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Fantastic work from our friend and collaborator Karine Le Roch at UC Riverside. Culmination of her many years of work to fight against malaria! 👏👏

#RSGDREAM2024 concluding after two fun days talking about gene regulation, regulatory genomics. Thank you all for coming! Don't forget to fill the survey forms.gle/4vvTypQG4TBXoS… Your feedback is really important for us!

It was a 4days of great scientific discussion, brainstorming and some fun along the way! Big thanks to U.S. National Science Foundation for funding & NSF-NCEMS leaders & organizers for a well-organized summit! All that was left for us was to turn coffee into ideas and proto-proposals :) #NCEMSSummit

After many zoom meetings, discussions & learning from one another about different ways to look at the same data/problem, our perspective article on regulatory genomics is out. We have a “hallmarks of gene regulation” figure which i am planning to use in my talks. Enjoy reading!

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Extremely happy to share that our work DiffHiChIP: a method to identify differential chromatin interactions from HiChIP (and any other chromatin interaction data such as Hi-C, ChIA-PET), is now online. Preprint in: biorxiv.org/content/10.110…

I posted a longer description on bluesky if you want to learn more about this: bsky.app/profile/ferhat…

Happy to share Dante Bolzan’s delicious new preprint-Soffritto. He developed a deep learning model that accurately predicts high-resolution replication timing data (16-fraction) using commonly available data types Creative name by Dante but i stopped him from forcing an acronym😂

Our new paper is finally out, showing that the same enhancer sequences - and likely the same transcription factors recruited to them - affect the activity of distal enhancers and their looping over to target gene promoters. nature.com/articles/s4146…

Please also check out two other papers using HiChIP and Hi-C to detect genetic associations with chromatin looping by Ferhat Ay's and Gisela Orozco's labs, which were submitted in parallel to ours and provide complementary insights: nature.com/articles/s4146…

medrxiv.org/content/10.110…

Comparison of CD30L and OX40L Reveals CD30L as a Promising Therapeutic Target in Atopic Dermatitis. First author: Rinkesh K. Gupta; corresponding author: Michael Croft Read the article here: doi.org/10.1111/all.16… This study investigated whether targeting the T cell

Perspective on recent developments and challenges in regulatory and systems genomics academic.oup.com/bioinformatics… is out, amazing to think about this with Julia Zeitlinger (@[email protected]), Ferhat Ay, Shaun Mahony, Anthony Mathelier, Alejandra Medina-Rivera, Jason Ernst!

🧬 Just out in Bioinformatics Advances: "Perspective on recent developments and challenges in regulatory and systems genomics" Find the full paper here: doi.org/10.1093/bioadv… Authors include: Julia Zeitlinger (@[email protected]), Sushmita Roy @sroyyors.bsky.social,genomic.social, Ferhat Ay, Anthony Mathelier, Alejandra Medina-Rivera, Shaun Mahony,