Petri-Netze und ihre Verwendung zum standardisierten Entwurf digitaler Steuerungen. - Rainer König (1980)

Chancen des Einsatzes öffentlicher Datennetze bei der umweltverträglichen Steuerung des Personennahverkehrs. - Peter Zoche; Rainer König (Informatik für den Umweltschutz, 1990)

Möglichkeiten und Grenzen von "Cooperative Work". - Rainer König; Peter Zoche (GI Jahrestagung, 1991)

Informationstechnik für den Verkehr - Medizin oder Droge? - Dirk-Michael Harmsen; Rainer König (Informatik cui bono?, 1992)

A Prototype of an Interface Bilder for the Common Lisp Interface Manager - CLIB. - Jan Hesse; Rainer König; Filippo Logi; Jens Herder (ACM SIGPLAN Notices, 1993)

Media Oriented Systems Transport (MOST®) - Standard für Multimedia Networking im Fahrzeug / Media Oriented Systems Transport - Standard for Multimedia Networking in Vehicle Environment. - Rainer König; Christian Thiel (Informationstechnik Tech. Inform., 1999)

Modelling of Information Flows in Cells. - Marco Weismueller; Rainer König; Roland Eils (ESM, 2002)

Gene expression analysis on biochemical networks with the potts spin model. - Rainer König; Roland Eils (German Conference on Bioinformatics, 2003)

Gene expression analysis on biochemical networks using the Potts spin model. - Rainer König; Roland Eils (Bioinform., 2004)

Applying Support Vector Machines for Gene ontology based gene function prediction. - Arunachalam Vinayagam; Rainer König; Jutta Moormann; Falk Schubert; Roland Eils; Karl-Heinz Glatting; Sándor Suhai (BMC Bioinform., 2004)

Pattern recognition of gene expression data on biochemical networks with simple wavelet transforms. - Gunnar Schramm; Marcus Oswald; Hanna Seitz; Sebastian Sager; Marc Zapatka; Gerhard Reinelt; Roland Eils; Rainer König (LWA, 2006)

Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms. - Rainer König; Gunnar Schramm; Marcus Oswald; Hanna Seitz; Sebastian Sager; Marc Zapatka; Gerhard Reinelt; Roland Eils (BMC Bioinform., 2006)

GOPET: A tool for automated predictions of Gene Ontology terms. - Arunachalam Vinayagam; Coral del Val; Falk Schubert; Roland Eils; Karl-Heinz Glatting; Sándor Suhai; Rainer König (BMC Bioinform., 2006)

Integrating Genomic and Transcriptomic Data into Graph Based Approaches for Defining Essential Reactions in the Metabolic Network of Escherichia Coli. - Kitiporn Plaimas; Marcus Oswald; Roland Eils; Rainer König (LWA, 2007)

Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli. - Gunnar Schramm; Marc Zapatka; Roland Eils; Rainer König (BMC Bioinform., 2007)

Machine learning based analyses on metabolic networks supports high-throughput knockout screens. - Kitiporn Plaimas; Jan-Phillip Mallm; Marcus Oswald; Fabian Svara; Victor Sourjik; Roland Eils; Rainer König (BMC Syst. Biol., 2008)

Haralick's Texture Features Computation Accelerated by GPUs for Biological Applications. - Markus Gipp; Guillermo Marcus Martinez; Nathalie Harder; Apichat Suratanee; Karl Rohr; Rainer König; Reinhard Männer (HPSC, 2009)

Analyzing the regulation of metabolic pathways in human breast cancer. - Eva-Maria Surmann; Gunnar Schramm; Stefan Wiesberg; Marcus Oswald; Gerhard Reinelt; Roland Eils; Rainer König (LWA, 2009)

PathWave: discovering patterns of differentially regulated enzymes in metabolic pathways. - Gunnar Schramm; Stefan Wiesberg; Nicolle Diessl; Anna-Lena Kranz; Vitalia Sagulenko; Marcus Oswald; Gerhard Reinelt; Frank Westermann; Roland Eils; Rainer König (Bioinform., 2010)

Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images. - Apichat Suratanee; Ilka Rebhan; Petr Matula; Anil Kumar 006; Lars Kaderali; Karl Rohr; Ralf Bartenschlager; Roland Eils; Rainer König (Bioinform., 2010)

Identifying essential genes in bacterial metabolic networks with machine learning methods. - Kitiporn Plaimas; Roland Eils; Rainer König (BMC Syst. Biol., 2010)

Regulation patterns in signaling networks of cancer. - Gunnar Schramm; Nandakumar Kannabiran; Rainer König (BMC Syst. Biol., 2010)

RIP: the regulatory interaction predictor - a machine learning-based approach for predicting target genes of transcription factors. - Tobias Bauer; Roland Eils; Rainer König (Bioinform., 2011)

Cell Tracking for Automatic Migration and Proliferation Analysis in High-Throughput Screens. - Nathalie Harder; Richa Batra; Sina Gogolin; Nicolle Diessl; Roland Eils; Frank Westermann; Rainer König; Karl Rohr (Bildverarbeitung für die Medizin, 2012)

SplicingCompass: differential splicing detection using RNA-Seq data. - Moritz Aschoff; Agnes Hotz-Wagenblatt; Karl-Heinz Glatting; Matthias Fischer 003; Roland Eils; Rainer König (Bioinform., 2013)

Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities. - Rosario M. Piro; Ivan Molineris; Ferdinando Di Cunto; Roland Eils; Rainer König (Bioinform., 2013)

Estimating the activity of transcription factors by the effect on their target genes. - Theresa Schacht; Marcus Oswald; Roland Eils; Stefan B. Eichmüller; Rainer König (Bioinform., 2014)

Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling. - Rosario M. Piro; Stefan Wiesberg; Gunnar Schramm; Nico Rebel; Marcus Oswald; Roland Eils; Gerhard Reinelt; Rainer König (BMC Syst. Biol., 2014)

Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen. - Apichat Suratanee; Martin H. Schaefer 001; Matthew J. Betts; Zita Soons; Heiko A. Mannsperger; Nathalie Harder; Marcus Oswald; Markus Gipp; Ellen Ramminger; Guillermo Marcus Martinez; Reinhard Männer; Karl Rohr; et al. (PLoS Comput. Biol., 2014)

The Use of Tools, Modelling Methods, Data Types, and Endpoints in Systems Medicine: A Survey on Projects of the German e: Med-Programme. - Matthias Gietzelt; Thomas Höfer; Petra Knaup-Gregori; Rainer König; Martin Löpprich; Alexandra Poos; Matthias Ganzinger (MIE, 2016)

Segmentation of cell structures using Model-Based Set Covering with iterative reweighting. - Peter Markowsky; Svenja Reith; Tabea E. Zuber; Rainer König; Karl Rohr; Christoph Schnörr (ISBI, 2017)

Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach. - Alexandra Poos; Theresa Kordaß; Amol Kolte; Volker Ast; Marcus Oswald; Karsten Rippe; Rainer König (BMC Bioinform., 2019)

Reprogramming of macrophages employing gene regulatory and metabolic network models. - Franziska Hörhold; David Eisel; Marcus Oswald; Amol Kolte; Daniela Röll; Wolfram Osen; Stefan B. Eichmüller; Rainer König (PLoS Comput. Biol., 2020)

Evaluating the effects of automation components in service networks of rail freight. - Tobias Pollehn; Moritz Ruf; Rainer König (J. Rail Transp. Plan. Manag., 2021)

Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis. - Kulwadee Thanamit; Franziska Hörhold; Marcus Oswald; Rainer König (BMC Bioinform., 2022)