@RNAnerd
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Genomics in Plants and Yeast, Assistant Professor
Joined January 2012
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- Following659
- Followers465
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Josh Cuperus retweeted
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
Josh Cuperus retweeted
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…
Josh Cuperus retweeted
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
Josh Cuperus retweeted
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…
Josh Cuperus retweeted
Mapping genetic modifiers of epimutation rates reveals a punctuated-equilibrium model of CG methylome evolution biorxiv.org/content/10.1101/…
Josh Cuperus retweeted
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…
Josh Cuperus retweeted
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.
Josh Cuperus retweeted
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…
Josh Cuperus retweeted
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/…
Josh Cuperus retweeted
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/…
Josh Cuperus retweeted
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
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…
Josh Cuperus retweeted
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…
Josh Cuperus retweeted
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/…
Josh Cuperus retweeted
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…
Josh Cuperus retweeted
IN BRIEF: Dissecting and redesigning enhancers of photosynthesis genes (Peng Liu) buff.ly/49TCLyH @RNAnerd @ASPB #PlantSci
Josh Cuperus retweeted
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…
Check out our new work!
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
Josh Cuperus retweeted
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