T
Thomas Manke
Researcher at Max Planck Society
Publications - 133
Citations - 13368
Thomas Manke is an academic researcher from Max Planck Society. The author has contributed to research in topics: Quantum chromodynamics & Promoter. The author has an hindex of 42, co-authored 125 publications receiving 9366 citations. Previous affiliations of Thomas Manke include University of Cambridge & Columbia University.
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deepTools2: a next generation web server for deep-sequencing data analysis
Fidel Ramírez,Devon Ryan,Björn Grüning,Vivek Bhardwaj,Fabian Kilpert,Andreas S. Richter,Steffen Heyne,Friederike Dündar,Thomas Manke +8 more
TL;DR: An update to the Galaxy-based web server deepTools, which allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches, is presented.
Journal ArticleDOI
deepTools: a flexible platform for exploring deep-sequencing data
TL;DR: A Galaxy based web server for processing and visualizing deeply sequenced data, called deepTools, that enables users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting and can be used without registration.
Journal ArticleDOI
High-resolution TADs reveal DNA sequences underlying genome organization in flies.
Fidel Ramírez,Vivek Bhardwaj,Vivek Bhardwaj,Laura Arrigoni,Kin Chung Lam,Björn Grüning,Jose M. Villaveces,Bianca Habermann,Asifa Akhtar,Thomas Manke +9 more
TL;DR: Software to identify high-resolution TAD boundaries and reveal their relationship to underlying DNA motifs is developed and it is demonstrated that boundaries can be accurately predicted using only the motif sequences at open chromatin sites.
Journal ArticleDOI
DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome
Tugce Aktas,Ibrahim Avsar Ilik,Daniel Maticzka,Vivek Bhardwaj,Vivek Bhardwaj,Cecilia Pessoa Rodrigues,Cecilia Pessoa Rodrigues,Gerhard Mittler,Thomas Manke,Rolf Backofen,Asifa Akhtar +10 more
TL;DR: It is proposed that DHX9 acts as a nuclear RNA resolvase that neutralizes the immediate threat posed by transposon insertions and allows these elements to evolve as tools for the post-transcriptional regulation of gene expression.
Journal ArticleDOI
Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells
Aydan Bulut-Karslioglu,Inti A. De La Rosa-Velázquez,Fidel Ramírez,Maxim Barenboim,Megumi Onishi-Seebacher,Julia Arand,Carmen Galán,Georg E. Winter,Bettina Engist,Borbala Gerle,Roderick J. O'Sullivan,Joost H.A. Martens,Jörn Walter,Thomas Manke,Monika Lachner,Thomas Jenuwein +15 more
TL;DR: A function for Suv39h-dependent H3K9me3 chromatin to specifically repress intact LINE elements in the ESC epigenome is provided.