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TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions

Clémentine Leporcq, Yannick Spill, Delphine Balaramane, Christophe Toussaint, Michaël Weber, Anaïs Flore Bardet
2020 Nucleic Acids Research  
Despite the availability of hundreds of known TF motifs in databases, it remains non-trivial to quickly query and visualize the enrichment of known TF motifs in genomic regions of interest.  ...  TFmotifView will contribute to the integration of TF motif information with a wide range of genomic datasets towards the goal to better understand the regulation of gene expression by transcription factors  ...  ACKNOWLEDGEMENTS The authors thank the many beta testers of the web application for useful feedback and the Weber lab for helpful discussions.  ... 
doi:10.1093/nar/gkaa252 pmid:32324215 pmcid:PMC7319436 fatcat:hkx3ficd5nbtxc6ee4zghyaudq

Pan-cancer predictions of transcription factors mediating aberrant DNA methylation

Dylane Detilleux, Yannick G. Spill, Delphine Balaramane, Michaël Weber, Anaïs Flore Bardet
2022 Epigenetics & Chromatin  
We identified differentially methylated regions between cancer and matching healthy samples, searched for transcription factor motifs enriched in those regions and selected transcription factors with corresponding  ...  Results Here, we integrated the massive amount of data available from The Cancer Genome Atlas to predict transcription factors driving aberrant DNA methylation in 13 cancer types.  ...  Acknowledgements The authors thank the Weber lab for helpful discussions and Éléa Héberlé for initiating the experiments.  ... 
doi:10.1186/s13072-022-00443-w pmid:35331302 pmcid:PMC8944071 fatcat:hz6nzm3vrfhefembcpaqi4zmny

Editorial: the 18th annual Nucleic Acids Research web server issue 2020

2020 Nucleic Acids Research  
As in the past, proposals were first editorially checked for their suitability and afterwards, websites or stand-alone tools were tested before allowing the submission of a manuscript.  ...  These are our current website examiners: • Adam Simpkin holds a PhD in X-ray crystallography and is at the University of Liverpool, UK. • Piotr Grabowski owns a PhD in computational systems biology and  ...  /tfmotifview/ Visualization of transcription factor motifs in genomic regions RiboToolkit http://rnabioinfor.tch.harvard.edu/ RiboToolkit Decoding RNA translation Short title URL Short description TeamTat  ... 
doi:10.1093/nar/gkaa528 pmid:32589733 fatcat:2sfy5ppbvnbdlptyqgyt5gqj3y