Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.
The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...
Figure 1 shows they key result
Weighted Gene Co-expression Network Analysis (WGCNA) has been the go to program for analysis of gene expression modules for nearly two decades but it is a difficult to implement. To make it easier to use WGCNA, I used Codex to build a human in the loop agentic workflow. github.com/lowrylab/WGC...
Open to anyone working with wheat, join us at the next Wheat Genetic Improvement Network (WGIN) meeting on March 11th at the John Innes Centre and online
Register: https://www.rothamsted.ac.uk/event/23rd-wheat-genetic-improvement-network-wgin-stakeholders-meeting
#wheat #arable #farming #agriculture
This paper is great. It describes a method to generate DNA binding proteins de novo: www.nature.com/articles/s41...
I wish there is a web server where you can punch in DNA sequences, submit a job, then it generates the cDNA of your DNA binders, and you can go straight for synthesis & testing.
🌾 Pleased to invite you to a pathogens webinar!
Dr. Xianming Chen (USDA), presenting on stripe rust epidemiology and host resistance
📅Friday, FEB 27, 7:00 PM CET / 11:00 AM MST
Have a look here: wheatinitiative.org/new-events/2...
@karchuntan.bsky.social
@ReemWheat.bsky.social
Exploring #abiotic stress resilience module for #molecular design in #rice
www.sciencedirect.com/science/arti...
#PlantStress @elsevierconnect.bsky.social @researcheracad.bsky.social @oryzasativum.bsky.social @sse-evolution.bsky.social @albertvilella.bsky.social @molplantsci.bsky.social
🧪🌱 Our paper on Genomics of Botanical Collections for the #TeachingTools collection of @theplantcell.bsky.social is out! 🎉 A wonderful publishing experience because we made a great team producing the paper but also thanks to the invaluable help of @plantteaching.bsky.social with the editing.
The last 2025 One Hour NUE webinar is now live.
Featuring Clint Della Bosca on improving NUE in low rainfall environments.
Watch: www.wheatinitiative.org/ewg-nutrient
image of a maize inflorescence meristem that is labeled by the plasma membrane marker PIP2-CFP and BAM1D-YFP.
nph.onlinelibrary.wiley.com/share/JAIVZX...
Excited to share my latest work in @newphyt.bsky.social. Here, we used TurboID proximity labeling with CLAVATA receptors FEA3 and BAM1D in maize meristems to better understand the signaling pathways important for meristem regulation. #PlantScience
Modification of starch synthesis in food crops using CRISPR/Cas9 gene editing technology for changing climate
Liangjie Niu, Hui Liu … Xiuli Hu & Wei Wang
link.springer.com/article/10.1...
#Crops #Biosynthesis #ClimateResilience #GeneEditing
New Brief Communication: "A CRISPR-based sequence proximity binding protein labelling system for scanning upstream regulatory proteins" rdcu.be/eZLUP
CRISPR-based proximity labelling system to profile DNA-binding proteins such as PIF4 transcription factor .
Join the EWG Wheat Breeding Methods and Strategies webinar on HB4 Wheat with Martín Mariani Ventura from Bioceres Crop Solutions.
👉 Learn more: wheatinitiative.org/new-events/e...
Jan 21, 2026!
Long-range PCR amplification and nanopore sequencing of 8-10 kb mitochondrial fragments from environmental DNA https://www.biorxiv.org/content/10.64898/2026.01.13.699327v1
The use of synthetic communities to enhance plant health remains challenging due, in part, to a shortage of long-term studies demonstrating effectiveness of translational microbiome efforts in agricultural systems. However, costs of this research is dropping and advancements are promising.
Fixing Hybrid Rice: >99% Efficient Apomixis with Near-Normal Seed Set https://www.biorxiv.org/content/10.1101/2025.10.16.682968v1
🚀 Our new paper on Alignoth just published in Bioinformatics!
Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows.
📄 doi.org/10.1093/bioi...
#bioinformatics #genomics #rust @johanneskoester.bsky.social
Our lab has just posted a review on wheat spike development, with an emphasis on the regulation of the number of spikelets per spike on bioRxiv.
Can one map the genome-wide binding (1) and its protein partners (2) simultaneously from the same sample?
Yes, one can. with CUT&ID ✂️🪪
Spearheaded — singlehandedly — by @annanordin.bsky.social
No need of transgenesis, cloning and overexpression.
Check it out, it's fast and its works.
The National Association for Plant Breeding (NAPB) will be hosting its annual meeting in College Station from June 14-18, 2026. A fantastic opportunity for everyone involved in plant breeding to come together, share knowledge, and network with professionals nationwide. napbannualmeeting.org
Fig. 1.Schematic overview of pattern-triggered immunity (PTI) in plants upon pest infestation. Cell wall-degrading enzymes (CWDEs) secreted by herbivory disrupt cell wall integrity, releasing damage-associated molecular patterns (DAMPs). The defence response is activated by the recognition of these DAMPs, as well as herbivore-associated molecular patterns (HAMPs), by pattern recognition receptor complexes (PRRs and co-PRRs). Elicitor binding to PRRs leads to a series of signalling events, such as membrane depolarization (Vm), activation of Ca2+ channels and influx of Ca2+ into the cytosol, burst of reactive oxygen species (ROS) via activation of RBOHD, membrane depolarization, and activation of the mitogen-activated protein kinase (MAPK) cascade. MAPK and Ca2+-dependent kinase (CDPK) cascades trigger transcriptional reprogramming, activating phytohormone (SA, JA, and ET) signalling, transcription regulatory factors, and synthesis of defensive compounds.
🪲 REVIEW 🪲
This review uncovers the critical role of the plant cell wall in pest defence, integrating structural, molecular, and genetic insights to highlight its emerging significance in plant–pest interactions during herbivory - Perez-Alonso et al.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
🚀 New preprint!
We introduce K-PROB, a k-mer–based Bayesian framework that mines pangenomic promoter and expression diversity to predict cis-regulatory elements driving gene expression variation in crops 🌽🌱
🔗 biorxiv.org/content/10.1101/2025.10.27.684862v1
#Genomics #GeneRegulation #Maize #Soybean
Fig. 5 (shortened, full legend in paper): Brassinosteroid induces BHB1 expression in Arabidopsis. (A) Relative expression of endogenous BHB1 in Col-0 seedlings grown on medium for 10 d and then treated with either 100 nM brassinolide (BL) or 3 µM brassinazole (Brz). Samples were taken 3 h after treatment. EtOH and DMSO represent the mock control treatments. Expression was determined by qRT-PCR and is relative to that in the controls, the value of which was set as 1. Data are means (±SD), and the numbers of replicates are indicated. Significant differences compared with the WT were determined using Student’s t-test and are also indicated. (B) GFP fluorescence showing BHB1 expression in rosette leaves of plants transformed with pBHB1::GFP and treated with BL. Scale bars are 1 mm. Plants at 25-day-old were treated with either 100 nM BL (+BL) or mock solution (–BL) and the images were taken after 7 d l.
🧂🌱 RESEARCH 🌱🧂
The transcription factor BRASSINOSTEROID-RELATED HOMEOBOX 1 acts as a hub in mediating crosstalk between salt stress and brassinosteroid signaling in Arabidopsis - Hasegawa et al.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
Fig. 4.Illustration of the co-evolutionary arms race between plants and insects through triterpene-based defence versus insect counter-measures. Plants deploy diverse triterpene-based defence strategies, including antifeedancy, stunted growth, protease inhibition, cytotoxicity, and indirect defence to deter herbivores. In response, insects have evolved sophisticated adaptations such as behavioural avoidance, enzymatic detoxification, sequestration of toxic compounds, microbial symbiosis, and genetic modifications to bypass plant defences. This ongoing evolutionary battle shapes the dynamic interplay between plant immunity and insect survival strategies.
🪲🌿 REVIEW 🌿🪲
Beyond bitter: plant triterpenoids in the battle against herbivorous insects. Mathur et al. explore triterpenoids as key players in plant defence & crop protection 🪲
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
NEWS & VIEWS: Jasmonic Acid Oxidase (JAO): Balancing growth and defense in rice (Marcella Alves Teixeira) doi.org/10.1093/plph... #PlantScience @aspbofficial
Working model of SR45-interacting salivary protein (SISP) regulating plant immunity.
Insect salivary proteins alter the stability of plant splicing factors
Haoli Gao, et al.
📖 nph.onlinelibrary.wiley.com/share/3PX4GV...
#planthopper #PlantScience
Another gene that could cause multiovary in grasses. In barley, at least three multiovary loci (mov1, mov2 and mov5 (HvLFY)) have been reported doi.org/10.1101/2022...
Excited by this breakthrough work led by Dr. Lauren Stanley (now Assistant Professor at Central Michigan University). Lauren was able to develop for the first time floral dip/spray transformation methods in the yellow monkeyflower (Mimulus guttatus). bsapubs.onlinelibrary.wiley.com/doi/10.1002/...
Our Genome Biology paper on wheat spike development integrating single cell and spatial transcriptomics is now published! Check out the paper here: doi.org/10.1186/s130... and enjoy the beautiful pictures (including our 44 supplementary figures)! Be sure to check out some of our tools below!
Exciting news in wheat science!
A new study in @natcomms.nature.com shows the first wheat pan-transcriptome: uncovering hidden diversity across modern wheat lines 🌾
Congrats to @earlhaminst.bsky.social & @helmholtzmunich.bsky.social for this major advance!
➡️ buff.ly/XEQlCnT
#WheatConnect
UNC Chapel Hill is hiring an Assistant Professor in Plant Molecular Biology. Per Jeff
Dangl MPMI candidates are also highly desired in the search. unc.peopleadmin.com/postings/307...
