Head of Facility

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Dr. Thomas Manke
Phone:+49 761 5108 738
Email:manke@...

Selected Publications

1.
Ramírez, F.*, Lingg, T.*, Toscano, S.*, Lam, K. C.*, Georgiev, P., Chung, H.-R., Lajoie, B.,de Wit, E.,Zhan, Y., de Laat, W., Dekker, J., Manke, T.,Akhtar, A.
High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila.
2.
Bulut-Karslioglu A, De La Rosa-Velázquez IA, Ramirez F, Barenboim M,Onishi-Seebacher M, Arand J, Galán C, Winter GE, Engist B, Gerle B, O'Sullivan RJ, Martens JH, Walter J, Manke T, Lachner M, Jenuwein T.
Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells.
3.
Chelmicki T, Dündar F, Turley MJ, Khanam T, Aktas T, Ramírez F, Gendrel AV, Wright PR, Videm P, Backofen R, Heard E, Manke T, Akhtar A.
MOF-associated complexes ensure stem cell identity and Xist repression.
4.
Ramirez F*, Dündar F*, Diehl S, Grüning B J and Manke T (2014) *equal contribution
deepTools: a flexible platform for exploring deep-sequencing data.
5.
Barenboim M, Manke T.
ChroMoS: an integrated web tool for SNP classification,prioritization and functional interpretation.
6.
Bulut-Karslioglu A, Perrera V, Scaranaro M, de la Rosa-Velazquez IA, van de Nobelen S, Shukeir N, Popow J, Gerle B, Opravil S, Pagani M, Meidhof S, Brabletz T, Manke T, Lachner M, Jenuwein T.
A transcription factor-based mechanism for mouse heterochromatin formation.
7.
Lam KC, Mühlpfordt F, Vaquerizas JM, Raja SJ, Holz H, Luscombe NM, Manke T, Akhtar A.
The NSL Complex Regulates Housekeeping Genes in Drosophila
8.
Thomas-Chollier M, Hufton A, Heinig M, O'Keeffe S, Masri NE, Roider HG, Manke T, Vingron M. (2011)
Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.

Bioinformatics Facility

Bioinformatics Facility

The regulation of gene expression is controlled by multiple mechanisms, such as the sequence-specific binding of transcription factors to DNA, epigenetic signals and a dynamic chromatin state. An unbiased understanding of these processes requires access to large-scale experiments and the capacity to analyze genome-wide data. In close interaction with the Deep-Sequencing Facility of the MPI-IE, we streamline the primary analysis and quality control of data, which emerges at an unprecedented rate and resolution from a wide range of new sequencing experiments. 

In the context of scientific collaborations we are also developing new methods and tools for quality control, analysis and visualization of deep-sequencing data (à deepTools2). Together with the Deep-Sequencing Facility, we actively contribute to larger networks of epigenomic research (German Epigenome Programme DEEP and CRC992 "Medical Epigenetics") and support these projects with our expertise in deep-sequencing data generation and analysis.

The Bioinformatics Group is operating a powerful Data Center (more than 500 cores and 200TB storage) for the primary analysis of sequencing data and other large-scale biocomputing. For our internal users we host extensive web services, workflows and customized tools that help with data management, visualizations, standardized analyses and data sharing.

To help our colleagues with the interpretation of genome-wide data, the group offers regular training courses and interactive tutorials.

<p class="p1">Heatmaps are useful tools to visualize genome-wide data, such as important histone marks around all human genes.</p> Zoom Image

Heatmaps are useful tools to visualize genome-wide data, such as important histone marks around all human genes.

 
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