Geoff Fudenberg
@gfudenberg
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chromosome organization, computational biology, genomics, physics
Los Angeles, CA
Joined August 2015
This movie-- sped up 10x from real time-- illustrates how regulator exchange brings us to a picture of cohesin as a multi-state motor complex, which only actively extrudes in a NIPBL co-bound state.
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Looking forward to this seminar! Also currently migrating to the other site. Looking forward to getting in touch over there as well!
New Webinar alert! 📣 Join us for the next Webinar on Tuesday, Jan. 28th at 12:00 E.T. for two exciting talks by @DansPablo and @gfudenberg. See you all there! (Link on the tweet below)
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New Webinar alert! 📣 Join us for the next Webinar on Tuesday, Jan. 28th at 12:00 E.T. for two exciting talks by @DansPablo and @gfudenberg. See you all there! (Link on the tweet below)
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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?
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This is a really interesting preprint the comprehensively studies how having dynamic CTCF boundaries effect 3D genome organization, demonstrating that residence time in addition to %occupancy has important regulatory functions:
Happy to share work with Hadi, Yao & @Maxime_Tortora characterizing the impact of dynamic CTCF barriers for cohesin loop extrusion https://t.co/iiaiJg2ZeB
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One use of barriers with much more rapid exchange than cohesins might be to equalize contact frequencies across a large genomic locus, as suggested at PCDH by @LeaKiefer138 @SimonMJGaudin et al. See animation from the GitHub: https://t.co/sED5kPlrwR
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Barrier dynamics thus leave distinct signatures even in static population averaged snapshots from genomic data!
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Even at constant occupancy, we find that cohesin positioning (by ChIP) and 3D genome folding (by Hi-C or imaging) are quite sensitive to the bound time of the barrier
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Happy to share work with Hadi, Yao & @Maxime_Tortora characterizing the impact of dynamic CTCF barriers for cohesin loop extrusion https://t.co/iiaiJg2ZeB
biorxiv.org
In mammalian interphase cells, genomes are folded by cohesin loop extrusion limited by directional CTCF barriers. This interplay leads to the enrichment of cohesin at barriers, isolation between...
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Great opportunity for new PhD students to join us @qcb_usc!
The USC/QBIO department is now accepting applications for the CBB PhD program. Please share with any interested undergraduate and Master's students. https://t.co/VSHj6z2dUe We will have zoom information sessions Nov 1 and 15, please contact me directly for a registration link.
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News flash!
(17) So it’s not that complicated in the end: If you rely on an enhancer, you will need cohesin extrusion beyond ~18kb. UNLESS you have a promoter-proximal regulatory element that can synergize with your distal enhancer – which happens independently of cohesin.
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Happy to share our work about DNA supercoiling, an understudied physical feature of the double helix and the chromatin. 1/5 https://t.co/dlUCjABLET
nature.com
Nature Structural & Molecular Biology - Here, the authors develop an assay to measure DNA supercoiling, revealing DNA supercoiling domains across the human genome that are modulated by...
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Great opportunity for a PhD with @golobor!
My lab is looking for PhD students with a background in physics and/or biochemistry/quantitative biology. If interested, please apply to the VBC graduate school. Deadline: Oct 15th.
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My lab is hiring a postdoc, don't hesitate to apply! Lots of opportunities to work on Hi-C/Micro-C and super-resolution imaging in Drosophila and mESCs.
📢 Job alert: Postdoc Position in the lab of Jumana AlHaj Abed (@JumanaAHA) – Fantastic opportunities at #MaxPlanck in #Freiburg to work on Hi-C & super-resolution imaging in #Drosophila and mESCs. Get all the details & apply until Sept. 27: https://t.co/HQa9hgoLYZ
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Our lab is looking for talented students passionate about experimentation and seeking challenging projects! Please apply!
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(1/n) From @ViraatGoel @Irate_Physicist et al. collab w @blobelgroup @leonidmirny
https://t.co/CdI7n2P31a RCMC at the M-to-G1 transition reveals strong microcompartments between CREs (E,P) in mitosis, that weaken upon G1 entry Sims reveal chromosome compaction as key regulator
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How do specific communications arise in chromatin? Here we determine condensin’s loop extrusion properties in budding yeast and identify various types of roadblock. It makes a conditional loop that allows mating-type switching to take place. https://t.co/aBdeXwV5Oo
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Registration for the 5th Annual Meeting on Advances in Nuclear Topology & 3D Chromatin Architecture in Cancer is NOW OPEN! Get ready to hear from an all-star lineup of speakers – you won't want to miss this. Register for free: https://t.co/xHZSamYZuq
#chromatin2024
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The video of my #BOSC2024 #ISMB2024 talk on Composable Bioinformatics is now available! Feat. amazing work from @trevmanz @jackh726 @Open2C_team and more! https://t.co/lxHB52AvTW
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