Josh T Cuperus
@rnanerd.bsky.social
Faculty in Genome Sciences at the University of Washington focusing on gene regulation tech dev, especially in plants.
Reposted by Josh T Cuperus
What an amazing assay.
DAF-seq, the evolution of Fiber-seq from the Andrew Stergachis group, using the @pacbio.bsky.social platform:
www.biorxiv.org/content/10.1...
This will revolutionise our understanding of transcriptional regulation and functional non-coding variants.
DAF-seq, the evolution of Fiber-seq from the Andrew Stergachis group, using the @pacbio.bsky.social platform:
www.biorxiv.org/content/10.1...
This will revolutionise our understanding of transcriptional regulation and functional non-coding variants.
Deaminase-assisted single-molecule and single-cell chromatin fiber sequencing
Gene regulation is mediated by the co-occupancy of numerous proteins along individual chromatin fibers. However, our tools for deeply profiling how proteins co-occupy individual fibers, especially at ...
www.biorxiv.org
October 4, 2025 at 12:06 PM
What an amazing assay.
DAF-seq, the evolution of Fiber-seq from the Andrew Stergachis group, using the @pacbio.bsky.social platform:
www.biorxiv.org/content/10.1...
This will revolutionise our understanding of transcriptional regulation and functional non-coding variants.
DAF-seq, the evolution of Fiber-seq from the Andrew Stergachis group, using the @pacbio.bsky.social platform:
www.biorxiv.org/content/10.1...
This will revolutionise our understanding of transcriptional regulation and functional non-coding variants.
Reposted by Josh T Cuperus
i'm glad it's posted now, but damn that's a gut-punch for any 2nd year students planning to apply this cycle
NSF GRFP solicitation is finally up. Life Sci deadline extended to Nov 10 but 2nd year grad students no longer eligible www.nsf.gov/funding/oppo...
NSF Graduate Research Fellowship Program (GRFP)
www.nsf.gov
September 26, 2025 at 9:35 PM
i'm glad it's posted now, but damn that's a gut-punch for any 2nd year students planning to apply this cycle
Reposted by Josh T Cuperus
Continuing efforts to hurt the research pipeline, the very late NSF GFRP solicitation no longer allows 2nd year PhD students to apply. Lots of these students chose not to apply last year because they were told they would have a better change once in their thesis lab www.nsf.gov/funding/oppo...
NSF Graduate Research Fellowship Program (GRFP)
www.nsf.gov
September 26, 2025 at 6:42 PM
Continuing efforts to hurt the research pipeline, the very late NSF GFRP solicitation no longer allows 2nd year PhD students to apply. Lots of these students chose not to apply last year because they were told they would have a better change once in their thesis lab www.nsf.gov/funding/oppo...
Reposted by Josh T Cuperus
The GRFP announcement from NSF cuts out an entire cohort of 2nd year students from consideration, without warning. This is so deeply unfair that it warrants a formal protest from the scientific community. If someone wants to work with me to craft an open letter and solicit signatures, LMK.
New: After a long wait, the GRFP solicitation is live! Deadlines have been extended to early November, so applicants have a bit over a month to submit. www.nsf.gov/funding/oppo...
NSF Graduate Research Fellowship Program (GRFP)
www.nsf.gov
September 26, 2025 at 5:10 PM
The GRFP announcement from NSF cuts out an entire cohort of 2nd year students from consideration, without warning. This is so deeply unfair that it warrants a formal protest from the scientific community. If someone wants to work with me to craft an open letter and solicit signatures, LMK.
Reposted by Josh T Cuperus
Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment.
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
jasonjwilliamsny.github.io
September 25, 2025 at 10:09 PM
Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment.
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
Reposted by Josh T Cuperus
Carrington lab reunion, Oregon State edition
September 16, 2025 at 1:38 PM
Carrington lab reunion, Oregon State edition
Here ends our foray into rDNA variation in model organisms—w/ Christine Queitsch, Bonnie Brewer, and many others. Especially Ashley Hall and Elizabeth Morton.
tl;dr: In natural ranges of rDNA copy number, phenotypes are rare (yeast + C. elegans).
But outside those ranges? Some things happen.
1/3
tl;dr: In natural ranges of rDNA copy number, phenotypes are rare (yeast + C. elegans).
But outside those ranges? Some things happen.
1/3
June 4, 2025 at 5:40 PM
Here ends our foray into rDNA variation in model organisms—w/ Christine Queitsch, Bonnie Brewer, and many others. Especially Ashley Hall and Elizabeth Morton.
tl;dr: In natural ranges of rDNA copy number, phenotypes are rare (yeast + C. elegans).
But outside those ranges? Some things happen.
1/3
tl;dr: In natural ranges of rDNA copy number, phenotypes are rare (yeast + C. elegans).
But outside those ranges? Some things happen.
1/3
Reposted by Josh T Cuperus
Proposed cut to NSF Biology budget is 70%.
70%. Seventy.
Call your senators & reps nonstop. Give them numbers on NSF impact for state/district. tableau.external.nsf.gov/views/NSFbyN... explain this will decimate the economy if their districts, especially if it has a major research univ. 🧪
70%. Seventy.
Call your senators & reps nonstop. Give them numbers on NSF impact for state/district. tableau.external.nsf.gov/views/NSFbyN... explain this will decimate the economy if their districts, especially if it has a major research univ. 🧪
May 31, 2025 at 12:58 AM
Proposed cut to NSF Biology budget is 70%.
70%. Seventy.
Call your senators & reps nonstop. Give them numbers on NSF impact for state/district. tableau.external.nsf.gov/views/NSFbyN... explain this will decimate the economy if their districts, especially if it has a major research univ. 🧪
70%. Seventy.
Call your senators & reps nonstop. Give them numbers on NSF impact for state/district. tableau.external.nsf.gov/views/NSFbyN... explain this will decimate the economy if their districts, especially if it has a major research univ. 🧪
Reposted by Josh T Cuperus
important historical perspective on the value of federal funding of basic research at universities: "These are the building blocks of America's extraordinary strength, created over the last 100 years, and they are now being dismantled in 100 days" 🧪
www.youtube.com/watch?v=0Qk4...
www.youtube.com/watch?v=0Qk4...
Fareed’s Take: Trump is gutting what made American science great
YouTube video by CNN
www.youtube.com
May 13, 2025 at 5:12 PM
important historical perspective on the value of federal funding of basic research at universities: "These are the building blocks of America's extraordinary strength, created over the last 100 years, and they are now being dismantled in 100 days" 🧪
www.youtube.com/watch?v=0Qk4...
www.youtube.com/watch?v=0Qk4...
Reposted by Josh T Cuperus
Trump’s war on science is an attack against anyone who has ever loved someone with cancer.
The American people do not want us to slash cancer research in order to give more tax breaks for billionaires.
The American people do not want us to slash cancer research in order to give more tax breaks for billionaires.
May 13, 2025 at 9:02 PM
Trump’s war on science is an attack against anyone who has ever loved someone with cancer.
The American people do not want us to slash cancer research in order to give more tax breaks for billionaires.
The American people do not want us to slash cancer research in order to give more tax breaks for billionaires.
www.biorxiv.org/content/10.1... new paper out!
Phenotypic tolerance for rDNA copy number variation within the natural range of C. elegans
The genes for ribosomal RNA (rRNA) are encoded by ribosomal DNA (rDNA), whose structure is notable for being present in arrays of tens to thousands of tandemly repeated copies in eukaryotic genomes. T...
www.biorxiv.org
March 29, 2025 at 1:38 AM
www.biorxiv.org/content/10.1... new paper out!
Thrilled to present our collaboration w/ Stergachis lab members “The regulatory potential of transposable elements in maize”. Single-molecule Fiber-seq - accurate and sensitive accessibility in maize. New open chromatin regions in LTRs and much more! www.biorxiv.org/content/10.1...
The regulatory potential of transposable elements in maize
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
July 16, 2024 at 10:13 PM
Thrilled to present our collaboration w/ Stergachis lab members “The regulatory potential of transposable elements in maize”. Single-molecule Fiber-seq - accurate and sensitive accessibility in maize. New open chromatin regions in LTRs and much more! www.biorxiv.org/content/10.1...