Joined January 2012
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- Following 662
- Followers 467
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100 Photos and videos
Our lab's new paper is out!
We introduce ENTRAP-seq, a high-throughput in planta assay for multiplexed profiling of protein-coding libraries. Using ENTRAP-seq and machine learning, we discovered transcriptional regulators from ~1,500 plant viral genomes.
go.nature.com/4pw5cL1
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Josh Cuperus retweeted
1 Jul 2025
Genetically engineered chestnut tree, grown in Syracuse, moves one step closer to release 🧬🌳 | If approved, Darling-54 -a fungus resistant event- would be the first genetically engineered tree made for large-scale reforestation, and could save the American chestnut from the brink of extinction. syracuse.com/outdoors/2025/0…
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Josh Cuperus retweeted
18 Jun 2025
What are the fitness consequences of rDNA copy number variation within and outside the lab conditions? Do fitness effects change when growth conditions differ?
In the new #GENETICS study @RNAnerd and colleagues answer these questions using #yeast: buff.ly/gxFNCbA
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Josh Cuperus retweeted
17 Jun 2025
Our latest paper is out in its final form in
@ThePlantCell
We show that in plants the same DNA sequence can act as an insulator or silencer depending on the surrounding regulatory context. Read the full paper at: doi.org/10.1093/plcell/koaf0…
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Josh Cuperus retweeted
16 Jun 2025
Mapping genetic modifiers of epimutation rates reveals a punctuated-equilibrium model of CG methylome evolution biorxiv.org/content/10.1101/…
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Josh Cuperus retweeted
14 Oct 2024
New preprint! An atlas of conserved TF binding sites across flowering plants generated with multiplexed DAP-seq. When integrated with multi-species snRNA- and snATAC-seq reveals how TF activity shapes development and stress responses at the cellular level.biorxiv.org/cgi/content/shor…
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Josh Cuperus retweeted
27 Sep 2024
Our lab is looking for a postdoc @uwgenome/@UW/@UWISCRM!
We tackle a wide range of biological Qs from cell-specific responses to perturbation to molecular consequences of aging.
We also work hard on new #TeamMassSpec methods to scale the # of proteomics samples we can analyze.
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Josh Cuperus retweeted
19 Sep 2024
Out now on biorxiv: We studied the activity of enhancer-blocking insulators in plants and found that they also act as silencers when placed upstream of moderate to weak enhancers.
biorxiv.org/cgi/content/shor…
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Josh Cuperus retweeted
19 Aug 2024
Excited to share our latest work investigating the consequences of extant genetic variation in cis-regulatory elements at single-cell resolution.
A short 🧵
biorxiv.org/content/10.1101/…
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Josh Cuperus retweeted
20 Jul 2024
Are CpG methylation and chromatin accessibility polar opposites? #Fiberseq proves they are not in #maize – transposon enhancers can have simultaneous single-molecule hyper-mCpG AND chromatin accessibility. Wonderful collaboration w/ Queitsch lab & @RNAnerd
biorxiv.org/content/10.1101/…
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Josh Cuperus retweeted
16 Jul 2024
Climate change be damned! Out in @NatureComms, we interrogated over 54k plant terminator sequences to synthetically design robust terminators for crop engineering. tinyurl.com/d63n894r
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16 Jul 2024
Thrilled to present our collaboration w/ @stergachislab 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! biorxiv.org/cgi/content/shor…
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Josh Cuperus retweeted
1 Jul 2024
I'm thrilled to announce the complete program for #ICAR2024SanDiego!
👉🏽Please check out the amazing line of up over 300 speakers in nearly 50 sessions! I hope to see you soon in San Diego..
icar2024.weebly.com/full-pro…
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Josh Cuperus retweeted
3 Jun 2024
I understand imitation is the sincerest form of flattery, but as junior faculty it is frustrating when @nanopore copies the figures of your work verbatim without any credit.
youtube.com/watch?v=1NkBr3oZ…
Figure 1: biorxiv.org/content/10.1101/…
Figure 4: biorxiv.org/content/10.1101/…
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Josh Cuperus retweeted
12 May 2024
Please join us for a tribute symposium on May 17 to Philip Benfey, a luminary in plant biology. Details and Zoom link here: as.nyu.edu/departments/biolo…
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Josh Cuperus retweeted
25 Apr 2024
IN BRIEF: Dissecting and redesigning enhancers of photosynthesis genes (Peng Liu) buff.ly/49TCLyH @RNAnerd @ASPB #PlantSci
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Josh Cuperus retweeted
22 Mar 2024
Josh Cuperus- Univ of Washington-Seattle, @RNAnerd is organizing the "Chromatin at Single-cell & Single-molecule Resolution" session at #ICAR2024SanDiego. Submit your abstract by 15 April.
See session description (#7) here- icar2024.weebly.com/mini-sym…
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Check out our new work!
22 Mar 2024
Plant enhancers exhibit both cooperative and additive interactions among their functional elements (Tobias Jores, Jackson Tonnies, Nicholas A Mueth, Andrés Romanowski, Stanley Fields, Josh T Cuperus, Christine Queitsch) buff.ly/3vlf2t0 @RNAnerd @ASPB #PlantSci
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Josh Cuperus retweeted
22 Mar 2024
Plant enhancers exhibit both cooperative and additive interactions among their functional elements (Tobias Jores, Jackson Tonnies, Nicholas A Mueth, Andrés Romanowski, Stanley Fields, Josh T Cuperus, Christine Queitsch) buff.ly/3vlf2t0 @RNAnerd @ASPB #PlantSci
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