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Citations since 2016
6 Research Items
While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational tool able to conduct different levels of footprinting analysis has so-far hindered the widespread application of this method. Here we present TOBIAS, a comprehensive, accurate, and fast footprinting f...
While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational method implementing both footprinting, visualization and downstream analysis has hindered the widespread application of this method. Here we present TOBIAS, a comprehensive footprinting framework enab...
The annotation of genomic ranges such as peaks resulting from ChIP-seq/ATAC-seq or other techniques represents a fundamental task of bioinformatics analysis with considerable impact on many downstream analyses. In our previous work, we introduced the Universal Robust Peak Annotator (UROPA), a flexible command line based tool which improves upon the...
The annotation of genomic ranges of interest represents a recurring task for bioinformatics analyses. These ranges can originate from various sources, including peaks called for transcription factor binding sites (TFBS) or histone modification ChIP-seq experiments, chromatin structure and accessibility experiments (such as ATAC-seq), but also from...
Ecological power management is currently facing three major challenges: the storage of electrical power, the development of renewable energy resources and the increase of atmospheric carbon dioxide due to the use of fossil fuels. Especially, when considering the decreasing fossil fuel reserves and the increasing consumption, new solutions are urgen...
Ecological power management is currently facing three challenges: the storage of electrical power, the development of renewable energy resources, which are not timely and locally synced with demand, and the increase of atmospheric carbon dioxide due to the use of fossil fuels. We address these challenges by implementing a proof of concept productio...
Regions of high coverage of reads(Peaks) produced by chromatin immunoprecipitation and sequencing (ChIP-seq) method, or by other chromatin-accessible assays(e.g. ATACseq ) are investigated in order to to interpret the state of chromatin and potential histone modifications(e.g. methylation), responsible for gene regulation, not evident by DNA analysis. When a gene regulation is affected by transcription factors acting from further distance than the gene's promoter, or when more than one genes are co-located in a peak, annotation becomes more complex to resolve. For these ambiguous cases this tool is developed and supposed to better indicate the genes affected by histone marks. It offers flexibility of choice in a number of parameters and is based on command-line but user-friendly.