Josh Cuperus

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

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/…

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

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…

Mapping genetic modifiers of epimutation rates reveals a punctuated-equilibrium model of CG methylome evolution biorxiv.org/content/10.110…

@cshperspectives How does one become an affiliate, I would be interested in volunteering

bioRxiv bat signal to Affiliates! We have a big backlog of submissions. If any of you have time to go in and screen a few papers, we'd be immensely grateful - as would the authors! 🙏

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/sh…

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.

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/sh…

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/10.110…

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/10.110…

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/sh…

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-program.h…

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=1NkBr3… Figure 1: biorxiv.org/content/10.110… Figure 4: biorxiv.org/content/10.110…

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/bi…

IN BRIEF: Dissecting and redesigning enhancers of photosynthesis genes (Peng Liu) buff.ly/49TCLyH @RNAnerd @ASPB #PlantSci

@DoctorZen @jedward_s #1 seems to happen more often these days

@jedward_s Many things could be true. 1. If authors resubmit, this can be treated as a new submission, so “average time from submission to publication” is kept artificially short. 2. Editors aren’t (and shouldn’t!) blindly compiling reviews. They are using their own judgment.

I’ve reviewed three papers in a row for solid mid-tier journals where all reviewers recommended revisions and the editors just flat rejected. What is going on with this? Seems like a huge waste of everyone’s time

@HarmitMalik @ChenxinLi2 Transient assays tell us that the free floating dsDNA is transcribed and follow most rules of chromosomal genes

@ChenxinLi2 If it's in the nucleus (which it is) it is chromatinized.

What kind of chromatin does an extrachromosomal T-DNA have? I assume it doesn’t have histone, but I reckon it isn’t naked, no?