Preprint of our tidyverse+graph theory based gene coexpression analysis workflow is online! Tidyverse functions produce nodes & edges, and graph based clustering (Leiden) detects tight gene coexpression modules. biorxiv.org/content/10.110… Tutorial: github.com/cxli233/Simple…

HOWEVER. During our 5 day stay, there were multiple occasions where we arrived at a station and the lift was out of service so we couldn’t exit. We had go to next station and get a bus back. There was no warning about this at other stations, and no announcements on the train.

To the biology tweeps: To finish off 2022, Oded Rechavi and I thought it would be fun to hear from you about one paper from 2022 that you think we should all read. One paper per person. A few words why you think is important would be great too.

Our pre-print is now published online at New Phytologist; Effective root responses to salinity stress include maintained cell expansion and carbon allocation nph.onlinelibrary.wiley.com/doi/10.1111/np… Wonderful collaboration @PPH_WUR WUR Plant Diana Santelia Kilian Duijts @jasper_lamers Yanxia Zhang

📢Please RT‼️ #Preprint Seminar by Travis Lee (Joe Ecker Salk Institute) on Seed to seed single cell nuclei atlas of Arabidopsis 🤯. Wanna hear more, join us‼️ When: 11th of April, 4 pm (European), Where: ZOOM. DM for the link. biorxiv.org/content/10.110…

We show that salt activates LBD16 independent of auxin-ARF7/19: a ZAT6-dependent pathway enables root branching while the canonical pathway is inhibited by salt! Yanxia Zhang Kilian Duijts Laboratory of Plant Physiology, Wageningen U&R Dorota Kawa Aalt-Jan van Dijk WUR Plant & many others biorxiv.org/content/10.110…

This is really cool! Thanks for sharing!

One of my favorite papers in recent years included this diagram. It shows the impact of controlling for three different types of variables: confounders, colliders, and mediators. With confounders, control is good. With the others, you ruin your result by controlling.

Are you a PhD student and crazy about plant sciences? Don't miss out the European Plant Sciences Retreat!!!

📢 To all users of GreenGate, the 🌱 modular cloning system: Very happy to introduce GreenGate 2.0 (GG2.0) 🎉 a backwards-compatible addon for the assembly of complex transcriptional units and their stacking. A short 🧵 for more details... biorxiv.org/content/10.110…

Tomorrow I will give a talk about #ImageForensics and #ScienceMisconduct at the European Plant Sciences Retreat #EPSR2023 in Wageningen. I hope to see some of you there! graduateschool-eps.info/european-plant…

In a recent Cell Stem Cell paper, the authors write the following about this UMAP: "bEPI and bTE derivatives were separated along UMAP-1, while trophoblast progenitor (bTE and bCTB) and differentiated cell types (bEVT, bSTB, and bPrSyn) were separated along UMAP-2" 👀👀👀👀 1/🧵

I regularly use the Mvista browser to check sequence conservation around my favorite genes. I would like to combine this information in plots of binding sites in promotors. Is there anyway to extract the Mvista plotting data of specific tracks? So I could replot it in python/R?

Does anyone still need a token for blsk? I've got a new batch.

I really enjoyed attending the EPSR last year. Here's a wonderful summary of some of the highlights from the event! Bringing Europe's early career plant scientists back together - Wittmer - New Phytologist - Wiley Online Library nph.onlinelibrary.wiley.com/doi/full/10.11…