Quinn Cowan

NIPBL dosage shapes genome folding by tuning the rate of cohesin loop extrusion Cohesin loop extrusion is a major driver of chromosome folding, but how its dynamics are controlled to shape the genome remains elusive. Here we disentangle the contributions of the cohesin cofactors ...

New preprint with @gfudenberg.bsky.social

We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding.

This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇

www.biorxiv.org/content/10.1...

16.08.2025 03:03 — 👍 113    🔁 52    💬 1    📌 6

BioMix red is a cheap Taq-base pol made with premixed with dye ready to run on gels. Or Phusion green if a high fidelity pol is needed for NGS!

01.11.2025 06:00 — 👍 1    🔁 0    💬 0    📌 0

Check out MitoScribe in our new preprint led by Linhan Wang: www.biorxiv.org/content/10.1...

It's an analog molecular recorder that uses neutral base edits to the mitochondrial genome to store information about historical signaling in a cell. Single cell resolution at scale (see next post)!

08.09.2025 17:13 — 👍 7    🔁 5    💬 1    📌 0

Balancing off-target and on-target considerations for optimized Cas9 CRISPR knockout library design The continued development of high-dimensional CRISPR screen readouts, such as single-cell RNA sequencing and high-content imaging, necessitates compact libraries to enable functional interrogation at ...

Doomscrolling pause to chat CRISPR libraries! Preprint describes our new, data-driven approach to combine on-target and off-target predictions much more intelligently for *selecting* guides, which we use to develop our newest Cas9 knockout library, Jacquere. Thread: www.biorxiv.org/content/10.1...

07.09.2025 17:02 — 👍 74    🔁 24    💬 2    📌 0

Flyer for the 2025 Next Generation Faculty Symposium (including QR code in top right corner). This symposium highlights the work of exceptional early-career scientists in the broad field of quantitative biological and biomedical sciences, with a track record of excellence in research, leadership, mentorship, and community engagement. These early career scientists are preparing to launch a faculty search. Applications are due May 30th, 2025.

Hello Community!
Are you a postdoc/grad student preparing to launch a faculty search? Do you have a track record of excellence in research, leadership, mentorship & community engagement? Apply to the 2025 Next Generation Faculty Symposium: www.berkeleystanfordnextgensymposium.com! Pls repost! (1/3)

21.04.2025 19:21 — 👍 93    🔁 84    💬 2    📌 4

Activity-based selection for enhanced base editor mutational scanning Base editing is a CRISPR-based technology that enables high-throughput, nucleotide-level functional interrogation of the genome, which is essential for understanding the genetic basis of human disease...

Happy Friday! New preprint to discuss, led by @ekaplan.bsky.social, entitled "Activity-based selection for enhanced base editor mutational scanning"

www.biorxiv.org/content/10.1...

A thread...

15.11.2024 13:17 — 👍 58    🔁 18    💬 7    📌 0

High throughput variant libraries and machine learning yield design rules for retron gene editors Abstract. The bacterial retron reverse transcriptase system has served as an intracellular factory for single-stranded DNA in many biotechnological applica

🚨New Pub: High throughput variant libraries and machine learning yield design rules for retron gene editors, now out in Nucleic Acids Research. This is a great one, and the last bit of Kate Crawford's PhD, who is off to David Bakar's Lab for a postdoc.
academic.oup.com/nar/advance-...

10.12.2024 18:42 — 👍 10    🔁 7    💬 0    📌 0

We just posted a new preprint where we found retrons in bacteria out in the real world, in dirt and water. We describe the first retrons in a handful of new species, show how they defend against phages, and use them to edit genomes. Read about it here: www.biorxiv.org/content/10.1...

30.01.2025 22:08 — 👍 10    🔁 4    💬 2    📌 1