iiinova — where your digital self keeps evolving

Reposted by Josh T Cuperus

Maitreya Dunham @maitreya.bsky.social · 24/09/2026

Exciting news: @uwgenome.bsky.social will be hiring for two tenure-track faculty positions this year, one open rank and one assistant professor. Both are “Genome Sciences” interpreted broadly so we welcome applicants working in a variety of fields and methods. Ad will be out shortly.

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Josh T Cuperus @rnanerd.bsky.social · 07/09/2026

Check out our preprint on Duckweed combo-stress responses and chromatin accessibility. ACRs have ⬆️ GC content much like maize, even with small genomes and low TE numbers. One speculation we had for this in maize was TE insertion avoidance, guess we were wrong. www.biorxiv.org/content/10.6...

biorxiv.org

Duckweeds as Multiplexable Plant Models for Exploring Abiotic Stress Responses

In nature, plants experience complex combinations of environmental stresses. Prior studies using Arabidopsis thaliana show that transcriptional responses to combinatorial stress are unique and cannot ...

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Reposted by Josh T Cuperus

Maitreya Dunham @maitreya.bsky.social · 28/08/2026

If you are thinking of applying to the @uwgenome.bsky.social PhD program this fall, we have a couple of zoom info sessions set up for Oct 6 and Oct 22. Please register at the link. Our website also has a ton of useful information about crafting your application. www.gs.washington.edu/news/graduat...

gs.washington.edu

Graduate Program Information Sessions – UW Genome Sciences

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Reposted by Josh T Cuperus

Sanjay Srivatsan @sanjaysrivatsan.bsky.social · 11/08/2026

A new blog post thinking through the parallels between protein structure prediction and virtual cell efforts. Many of our current approaches to collect data to build a virtual cell model lack the abstraction that links measurement and function. t.co/4sPSMaLWLL

Acknowledgement: Illustration by David S. Goodsell, RCSB Protein Data Bank and the Scripps Research Institute. doi: 10.2210/rcsb_pdb/goodsell-gallery-050

Kinetochores separate chromosomes when eukaryotic cells divide. This illustration shows a yeast kinetochore (green) attached to a disassembling microtubule (blue). Chromatin is shown at upper right with DNA in yellow and histones in orange.

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Reposted by Josh T Cuperus

AAUP @aaup.org · 12/05/2026

“The message, very clearly, they’re sending is, do not speak out on behalf of Chinese postdocs. If you do, you’re going to pay a penalty...It seems pretty obvious that this is an attempt by the current administration to silence people that question their activities." — Roger Innes, IU AAUP member

chronicle.com

A Professor Defended a Postdoc Who Was Deported. Now His Lab Has Been Suddenly Locked Down.

Work at an Indiana University biology lab was halted amid federal scrutiny, affecting dozens of researchers. “The damage is significant and mounting,” the department chair told The Chronicle.

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Josh T Cuperus @rnanerd.bsky.social · 03/05/2026

@vram142.bsky.social So are pioneer TFs displacing or moving nucleosomes? Or is that an unanswerable question.

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Josh T Cuperus @rnanerd.bsky.social · 30/04/2026

Check out the new paper from @tobiasjores.bsky.social, including @lampoona.bsky.social and many more of us!

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Reposted by Josh T Cuperus

PacBio @pacbio.bsky.social · 12/01/2026

Our #PacBio workshop at #PAG33 starts in one hour. ⏰ See how HiFi sequencing and SPRQ-Nx chemistry help researchers reveal chromatin features, explore genetic and epigenetic diversity, and resolve complex genomes. 🕐 January 12 | 12:50–3:00 PM 📍 Town and Country, Ballroom C

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Reposted by Josh T Cuperus

John Greally @greally.bsky.social · 04/10/2025

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.

biorxiv.org

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 ...

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Reposted by Josh T Cuperus

Jess McLaughlin, PhD (they/them) @jfmclaughlin92.bsky.social · 26/09/2025

i'm glad it's posted now, but damn that's a gut-punch for any 2nd year students planning to apply this cycle

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Reposted by Josh T Cuperus

@LaBonneLaB @labonnelab.bsky.social · 26/09/2025

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.gov

NSF Graduate Research Fellowship Program (GRFP)

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Reposted by Josh T Cuperus

Daniel Bolnick @danielbolnick.bsky.social · 26/09/2025

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.

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Reposted by Josh T Cuperus

Jason “Obstacle to Progress” Williams @jasonwilliamsny.bsky.social · 25/09/2025

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/

jasonjwilliamsny.github.io

An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program

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Josh T Cuperus @rnanerd.bsky.social · 16/09/2025

Carrington lab reunion, Oregon State edition

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Josh T Cuperus @rnanerd.bsky.social · 04/06/2025

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

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Reposted by Josh T Cuperus

Emilio M Bruna @brunalab.bsky.social · 31/05/2025

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. 🧪

tableau.external.nsf.gov

Tableau

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Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · 13/05/2025

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...

youtube.com

Fareed’s Take: Trump is gutting what made American science great

YouTube video by CNN

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Reposted by Josh T Cuperus

Senator Bernie Sanders @sanders.senate.gov · 13/05/2025

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.

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Josh T Cuperus @rnanerd.bsky.social · 16/07/2024

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...

biorxiv.org

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

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