V
Vivek Bhardwaj
Researcher at Max Planck Society
Publications - 30
Citations - 6237
Vivek Bhardwaj is an academic researcher from Max Planck Society. The author has contributed to research in topics: Gene & Chromatin. The author has an hindex of 12, co-authored 21 publications receiving 3539 citations. Previous affiliations of Vivek Bhardwaj include University of Freiburg & Council of Scientific and Industrial Research.
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Journal ArticleDOI
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
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.
Posted ContentDOI
High-resolution TADs reveal DNA sequences underlying genome organization in flies
Fidel Ramírez,Vivek Bhardwaj,Jose M. Villaveces,Laura Arrigoni,Björn Grüning,Kin Chung Lam,Bianca Habermann,Asifa Akhtar,Thomas Manke +8 more
TL;DR: It is demonstrated that boundaries can be accurately predicted using only the motif sequences, along with open chromatin, suggesting that DNA sequence encodes the 3D genome architecture in flies.
Journal ArticleDOI
pyGenomeTracks: reproducible plots for multivariate genomic datasets.
Lucille Lopez-Delisle,Leily Rabbani,Joachim Wolff,Vivek Bhardwaj,Rolf Backofen,Björn Grüning,Fidel Ramírez,Thomas Manke +7 more
TL;DR: PGT as discussed by the authors is a modular plotting tool that easily combines multiple genomic tracks and enables a reproducible and standardized generation of highly customizable and publication ready images, and it is available through a graphical interface on usegalaxy.eu and through the command line.