GMFilter and SXTestPlate: software tools for improving the SNPlexTM genotyping system. - Markus Teuber; Michael H. Wenz; Stefan Schreiber; Andre Franke (BMC Bioinform., 2009)

CNVineta: a data mining tool for large case-control copy number variation datasets. - Michael Wittig; Ingo Helbig; Stefan Schreiber; Andre Franke (Bioinform., 2010)

SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels. - Kristian Holm; Espen Melum; Andre Franke; Tom H. Karlsen (BMC Bioinform., 2010)

B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data. - Benjamin Kreck; George Marnellos; Julia Richter; Felix Krueger; Reiner Siebert; Andre Franke (Bioinform., 2012)

OscARsWelt: A Collaborative Augmented Reality Game. - Anna Katharina Hebborn; Milan Dilberovic; Adrian Derstroff; Andre Franke; Nils Höhner; Patrick Krechel; Lisa Prinz; Astrid Szirmai; Fabian Weigend; Stefan Müller 002 (AVR, 2015)

Haplotype synthesis analysis reveals functional variants underlying known genome-wide associated susceptibility loci. - André Lacour; David Ellinghaus; Stefan Schreiber; Andre Franke; Tim Becker (Bioinform., 2016)

Interdisciplinary approach towards a systems medicine toolbox using the example of inflammatory diseases. - Christian R. Bauer; Carolin Knecht; Christoph Fretter; Benjamin Baum; Sandra Jendrossek; Malte Rühlemann; Femke-Anouska Heinsen; Nadine Umbach; Bodo Grimbacher; Andre Franke; Wolfgang Lieb; Michael Krawczak; et al. (Briefings Bioinform., 2017)

Fine-mapping inflammatory bowel disease loci to single-variant resolution. - Hailiang Huang; Ming Fang; Luke Jostins; Masa Umicevic Mirkov; Gabrielle Boucher; Carl A. Anderson; Vibeke Andersen; Isabelle Cleynen; Adrian Cortes; François Crins; Mauro D'Amato; Valérie Deffontaine; et al. (Nat., 2017)

Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome. - Jens Christian Claussen; Jurgita Skieceviciene; Jun Wang 074; Philipp Rausch; Tom H. Karlsen; Wolfgang Lieb; John F. Baines; Andre Franke; Marc-Thorsten Hütt (PLoS Comput. Biol., 2017)

LitDB - Keeping Track of Research Papers From Your Institute Made Simple. - Jörn Bethune; Lars Kraemer; Ingo Thomsen; Andreas Keller; David Ellinghaus; Andre Franke (Source Code Biol. Medicine, 2017)

Comparing genome versus proteome-based identification of clinical bacterial isolates. - Valentina Galata; Christina Backes; Cedric Christian Laczny; Georg Hemmrich-Stanisak; Howard Li; Laura Smoot; Andreas E. Posch; Susanne Schmolke; Markus Bischoff; Lutz von Müller; Achim Plum; Andre Franke; et al. (Briefings Bioinform., 2018)

A high-resolution map of the human small non-coding transcriptome. - Tobias Fehlmann; Christina Backes; Julia Alles; Ulrike Fischer; Martin Hart; Fabian Kern; Hilde Langseth; Trine Rounge; Sinan Ugur Umu; Mustafa Kahraman; Thomas Laufer; Jan Haas; et al. (Bioinform., 2018)

Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11, 087 Clinical Isolates. - Valentina Galata; Cedric Christian Laczny; Christina Backes; Georg Hemmrich-Stanisak; Susanne Schmolke; Andre Franke; Eckart Meese; Mathias Herrmann; Lutz von Müller; Achim Plum; Rolf Müller 002; Cord Stähler; et al. (Genom. Proteom. Bioinform., 2019)

Amino acid encoding for deep learning applications. - Hesham ElAbd; Yana Bromberg; Adrienne Hoarfrost; Tobias Lenz; Andre Franke; Mareike Wendorff (BMC Bioinform., 2020)

Identification of Biomarkers Controlling Cell Fate In Blood Cell Development. - Maryam Nazarieh; Volkhard Helms; Marc P. Hoeppner; Andre Franke (CoRR, 2020)

A structural variation reference for medical and population genetics. - Ryan L. Collins; Harrison Brand; Konrad J. Karczewski; Xuefang Zhao; Jessica Alföldi; Laurent C. Francioli; Amit V. Khera; Chelsea Lowther; Laura D. Gauthier; Harold Wang; Nicholas A. Watts; Matthew Solomonson; et al. (Nat., 2020)

Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data. - Hesham ElAbd; Frauke Degenhardt; Tomás Koudelka; Ann-Kristin Kamps; Andreas Tholey; Petra Bacher; Tobias L. Lenz; Andre Franke; Mareike Wendorff (BMC Bioinform., 2021)

MAGScoT: a fast, lightweight and accurate bin-refinement tool. - Malte Rühlemann; Eike Matthias Wacker; David Ellinghaus; Andre Franke (Bioinform., 2022)

Pathogen detection in RNA-seq data with Pathonoia. - Anna-Maria Liebhoff; Kevin Menden; Alena Laschtowitz; Andre Franke; Christoph Schramm; Stefan Bonn (BMC Bioinform., 2023)