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Conference Paper

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

Technical Report (1.25 MB)

Journal Article

M. Kirchner, Saussen, B., Steen, H., Steen, J. A. J., and Hamprecht, F. A., “amsrpm: Robust Point Matching in Retention Time Alignment of LC/MS Data with R”, Journal of Statistical Software, vol. 18, pp. 1-12, 2007.

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

Technical Report (3.22 MB)

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

Technical Report (380.19 KB)

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

Technical Report (3.91 MB)

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

Technical Report (518.01 KB)

J. A. J. Steen, Steen, H., Georgi, A., Parker, K. C., Springer, M., Kirchner, M., Hamprecht, F. A., and Kirschner, M. W., “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, vol. 105, pp. 6069-6074, 2008.

Technical Report (173.02 KB)

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

Technical Report (619.11 KB)

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

Technical Report (125.18 KB)

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

Technical Report (643.89 KB)

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

Technical Report (444.6 KB)

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

Technical Report (1.16 MB)

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

Technical Report (2.2 MB)

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

Technical Report (1.47 MB)

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

Technical Report (901.78 KB)

Masters Thesis

M. Kirchner, “Spatial extensions to self-modeling curve resolution”, University of Heidelberg, 2004.

PhD Thesis

M. Kirchner, “Analysis of Spectral Data”. University of Heidelberg, 2008.