Happy to share that our work on how small set of motifs and rules explain most human promoters is published in Science Magazine I am very grateful for the chance to be part of a team of amazing scientists: Donghong Cai, Chenlai Shi,Jian Xu,Jian Zhou science.org/doi/10.1126/sc…

Excited to finally share my work with Charles Danko on the regulatory syntax governing transcription initiation and training genomic DL models on diverse genomes. doi.org/10.1101/2024.0…. Blurb thread below: 0/8

Delighted to announce our latest, led by the awesome Adam He. See the thread below for a fantastic explanation:
x.com/missing_a_rib/…

This is your friendly daily reminder to write your congressman and ask them to pass a Ukraine/ Israel aid package ASAP.

Reposting after reading rumors of another Jordan speaker vote, after threats against those in the Republican caucus who voted no.
x.com/charlesdanko/s…

Ithaca tweeps:

Congressman Marc Molinaro is voting for Jim Jordan as speaker. Consider sending a letter stating how you feel about this.

Contact here: molinaro.house.gov/contact/

Our district is no longer safe red. Molinaro may listen if enough of us write!

I am thrilled to share our work on nascent RNA sequencing in single cells.
I hope it will unlock the study of enhancer-gene coordination at the single-cell level.

Single-cell nascent RNA sequencing using click-chemistry unveils coordinated transcription biorxiv.org/content/10.110…

Thank you Charles. Your work over the last decade has paved the path for scGRO-seq development!

The rNTPs are available from Jena Biosciences.

Delighted to share that BayesPrism consistently ranks as the top-performing deconvolution approach in another independent benchmark studies. 🌟

If you or someone you know can benefit from my work, feel free to share this link:
nature.com/articles/s4301…

Another independent benchmark of deconvolution tools ranks BayesPrism as the top performing. Gratifying to see the many years Tinyi Chu spent developing BayesPrism paying off!
nature.com/articles/s4146…

Great to finally see a single cell GRO-seq assay! Hoping we can buy the clickable rNTPs soon.

Congratulations on this extremely creative approach to Jay Mahat and other members of the Sharp lab.
biorxiv.org/content/10.110…

New preprint from Lexi Morrissey in my lab describing Allo - a new tool for allocating multi-mapped reads in regulatory genomics experiments. 1/
biorxiv.org/content/10.110…

Super excited to share our study on the importance of proper epigenetic inheritance for cell identity and developmental competence, a fantastic collaboration with Anja Groth 🇺🇦 and Josh Brickman, led by Alice Wenger, Alva Biran, Nicolas Alcaraz, alboo nature.com/articles/s4158…

a while ago I posed this question...

1/

A Spatiotemporal Molecular Atlas of the Ovulating Mouse Ovary biorxiv.org/content/10.110…

Our studies of why genetic variant pathogenicity prediction algorithms leave much to be desired:
pnas.org/doi/10.1073/pn…

Very excited for the first machine learning model from our lab, named 3D-HiChAT developed by Alexander, that enables prediction of 3D complex regulatory relationships, including enhancer hierarchies and 3D hubs that control gene coregulation.

Noordermeer lab 🇺🇦 wrote a very interesting News&Views on our and Akis Papantonis recent papers in Nature Genetics on the role of Pol II in shaping enhancer-promoter interactions. Enjoy!

I wrote a News&Views on the recent studies in Nature Genetics from the Akis Papantonis and Charles Danko groups that definitively settle that mammalian RNA PolII helps to shape the 3D genome . Particularly when combined, very interesting insights emerge. rdcu.be/dgRk4

Nature research paper: Complementary Alu sequences mediate enhancer–promoter selectivity go.nature.com/3PWTMS7