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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RT @MGO_BPS: New Webinar alert! 📣 Join us for the next Webinar on Tuesday, Jan. 28th at 12:00 E.T. for two exciting talks by @DansPablo an….
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Join us over there!.
Also we are moving to the other site, find us at .
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RT @Open2C_team: Planning our move away from Slack! Considering Discord or Zulip. Any pros/cons for either of those for us as a group worki….
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RT @Anders_S_Hansen: This is a really interesting preprint the comprehensively studies how having dynamic CTCF boundaries effect 3D genome….
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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:
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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.
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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. 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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RT @chongyi_chen: Happy to share our work about DNA supercoiling, an understudied physical feature of the double helix and the chromatin. 1….
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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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RT @JumanaAHA: My lab is hiring a postdoc, don't hesitate to apply! Lots of opportunities to work on Hi-C/Micro-C and super-resolution imag….
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RT @BienkoMagda: Our lab is looking for talented students passionate about experimentation and seeking challenging projects! Please apply!….
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RT @Anders_S_Hansen: (1/n) From @ViraatGoel @Irate_Physicist et al. collab w @blobelgroup @leonidmirny . RCMC at th….
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RT @aurelepiazza: How do specific communications arise in chromatin? Here we determine condensin’s loop extrusion properties in budding yea….
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RT @jane_skok: Registration for the 5th Annual Meeting on Advances in Nuclear Topology & 3D Chromatin Architecture in Cancer is NOW OPEN! G….
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