Deltr: Digital embryo lineage tree reconstructor. - Xinghua Lou; Frederik O. Kaster; Martin S. Lindner; Bernhard X. Kausler; Ullrich Köthe; Burkhard Hockendorf; Jochen Wittbrodt; Heike Jänicke; Fred A. Hamprecht (ISBI, 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 Discrete Chain Graph Model for 3d+t Cell Tracking with High Misdetection Robustness. - Bernhard X. Kausler; Martin Schiegg; Björn Andres; Martin S. Lindner; Ullrich Köthe; Heike Leitte; Jochen Wittbrodt; Lars Hufnagel; Fred A. Hamprecht (ECCV (3), 2012)

Analyzing genome coverage profiles with applications to quality control in metagenomics. - Martin S. Lindner; Maximilian Kollock; Franziska Zickmann; Bernhard Y. Renard (Bioinform., 2013)

RNA-seq driven gene identification. - Franziska Zickmann; Martin S. Lindner; Bernhard Y. Renard (GCB, 2014)

Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics. - Anke Penzlin; Martin S. Lindner; Joerg Doellinger; Piotr Wojtek Dabrowski; Andreas Nitsche; Bernhard Y. Renard (Bioinform., 2014)

GIIRA - RNA-Seq driven gene finding incorporating ambiguous reads. - Franziska Zickmann; Martin S. Lindner; Bernhard Y. Renard (Bioinform., 2014)

DUDes: a top-down taxonomic profiler for metagenomics. - Vitor Piro; Martin S. Lindner; Bernhard Y. Renard (Bioinform., 2016)

HiLive: real-time mapping of illumina reads while sequencing. - Martin S. Lindner; Benjamin Strauch; Jakob M. Schulze; Simon H. Tausch; Piotr Wojtek Dabrowski; Andreas Nitsche; Bernhard Y. Renard (Bioinform., 2017)

LiveKraken–real-time metagenomic classification of illumina data. - Simon H. Tausch; Benjamin Strauch; Andreas Andrusch; Tobias P. Loka; Martin S. Lindner; Andreas Nitsche; Bernhard Y. Renard (Bioinform., 2018)