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The paper is now published in Genome Research, see the updated manuscript at genome.org/cgi/doi/10.110…

The first preprint of our PERICODE consortium: MPRA-trained deep learning provides insight into the regulatory logic of promoters and transcription factors. biorxiv.org/cgi/content/sh…

We generated a collection of new and optimised (and multiplexable) TF reporters for human and mouse cells: biorxiv.org/content/10.110…

Really awesome paper from gagneurlab on a new, clever interpretation approach showing that local DNA language models (trained on pre-defined functional elements across species) are capable of learning regulatory & structural syntax. biorxiv.org/content/10.110…

Thank you Lautenberg Center for Immunology and cancer ! and many thanks to all the students in my lab whose work made this possible.

The radial positioning of genomic loci, i.e. how far they are from the nuclear lamina has been associated with genome structure and function for several decades. But in genomics everything is correlated, e.g. radial positioning with genomic compartments with gene activity etc

Want to learn how transformers and large-language models can help to organize&understand single cell profiles? Led by Artur Szałata, we review current such approaches in single cell genomics and give perspectives towards foundation models etc. nature.com/articles/s4159…

Our single-cell, pan-cancer analysis of open chromatin in human cancers, done in collaboration with TCGA and the Chang and Corces labs (among others including Illumina), is out in Science today. Congrats to Laksshman Sundaram and all authors! science.org/doi/10.1126/sc…

In this new preprint, we do a deep dive into the temporal relationship between DNA #methylation, #chromatin and #enhancers. Amazing work by first author Lindsey Guerin and thanks to our collaborators @IhrieLab, Ken Lau Lab, & biomodal. biorxiv.org/content/10.110…

Great new paper using #3D #MERFISH to generate 3D genome cancer atlases of murine lung and pancreatic adenocarcinoma. Tracing the evolution of single-cell cancer 3D genomes: an atlas for cancer gene discovery biorxiv.org/content/10.110…

Great opportunity for postdocs! If you are interested in epigenetic and topologic dysregulation in disease consider joining our lab, see yotamdrier.ekmd.huji.ac.il for more details. We will help you apply to the Azrieli Fellowship :)

CTCF binding landscape is established by the epigenetic status of the nucleosome, well-positioned relative to CTCF motif orientation biorxiv.org/content/10.110…

Thrilled to report Patho-DBiT, just published in Cell 😊. It allows us to directly “see” all kinds of RNA species on the same clinical FFPE tissue slide, including mRNA, miRNA, snRNA, snoRNA, tRNA, etc, and splicing isoforms, genetic alterations (SNV, CNV, etc). Really a fun,

Excited with to share our new deep single-cell whole genome bisulfite sequencing technique with Hui Shen, along with some truly innovative DNA methylation analyses by lead author and talented MD/PhD student, Nathan Spix biorxiv.org/content/10.110…

Check out the newest version of our paper, now published in PNAS: pnas.org/cgi/doi/10.107…. A good way to start the new Hebrew year. Congratulations to all authors. More details in the thread below

Check out our review on an RNA-centric view of transcription and genome organization in an #RNA-focused issue of Molecular Cell! It was a delight to write with Richard Young. cell.com/molecular-cell…

The Vassilis Roukos lab led a new and detailed study of Topoisomerase II contribution to #3Dgenome folding in human cells and in different cell cycle phases -- my group and the MundlosLab contributed analyses/data. The paper is now published in Molecular Cell ...1/n

Thrilled to share our new preprint, 'A genome wide code to define cell-type specific CTCF binding and chromatin organization'. biorxiv.org/content/10.110…

New paper alert! The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and DNA repair efficiency academic.oup.com/nar/article/53….

Thanks!