The new OrthoFinder paper is out now! In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets www.nature.com/articles/s41... github.com/OrthoFinder/...

OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability - Nature Methods

The updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.

nature.com

Calling all OrthoFinder users! We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny. GLADE runs directly on OrthoFinder results. www.biorxiv.org/content/10.6... github.com/lauriebelch/... (1/10)

In our Forest of Biologists we fund the restoration and preservation of ancient woodland and dedicate these trees to our peer reviewers. There are now over 10,000 trees for peer reviews! Thank you to all our peer reviewers. Find out more: forest.biologists.com #PRW2025 @peerreviewweek.bsky.social

OrthoFinder just dropped a major update It’s faster, more accurate, and ready for thousands of genomes Let’s break it down (1/10) github.com/OrthoFinder/... www.biorxiv.org/content/10.1...

Researchers in @biology.ox.ac.uk and Wild Bioscience Ltd are to receive backing of a £6.7 million grant from the Advanced Research and Invention Agency (ARIA) to pioneer a new synthetic biology approach which promises to improve yields in potato and wheat. Read more ⬇️ #OxfordClimate

New ARIA award will aim to deliver a revolution in sustainable

Researchers in the University of Oxford’s Department of Biology and Wild Bioscience Ltd are to receive backing of a £6.7 million grant from the Advanced Research and Invention Agency (ARIA) to

ox.ac.uk

So true: "In a very short time, we have created not only silly systems of governance and regulation, but are also managing to subvert academic life through the creation of bullshit jobs and, I would argue, bullshit practices."

Ben Long@botbml.bsky.social · last yr.

touché. academic.oup.com/brain/articl...

Second writeup! This paper made me fall back in love with photosynthesis evolution. ❤️

Plantae.org@plantaeofficial.bsky.social · last yr.

Plant Science Research Weekly -- Review: The complexities of metabolite transport in C4 photosynthesis (The Plant Cell) @stevenkelly.bsky.social (Summary by Mae Mercado @maemercado.bsky.social‬ ) buff.ly/LyHf7qN #PlantaePSRW

Plant Science Research Weekly -- Review: The complexities of metabolite transport in C4 photosynthesis (The Plant Cell) @stevenkelly.bsky.social (Summary by Mae Mercado @maemercado.bsky.social‬ ) buff.ly/LyHf7qN #PlantaePSRW

Review: The complexities of metabolite transport in C4 photosynthesis | Plantae

C4 photosynthesis, an adaptive mechanism to spatially concentrate CO2 around Rubisco to enhance carbon fixation, has evolved independently at least 60 times in plants. This process spatially…

buff.ly

#PlantSci Research Weekly March 7 plantae.org/plant-scienc... Review: C4 metabolite transporters; Insights from Marchantia pangenome; cry1 & phot work synergistically; Plasmodesmata as MCS for intercellular communication; Developmental robustness from antagonizing cis-elements; (1/2)

@stevenkelly.bsky.social @pierremarcdelaux.bsky.social @dubcovskylab.bsky.social @williamsanu.bsky.social

Wild is hiring! If you’re passionate about making an impact in crop improvement using genomics and comp bio come join the team! jobs.recruit.charliehr.com/wildbioscien...

Lots of ✈️ traffic over Oxford today. Never seen so many before

In the May 2024 @ijpsjournal.bsky.social Endopolyploidy in the Leaf Cells of Rhodes Grass (Chloris gayana Kunth) Hidekazu Kobayashi, Takao Oi www.journals.uchicago.edu/doi/full/10....

Endopolyploidy in the Leaf Cells of Rhodes Grass (Chloris gayana Kunth) | International Journal of Plant Sciences: Vol 185, No 3

Premise of research. Endopolyploidy is the occurrence of different levels of ploidy in the cells of the somatic tissues of an organism. Although several cell functions have been associated with endopo...

journals.uchicago.edu

The first step on a path to C4 rice by genome editing ✂️🧬 www.biorxiv.org/content/10.1...

A preprint several years in the making… A holistic review of metabolite transport in C4 photosynthesis. Current understanding, key gaps, future directions and new molecular blueprints for NAD-ME. A masterpiece by former PhD student Oliver Mattinson ecoevorxiv.org/repository/v...

A quick visit to my (scientific) roots today… haven’t changed a bit 😂😂😂

Engineering the cyanobacterial ATP-driven BCT1 bicarbonate transporter for functional targeting to C3 plant chloroplasts https://www.biorxiv.org/content/10.1101/2024.02.14.580295v1

Engineering the cyanobacterial ATP-driven BCT1 bicarbonate transporter for functional targeting to C3 plant chloroplasts https://www.biorxiv.org/content/10.1101/2024.02.14.580295v1

The ATP-driven bicarbonate transporter BCT1, a four-component complex in the cyanobacteria CO2-conce

biorxiv.org

A surprising discovery - a role for lineage in leaf development. Great work by @chiaraperico.bsky.social

bioRxiv Plant Bio@biorxiv-plants.bsky.social · 3y ago

Spatial transcriptomics reveals distinct lineage identities for major and minor vein initiation during maize leaf development https://www.biorxiv.org/content/10.1101/2024.02.05.578898v1

The NHM was looking spectacular this evening 🦖

Musk’s Starlink satellite train just passed over Oxford.. satellites stretched horizon to horizon … I genuinely thought it was aliens!

Very pleased to have finally got this out there - many years work by the team - primarily Dana Vlad. Discovered that large vein ranks are actively repressed to allow smaller veins to develop. All grasses we looked at are the same. Allowed us to change patterns in rice - not quite C4 rice but closer

bioRxiv Plant Bio@biorxiv-plants.bsky.social · 3y ago

THE WIP6 TRANSCRIPTION FACTOR TOO MANY LATERALS SPECIFIES VEIN TYPE IN C4 AND C3 GRASS LEAVES https://www.biorxiv.org/content/10.1101/2023.12.20.572592v1

So it turns out that electroporation of exogenous DNA into organisms is entirely natural. peerj.com/articles/165...

Exciting opportunity at the Queen’s College Oxford in association with @oxfordbiology.bsky.social. The Browne JRF is a three year independent research fellowship available in any area of biology that complements Oxford Biology. www.queens.ox.ac.uk/vacancies/br... Please repost!

🚨Come join the lab🚨 to lead on developing Selaginella apoda as a genetic model system 🌿 1.5 yr PDRA, Deadline 13th Dec Full details: elxw.fa.em3.oraclecloud.com/hcmUI/Candid...

"People don't take climate action because they don't understand the science", someone said in a discussion yesterday. But why do we treat climate science different than medicine? If people are told they have diabetes, they don't go "I don't understand the endocrine system, yum, cake" do they? 🧪

Our prepring about comparative gene regulatory network analysis is available on bioRxiv! We focused on the regulation of C4 and C3 photosynthesis and identified conserved regulators for other pathways too. www.biorxiv.org/content/10.1... #Bioinformatics #generegulation #photosyntheis #PlantScience

Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

biorxiv.org

The genetic basis of dynamic non-photochemical quenching and photosystem II efficiency in fluctuating light reveals novel molecular targets for maize (Zea mays) improvement https://www.biorxiv.org/content/10.1101/2023.11.01.565118v1

The genetic basis of dynamic non-photochemical quenching and photosystem II efficiency in fluctuating light reveals novel molecular targets for maize (Zea mays) improvement https://www.biorxiv.org/content/10.1101/2023.11.01.565118v1

Maize is a major global crop species which uses C4 photosynthesis. Although C4 is typically consider

biorxiv.org

Seems as if Plan-S was only the beginning The continuous revolution in science publishing continues... www.nature.com/articles/d41...

Richard Sever@richardsever.bsky.social · 3y ago

Plan S revamp. Calls to make papers available immediately and abolish APCs. It begins to look like a preprint-driven system is desired www.nature.com/articles/d41...

This was a surprise - for years we thought GLK1 must function to regulate chloroplast development in mesophyll cells of maize given its expression profile - but it doesn’t. Great work by Julia Lambret (not yet on bsky)

Vinay Shukla@vinayshukla.bsky.social · 3y ago

Latest work from the Langdale lab @janelangdale.bsky.social GOLDEN2-like is sufficient but not necessary for chloroplast biogenesis in mesophyll cells of C4 grasses onlinelibrary.wiley.com/doi/full/10.... #plantscience

I determined the sequence of the NcoI recognition site as an undergraduate in Rich Robert’s lab in 1981 - one of my unknown claims to fame 🤣