Detecting Functional Modules of Transcription Factor Binding Sites in the Human Genome. - Thomas Manke; Christoph Dieterich; Martin Vingron (Regulatory Genomics, 2004)

Predicting transcription factor affinities to DNA from a biophysical model. - Helge G. Roider; Aditi Kanhere; Thomas Manke; Martin Vingron (Bioinform., 2007)

Prioritization of gene regulatory interactions from large-scale modules in yeast. - Ho-Joon Lee; Thomas Manke; Ricardo Bringas; Martin Vingron (BMC Bioinform., 2008)

Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions. - Thomas Manke; Helge G. Roider; Martin Vingron (PLoS Comput. Biol., 2008)

PASTAA: identifying transcription factors associated with sets of co-regulated genes. - Helge G. Roider; Thomas Manke; Sean O'Keeffe; Martin Vingron; Stefan A. Haas (Bioinform., 2009)

ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation. - Maxim Barenboim; Thomas Manke (Bioinform., 2013)

deepTools: a flexible platform for exploring deep-sequencing data. - Fidel Ramírez; Friederike Dündar; Sarah Diehl; Björn A. Grüning; Thomas Manke (Nucleic Acids Res., 2014)

deepTools2: a next generation web server for deep-sequencing data analysis. - Fidel Ramírez; Devon Patrick Ryan; Björn A. Grüning; Vivek Bhardwaj 002; Fabian Kilpert; Andreas S. Richter; Steffen Heyne; Friederike Dündar; Thomas Manke (Nucleic Acids Res., 2016)

DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome. - Tugçe Aktas; Ibrahim Avsar Ilik; Daniel Maticzka; Vivek Bhardwaj 002; Cecilia Pessoa Rodrigues; Gerhard Mittler; Thomas Manke; Rolf Backofen; Asifa Akhtar (Nat., 2017)

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. - Joachim Wolff; Vivek Bhardwaj 002; Stephan Nothjunge; Gautier Richard; Gina Renschler; Ralf Gilsbach; Thomas Manke; Rolf Backofen; Fidel Ramírez; Björn A. Grüning (Nucleic Acids Res., 2018)

Parkour LIMS: high-quality sample preparation in next generation sequencing. - Evgeny Anatskiy; Devon Patrick Ryan; Björn A. Grüning; Laura Arrigoni; Thomas Manke; Ulrike Bönisch (Bioinform., 2019)

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis. - Vivek Bhardwaj 002; Steffen Heyne; Katarzyna Sikora; Leily Rabbani; Michael Rauer; Fabian Kilpert; Andreas S. Richter; Devon Patrick Ryan; Thomas Manke (Bioinform., 2019)

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization. - Joachim Wolff; Leily Rabbani; Ralf Gilsbach; Gautier Richard; Thomas Manke; Rolf Backofen; Björn A. Grüning (Nucleic Acids Res., 2020)

pyGenomeTracks: reproducible plots for multivariate genomic datasets. - Lucille Lopez-Delisle; Leily Rabbani; Joachim Wolff; Vivek Bhardwaj 002; Rolf Backofen; Björn A. Grüning; Fidel Ramírez; Thomas Manke (Bioinform., 2021)