B Y, Kirchner, M, Steen, H, Steen, J A J and Hamprecht, F A (2008). NITPICK: Peak Identification for Mass Spectrometry Data. BMC Bioinformatics. 9 355

Technical Report (643.89 KB)

Renard, B Y, Xu, B, Kirchner, M, Zickmann, F, Winter, D, Korten, S, Brattig, N, Tzur, A, Hamprecht, F A and Steen, H (2012). Overcoming species boundaries in peptide identification with BICEPS. Molecular and Cellular Proteomics. 11

Technical Report (444.6 KB)

König, T, Menze, B H, Kirchner, M, Monigatti, F, Parker, K C, Patterson, T, Steen, J J, Hamprecht, F A and Steen, H (2008). Robust Prediction of the MASCOT Score for an Improved Quality Assessment in Mass Spectrometric Proteomics. Journal of Proteome Research. 7 3708-3717

Technical Report (1.16 MB)

Hanselmann, M, Voss, B, Renard, B Y, Lindner, M, Köthe, U, Kirchner, M and Hamprecht, F A (2011). SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists. Bioinformatics. 27 (7) 987-993

Technical Report (2.2 MB)

Hanselmann, M, Köthe, U, Kirchner, M, Renard, B Y, Amstalden, E R, Glunde, K, Heeren, R M A and Hamprecht, F A (2009). Towards Digital Staining using Imaging Mass Spectrometry and Random Forests. Journal of Proteome Research. 8 3558-3567

Technical Report (1.47 MB)

Renard, B Y, Kirchner, M, Monigatti, F, Ivanov, A R, Rappsilber, J, Winter, D, Steen, J A J, Hamprecht, F A and Steen, H (2009). When Less Can Yield More - Computational Preprocessing of MS/MS Spectra for Peptide Identification Preprocessing. Proteomics. 9 4978-4984

Technical Report (901.78 KB)

Masters Thesis

Kirchner, M (2004). Spatial Extensions To Self-Modeling Curve Resolution. University of Heidelberg

PhD Thesis

Kirchner, M (2008). Analysis of Spectral Data. University of Heidelberg