JVirGel: calculation of virtual two-dimensional protein gels. - Karsten Hiller; Max Schobert; Claudia Hundertmark; Dieter Jahn; Richard Münch (Nucleic Acids Res., 2003)

PRODORIC: prokaryotic database of gene regulation. - Richard Münch; Karsten Hiller; Heiko Barg; Dana Heldt; Simone Linz; Edgar Wingender; Dieter Jahn (Nucleic Acids Res., 2003)

PrediSi: prediction of signal peptides and their cleavage positions. - Karsten Hiller; Andreas Grote; Maurice Scheer; Richard Münch; Dieter Jahn (Nucleic Acids Res., 2004)

Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. - Richard Münch; Karsten Hiller; Andreas Grote; Maurice Scheer; Johannes Klein; Max Schobert; Dieter Jahn (Bioinform., 2005)

JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. - Andreas Grote; Karsten Hiller; Maurice Scheer; Richard Münch; Bernd Nörtemann; Dietmar C. Hempel; Dieter Jahn (Nucleic Acids Res., 2005)

MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data. - Boyke Bunk; Martin Kucklick; Rochus Jonas; Richard Münch; Max Schobert; Dieter Jahn; Karsten Hiller (Bioinform., 2006)

JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins. - Karsten Hiller; Andreas Grote; Matthias Maneck; Richard Münch; Dieter Jahn (Bioinform., 2006)

JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. - Maurice Scheer; Frank Klawonn; Richard Münch; Andreas Grote; Karsten Hiller; Claudia Choi; Ina Koch; Max Schobert; Elisabeth Härtig; Ulrich Klages; Dieter Jahn (Nucleic Acids Res., 2006)

SYSTOMONAS - an integrated database for systems biology analysis of Pseudomonas. - Claudia Choi; Richard Münch; Stefan Leupold; Johannes Klein; Inga Siegel; Bernhard Thielen; Beatrice Benkert; Martin Kucklick; Max Schobert; Jens Barthelmes; Christian Ebeling; Isam Haddad; et al. (Nucleic Acids Res., 2007)

An Emergent Self-Organizing Map Based Analysis Pipeline for Comparative Metabolome Studies. - Isam Haddad; Karsten Hiller; Eliane Frimmersdorf; Beatrice Benkert; Dietmar Schomburg; Dieter Jahn (Silico Biol., 2009)

NTFD - a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data. - Karsten Hiller; André Wegner; Daniel Weindl; Thekla Cordes; Christian M. Metallo; Joanne K. Kelleher; Gregory Stephanopoulos (Bioinform., 2013)

MIA: non-targeted mass isotopolome analysis. - Daniel Weindl; André Wegner; Karsten Hiller (Bioinform., 2016)

Continuous Live-Cell Culture Imaging and Single-Cell Tracking by Computational Lensfree LED Microscopy. - Gregor Scholz; Shinta Mariana; Agus Budi Dharmawan; Iqbal Syamsu; Philipp Hörmann; Carsten Reuse; Jana Hartmann; Karsten Hiller; Joan Daniel Prades; Hutomo Suryo Wasisto; Andreas Waag (Sensors, 2019)

MIAMI–a tool for non-targeted detection of metabolic flux changes for mode of action identification. - Christian-Alexander Dudek; Carsten Reuse; Regine Fuchs; Janneke Hendriks; Veronique Starck; Karsten Hiller (Bioinform., 2020)