NITPICK: peak identification for mass spectrometry data. - Bernhard Y. Renard; Marc Kirchner; Hanno Steen; Judith A. J. Steen; Fred A. Hamprecht (BMC Bioinform., 2008)

Multivariate Watershed Segmentation of Compositional Data. - Michael Hanselmann; Ullrich Köthe; Bernhard Y. Renard; Marc Kirchner; Ron M. A. Heeren; Fred A. Hamprecht (DGCI, 2009)

Computational protein profile similarity screening for quantitative mass spectrometry experiments. - Marc Kirchner; Bernhard Y. Renard; Ullrich Köthe; Darryl J. Pappin; Fred A. Hamprecht; Hanno Steen; Judith A. J. Steen (Bioinform., 2010)

Non-linear classification for on-the-fly fractional mass filtering and targeted precursor fragmentation in mass spectrometry experiments. - Marc Kirchner; Wiebke Timm; Peying Fong; Philine Wangemann; Hanno Steen (Bioinform., 2010)

Deuteration distribution estimation with improved sequence coverage for HX/MS experiments. - Xinghua Lou; Marc Kirchner; Bernhard Y. Renard; Ullrich Köthe; Sebastian Boppel; Christian Graf 002; Chung-Tien Lee; Judith A. J. Steen; Hanno Steen; Matthias P. Mayer; Fred A. Hamprecht (Bioinform., 2010)

libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data. - Marc Kirchner; Buote Xu; Hanno Steen; Judith A. J. Steen (Bioinform., 2011)

SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists. - Björn Voss; Michael Hanselmann; Bernhard Y. Renard; Martin S. Lindner; Ullrich Köthe; Marc Kirchner; Fred A. Hamprecht (Bioinform., 2011)

A Practical Guide to the FLEXIQuant Method. - Sasha Singh; Marc Kirchner; Judith A. J. Steen; Hanno Steen (Quantitative Methods in Proteomics, 2012)

Neo: Generalizing Confusion Matrix Visualization to Hierarchical and Multi-Output Labels. - Jochen Görtler; Fred Hohman; Dominik Moritz; Kanit Wongsuphasawat; Donghao Ren; Rahul Nair; Marc Kirchner; Kayur Patel (CHI, 2022)

On Efficient and Statistical Quality Estimation for Data Annotation. - Jan-Christoph Klie; Juan Haladjian; Marc Kirchner; Rahul Nair (ACL (1), 2024)