Surfin' NuRD
@surfinnurd.bsky.social
Ahh well-a everybody's heard
about the NuRD.
#NuRDistheWord
Cycling/Chromatin Remodelling/Transcription/Enhancers/StemCells
We've got it all.
Living Systems Institute, University of Exeter
https://lsi.exeter.ac.uk/groups/hendrich-group/
about the NuRD.
#NuRDistheWord
Cycling/Chromatin Remodelling/Transcription/Enhancers/StemCells
We've got it all.
Living Systems Institute, University of Exeter
https://lsi.exeter.ac.uk/groups/hendrich-group/
Always been tempted to say during a talk "...and in experiments carried out by my average, lacklustre PhD student...."
(But not yet confident the student would get the joke.)
(But not yet confident the student would get the joke.)
November 13, 2025 at 8:15 AM
Always been tempted to say during a talk "...and in experiments carried out by my average, lacklustre PhD student...."
(But not yet confident the student would get the joke.)
(But not yet confident the student would get the joke.)
I agree This is WHY some falsehoods get established in the field: people tend to believe what they read, particularly if it's published in a glam journal. Or, more often in my field, causation is inferred from correlation and then becomes "established".
November 11, 2025 at 9:06 AM
I agree This is WHY some falsehoods get established in the field: people tend to believe what they read, particularly if it's published in a glam journal. Or, more often in my field, causation is inferred from correlation and then becomes "established".
This is my concern. What if research doesn't fit the mould? Will AI identify truly original research that counters prevailing trends/models that are nevertheless incorrect?
November 11, 2025 at 8:08 AM
This is my concern. What if research doesn't fit the mould? Will AI identify truly original research that counters prevailing trends/models that are nevertheless incorrect?
Ahem. www.nature.com/articles/s42...
Will this trend of using AI further homogenise papers?
Will truly original thinking 'fit' with the algorithm?
Will this trend of using AI further homogenise papers?
Will truly original thinking 'fit' with the algorithm?
Language models cannot reliably distinguish belief from knowledge and fact - Nature Machine Intelligence
Suzgun et al. find that current large language models cannot reliably distinguish between belief, knowledge and fact, raising concerns for their use in healthcare, law and journalism, where such disti...
www.nature.com
November 7, 2025 at 5:04 PM
Ahem. www.nature.com/articles/s42...
Will this trend of using AI further homogenise papers?
Will truly original thinking 'fit' with the algorithm?
Will this trend of using AI further homogenise papers?
Will truly original thinking 'fit' with the algorithm?
Recognise anyone?
October 31, 2025 at 5:12 PM
Recognise anyone?
Reposted by Surfin' NuRD
about PAE #alphafold
PAE viewer pae-viewer.uni-goettingen.de
PAE Figure editor thecodingbiologist.com/tools/pae.html
PAE viewer pae-viewer.uni-goettingen.de
PAE Figure editor thecodingbiologist.com/tools/pae.html
October 27, 2025 at 7:27 AM
about PAE #alphafold
PAE viewer pae-viewer.uni-goettingen.de
PAE Figure editor thecodingbiologist.com/tools/pae.html
PAE viewer pae-viewer.uni-goettingen.de
PAE Figure editor thecodingbiologist.com/tools/pae.html
Cool stuff Kashyap. Congrats!
October 24, 2025 at 11:40 AM
Cool stuff Kashyap. Congrats!
...and now I see that's YOUR paper. Very nice!
October 23, 2025 at 6:55 AM
...and now I see that's YOUR paper. Very nice!
Thanks! Agree re: Takaku/Wade paper, they certainly saw this. You are also so right about the Fuller/Brehm paper, which I'd neglected to cite. Really looks like a similar thing. Thanks for pointing it out!
October 23, 2025 at 6:46 AM
Thanks! Agree re: Takaku/Wade paper, they certainly saw this. You are also so right about the Fuller/Brehm paper, which I'd neglected to cite. Really looks like a similar thing. Thanks for pointing it out!
Thanks! Will re-read that paper with this in mind. Very cool that new methods are shedding light on old questions!
October 23, 2025 at 6:41 AM
Thanks! Will re-read that paper with this in mind. Very cool that new methods are shedding light on old questions!
No idea why the hands are there, btw.
October 17, 2025 at 9:07 AM
No idea why the hands are there, btw.
We find the opposite is true for a chromatin remodeller, where the biggest effects on chromatin accessibility are seen at low enrichment sites. We see something similar for a TF. So in my experience, it's not a good idea to exclude those low enrichment sites.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The chromatin remodeller CHD4 regulates transcription factor binding to both prevent activation of silent enhancers and maintain active regulatory elements
Chromatin organisation and transcriptional regulation are tightly coordinated processes that are essential for maintaining cellular identity and function. ATP-dependent chromatin remodelling proteins ...
www.biorxiv.org
October 14, 2025 at 1:06 PM
We find the opposite is true for a chromatin remodeller, where the biggest effects on chromatin accessibility are seen at low enrichment sites. We see something similar for a TF. So in my experience, it's not a good idea to exclude those low enrichment sites.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...