Selected Publications

Despite an abundance of new studies about topologically associating domains (TADs), the role of genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer ( to annotate >2800 high-resolution (570 bp) TAD boundaries in Drosophila melanogaster. We identify eight DNA motifs enriched at boundaries, including a motif bound by the M1BP protein, and two new boundary motifs. In contrast to mammals, the CTCF motif is only enriched on a small fraction of boundaries flanking inactive chromatin while most active boundaries contain the motifs bound by the M1BP or Beaf-32 proteins. We demonstrate that boundaries can be accurately predicted using only the motif sequences at open chromatin sites. We propose that DNA sequence guides the genome architecture by allocation of boundary proteins in the genome. Finally, we present an interactive online database to access and explore the spatial organization of fly, mouse and human genomes, available at
In Nature Communications

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Galaxy HiCExplorer article to be published in NAR Are you a biologist looking for an easy way to understand and perform HiC data analsis? Galaxy HiCExplorer is the solution! It’s a user-freiendly galaxy webserver that utilizes HiCExplorer along with multiple other tools dor analysis of HiC data. The project was performed in collaboration with the galaxy team (Joachim Wolff and Bjoern Gruening) at University of Freiburg. Galaxy HiCExplorer has been accepted for publication in the next NAR webserver issue (July 2018) and is already available to use here.


HiCExplorer article comes online in nature communications Our article on DNA sequence behind Drosophila (Fly) genome architecture is now published in Nature Communications. The preprint has already been available on biorXiv since march 2017. In this article, we introduce HiCExplorer: An easy to use tool for HiC data analysis, also available in galaxy. We also introduce HiCBrowser : A standalone software to visualize HiC along with other genomic datasets. Based on HiCExplorer and HiCBrowser, we built a useful resource for anyone to browse and download the chromosome conformation datasets in Human, Mouse and Flies.




I am part of the team of HiCBrowser : A simple web-browser to visualize Hi-C and other genomic data sets.


I am part of the team of HiCExplorer : Tools to process and analyze Hi-C data.

deepTools 2

I am part of the team of deepTools2 : Tools to process and analyze deep sequencing data.



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