Thomas Manke
Thomas Manke
Head of Bioinformatics and Deep-Sequencing Unit, Max Planck Institute for Immunobiology and
Verified email at
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deepTools2: a next generation web server for deep-sequencing data analysis
F Ramírez, DP Ryan, B Grüning, V Bhardwaj, F Kilpert, AS Richter, ...
Nucleic acids research 44 (Web Server issue), W160, 2016
deepTools: a flexible platform for exploring deep-sequencing data
F Ramírez, F Dündar, S Diehl, BA Grüning, T Manke
Nucleic acids research 42 (W1), W187-W191, 2014
High-resolution TADs reveal DNA sequences underlying genome organization in flies
F Ramírez, V Bhardwaj, L Arrigoni, KC Lam, BA Grüning, J Villaveces, ...
Nature communications 9 (1), 189, 2018
The International Human Epigenome Consortium: a blueprint for scientific collaboration and discovery
HG Stunnenberg, S Abrignani, D Adams, M de Almeida, L Altucci, V Amin, ...
Cell 167 (5), 1145-1149, 2016
DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome
T Aktaş, İ Avşar Ilık, D Maticzka, V Bhardwaj, C Pessoa Rodrigues, ...
Nature 544 (7648), 115-119, 2017
Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells
A Bulut-Karslioglu, A Inti, F Ramirez, M Barenboim, M Onishi-Seebacher, ...
Molecular cell 55 (2), 277-290, 2014
pyGenomeTracks: reproducible plots for multivariate genomic datasets
L Lopez-Delisle, L Rabbani, J Wolff, V Bhardwaj, R Backofen, B Grüning, ...
Bioinformatics 37 (3), 422-423, 2021
Robustness and network evolution—an entropic principle
L Demetrius, T Manke
Physica A: Statistical Mechanics and its Applications 346 (3-4), 682-696, 2005
Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs
M Thomas-Chollier, A Hufton, M Heinig, S O'keeffe, NE Masri, HG Roider, ...
Nature protocols 6 (12), 1860-1869, 2011
Predicting transcription factor affinities to DNA from a biophysical model
HG Roider, A Kanhere, T Manke, M Vingron
Bioinformatics 23 (2), 134-141, 2007
A genome-wide association study identifies GLT6D1 as a susceptibility locus for periodontitis
AS Schaefer, GM Richter, M Nothnagel, T Manke, H Dommisch, G Jacobs, ...
Human molecular genetics 19 (3), 553-562, 2010
Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization
J Wolff, L Rabbani, R Gilsbach, G Richard, T Manke, R Backofen, ...
Nucleic acids research 48 (W1), W177-W184, 2020
Epigenomic profiling of human CD4+ T cells supports a linear differentiation model and highlights molecular regulators of memory development
P Durek, K Nordström, G Gasparoni, A Salhab, C Kressler, M De Almeida, ...
Immunity 45 (5), 1148-1161, 2016
The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle
HJ Warnatz, D Schmidt, T Manke, I Piccini, M Sultan, T Borodina, ...
Journal of Biological Chemistry 286 (26), 23521-23532, 2011
A transcription factor–based mechanism for mouse heterochromatin formation
A Bulut-Karslioglu, V Perrera, M Scaranaro, IA De La Rosa-velazquez, ...
Nature structural & molecular biology 19 (10), 1023-1030, 2012
Community-driven data analysis training for biology
B Batut, S Hiltemann, A Bagnacani, D Baker, V Bhardwaj, C Blank, ...
Cell systems 6 (6), 752-758. e1, 2018
Nuclear architecture organized by Rif1 underpins the replication-timing program
R Foti, S Gnan, D Cornacchia, V Dileep, A Bulut-Karslioglu, S Diehl, ...
Molecular cell 61 (2), 260-273, 2016
Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
J Wolff, V Bhardwaj, S Nothjunge, G Richard, G Renschler, R Gilsbach, ...
Nucleic acids research 46 (W1), W11-W16, 2018
PASTAA: identifying transcription factors associated with sets of co-regulated genes
HG Roider, T Manke, S O'Keeffe, M Vingron, SA Haas
Bioinformatics 25 (4), 435-442, 2009
Mutational characterization of the bile acid receptor TGR5 in primary sclerosing cholangitis
JR Hov, V Keitel, JK Laerdahl, L Spomer, E Ellinghaus, A ElSharawy, ...
PloS one 5 (8), e12403, 2010
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