@gfudenberg.bsky.social
https://fudenberg.team
🚨 Preprint alert 🚨
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...
2 interns available in my team!! www.linkedin.com/posts/activi...
27.01.2025 23:03 — 👍 3 🔁 4 💬 0 📌 0Looking forward to sharing some of our recent work !
For more details please check out our preprints:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
BPS Multiscale Genome Organization Webinar Jan. 28th, 2025 @ 12-1 PM ET Pablo Dans, PhD University of the Republic Geoff Fudenberg, PhD University of Southern California
The Multiscale Genome Organisation is now on Bluesky!
Our first post is to announce our next webinar. Join us next week on Tuesday, Jan. 28th at 12:00 E.T. for two exciting talks by Pablo Dans and @gfudenberg.bsky.social
See you all there!
Link:
mit.zoom.us/j/91715298970
In addition to coming here, we are planning our move away from Slack! Considering Discord or Zulip. Any pros/cons for either of those for us as a group working on open source software for biological data analysis?
16.01.2025 11:12 — 👍 3 🔁 1 💬 1 📌 1
January 31 at 12pm CT, Job Dekker, PhD of UMass Chan Medical School presents the Monthly Seminar on Physical Genomics: "Mechanisms of Chromosome Folding", live on Zoom. Join us!
Registration is free: tinyurl.com/5n6ep25m
#chromatin #genomics #chromosomes #science #dna #northwestern #biology #umass
Read all about this new discovery here: www.sciencedirect.com/science/arti...
9/9
Excited to share James Jusuf's preprint:
By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%)
We quantify mESC 36k loops: <loops> are generally rare (2.3%)
www.biorxiv.org/content/10.1...
Do you have a new and exciting chromatin/transcription story that you'd like to share with an enthusiastic audience?
If so, you should apply to give a talk in the 2025 Fragile Nucleosome seminar series: forms.gle/fwMYPFDf4az3...!
We're open to scientists at all stages of their careers!
Important independent calibration of Hi-C data:
www.biorxiv.org/content/10.1...
Happy New Year, blue-sci-peeps!
My piece in Annual Review of Biophysics on chromatin replication is now available online.
doi.org/10.1146/annu...
If you have paywall issues, try this link:
madhanilab.ucsf.edu/s/annurev-bi...
The only thing I am missing here is Epigenetic Hulk account.
22.11.2024 15:23 — 👍 23 🔁 3 💬 0 📌 0
Closing 2024 with a review! Excited to share the latest (short) review from our lab, written by amazing Ramani/Narlikar lab grad student Aaron Corin in collaboration with @elphegenoralab.bsky.social! We focus on CTCF's myriad functions beyond regulating loop extrusion; tons to dig into!
27.12.2024 21:00 — 👍 13 🔁 2 💬 1 📌 0After a month of hard work to create a pool of over 50 fantastic mentors, we have opened the call for mentee applications!
If you are an early career researcher and need help navigating the career path (be it academia or industry, or anything else), see if there is a mentor for you and apply!
in case of use (or if folks in your group would be interested in contributing) we have been developing a Snakemake pipeline that processes fastqs either with or without Spike-in github.com/Fudenberg-Re... -- we've used it to compute FRiPs for cohesin in CTCF peaks to compare with extrusion models
03.12.2024 19:59 — 👍 4 🔁 2 💬 0 📌 0
