Reposted by Geoff Fudenberg
🚨 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...
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...
Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics
Antibodies (Ab) are essential for detecting specific epitopes in microscopy and genomics, but can produce artifacts leading to erroneous interpretations. Here, we characterize a novel artifact, Ab-tra...
doi.org
April 14, 2025 at 8:08 PM
🚨 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...
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...
Reposted by Geoff Fudenberg
2 interns available in my team!! www.linkedin.com/posts/activi...
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www.linkedin.com
January 27, 2025 at 11:03 PM
2 interns available in my team!! www.linkedin.com/posts/activi...
Looking 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...
For more details please check out our preprints:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
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
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
January 28, 2025 at 12:46 AM
Looking 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...
For more details please check out our preprints:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Geoff Fudenberg
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
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
January 20, 2025 at 11:47 AM
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
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
Reposted by Geoff Fudenberg
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?
January 16, 2025 at 11:12 AM
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?
Reposted by Geoff Fudenberg
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
Registration is free: tinyurl.com/5n6ep25m
#chromatin #genomics #chromosomes #science #dna #northwestern #biology #umass
January 15, 2025 at 8:04 PM
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
Registration is free: tinyurl.com/5n6ep25m
#chromatin #genomics #chromosomes #science #dna #northwestern #biology #umass
Reposted by Geoff Fudenberg
January 16, 2025 at 4:17 PM
Reposted by Geoff Fudenberg
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: are generally rare (2.3%)
www.biorxiv.org/content/10.1...
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:
www.biorxiv.org/content/10.1...
January 16, 2025 at 1:35 PM
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: are generally rare (2.3%)
www.biorxiv.org/content/10.1...
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:
www.biorxiv.org/content/10.1...
Reposted by Geoff Fudenberg
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!
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!
Application to speak in the Fragile Nucleosome series
Thank you for your interest in our seminar series!
We use a variety of different session formats but, in general, trainees can plan for a ~15 min talk + 5min Q/A and PIs can plan for a ~25min talk +...
forms.gle
January 16, 2025 at 8:34 PM
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!
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!
Reposted by Geoff Fudenberg
Reposted by Geoff Fudenberg
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...
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...
Mechanisms of Inheritance of Chromatin States: From Yeast to Human | Annual Reviews
In this article I review mechanisms that underpin epigenetic inheritance of CpG methylation and histone H3 lysine 9 methylation (H3K9me) in chromatin in fungi and mammals. CpG methylation can be faith...
doi.org
January 7, 2025 at 1:22 AM
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...
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...
Reposted by Geoff Fudenberg
The only thing I am missing here is Epigenetic Hulk account.
November 22, 2024 at 3:23 PM
The only thing I am missing here is Epigenetic Hulk account.
Reposted by Geoff Fudenberg
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!
Beyond genomic weaving: molecular roles for CTCF outside cohesin loop extrusion
CCCTC-binding factor (CTCF) is a key regulator of 3D genome organization and transcriptional activity. Beyond its well-characterized role in facilitat…
www.sciencedirect.com
December 27, 2024 at 9:00 PM
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!
Reposted by Geoff Fudenberg
After 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!
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!
📢We have opened the call for #mentees!
Apply and become a mentee: scisteps.org/call-2025
Sci.STEPS mentors share with you their knowledge and insights on studying abroad, navigating relocations, building careers, and transitioning between fields!💙
@phdvoice.bsky.social @dragonflymh.bsky.social
Apply and become a mentee: scisteps.org/call-2025
Sci.STEPS mentors share with you their knowledge and insights on studying abroad, navigating relocations, building careers, and transitioning between fields!💙
@phdvoice.bsky.social @dragonflymh.bsky.social
December 6, 2024 at 1:44 PM
After 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!
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!