Happy to share our🆕invited #OpenAccess article "​From the #genome to super- #pangenome🧬: a new paradigm for accelerated #crop improvement🌾🌿🪴" is out in 𝙣𝙥𝙟 𝙎𝙘𝙞𝙚𝙣𝙘𝙚 𝙤𝙛 𝙋𝙡𝙖𝙣𝙩𝙨 @natureportfolio.nature.com🤩🎉 🔗 www.nature.com/articles/s44... #PlantScience @tpg-sssa.bsky.social @planteditors.bsky.social

“At 14 research agencies Science examined in detail, departures outnumbered new hires last year by a ratio of 11 to one, resulting in a net loss of 4224 STEM Ph.D.s. “ www.science.org/content/arti...

📘 @springernature.com has published Deep Learning for Life Scientists by Filippo Biscarini & Nelson Nazzicari—the first volume of the new Decoding Evolution series. Based on Physalia-courses, it bridges theory and practice in AI, bioinformatics & genomics 🚀 🧵

We are pleased to announce the official release of PLAZA 5.1, our plant genomics platform, which comes with a major front-end redesign. This results in improved performance, enhanced visualization tools, and refined Toolboxes. Src: www.vandepoelelab.be/plaza/news#28

Are you excited about pangenomics? If so, join us in Edinburgh on 8-9th June to discuss the latest methods & insights from using these approaches across biodiversity! More details here: royalsociety.org/science-even... Organised together with @henrylnorth.bsky.social & @joanameier.bsky.social!

Made a site comparing the sizes of living things :) The great Julius Csotonyi spent 5 months painting over 60 illustrations for the site, no ai used > neal.fun/size-of-life/

Now on Bluesky: @darwin-online.bsky.social. Give 'em a follow! #HPS #histsci

Lovely new review on H3K27me3 dynamics and potential functions in #plantscience by @drosborneplantsci.bsky.social nph.onlinelibrary.wiley.com/doi/10.1111/...

The hidden danger of Biorender (& the death of scientific illustration) A short thread 🧵

A really nice article in The Scientist about q.e.d! @qedscience.bsky.social - If you're not using it yet, now's the time! www.the-scientist.com/q-e-d-an-ai-...

Our latest paper has just been published in Cell! doi.org/10.1016/j.ce... We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.

I am looking for a PhD student to start in my lab at UCSB in Fall 2026, studying evolutionary biology. See attached flyer for more information. Please also share with potentially interested students. Thanks!

I'm recruiting PhD students for the Barker Lab @uofa-eeb.bsky.social We study plant evolutionary genomics - polyploidy, hybridization & machine learning for genome evolution. Work with Selaginella, Xanthisma, Brassica & more. Funding available via CAMBIUM Fellowships. Reach out if interested! 🧬🌵🤖

Chromatin organization is measured in single cells using droplet microfluidics go.nature.com/3NCqwO1 rdcu.be/eNah5

🚀 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

Our new publication on HOBIT, a software tool for polyploid gene expression analysis. Compared with our previous method HomeoRoq (2014), HOBIT enables direct and higher-quality analysis of complex allohexaploid species such as bread wheat.

Please spread the word to anyone who might be interested! #PhD available in our group

Pre-phasing long reads improves structural variant genotyping. #LongReads #Sequencing #ReadsPhasing #StructuralVariants #Genotyping #Genomics #Bioinformatics academic.oup.com/bioinformati...

Published today: One of the biggest #science #communication studies to date. We asked 71,922 people in 68 countries how they #engage with information about #science and combined the data with several country-level factors: journals.sagepub.com/doi/10.1177/... #OpenAccess

Lunch today halfway around the world in Hangzhou and met a new asst professor who was very thankful for this resource. Please help out folks like them and other early career scientists with examples of job apps. Submit yours! github.com/RILAB/statem...

Today we have published a new analysis of UK immigration costs, comparing the 2025 costs of skilled worker, researcher and student visas in the UK and 17 other leading science nations. This updates previous analysis from 2019, 2021 and 2024: royalsociety.org/news-resourc...

Here's the link to the system, try it! qedscience.com @qedscience.bsky.social

We extended the functionality of DMRcaller ( bioconductor.org/packages/DMR...) to incorporate ONT data directly from Dorado aligned bam files and maintain the information of the read the modification was detected on.

Apple is entering the protein folding arena. SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...

I get that the news cycle is packed right now, but I just heard from a colleague at the Smithsonian that this is fully a GIANT SQUID BEING EATEN BY A SPERM WHALE and it’s possibly the first ever confirmed video according to a friend at NOAA 10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)

Later TODAY at 15:00 CEST! Efficient evidence-based genome annotation with EviAnn 🧬 👉 www.erga-biodiversity.eu/post/efficie... #genomeannotation #genomes #seminar #research #EviAnn @ebpgenome.bsky.social

StackOverflow AI stackoverflow.ai

I am editing a collection on "plant epigenetic regulation" for BMC Plant Biology. If you think that your paper might fit there please contact me or send it through the submission system to our collection: www.biomedcentral.com/collections/...

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

I'm looking to recruit a PhD student to study patterns of local adaptation and introgression across the spruce hybrid zone in the Rockies near Calgary. Projects can include field work, bioinformatics, pop gen theory, or comparison to plant/ conifer species yeamanlab.weebly.com/uploads/5/7/...

Postdoc opportunity with @tomasbruna.bsky.social here at @jgi.doe.gov @berkeleylab.lbl.gov: Develop, benchmark, and apply Plant Genomic Language Models (gLMs) 🌿🧬💻 jobs.lbl.gov/jobs/computa... #AI #PlantGenomics #gLMs #Postdoc

Happy to be able to finally share our NLR pangenome paper, out now in CHM. "Pangenomic context reveals the extent of intraspecific plant NLR evolution" www.cell.com/cell-host-mi... #plantscience #plantimmunity #pangenomes #science #nlr

Prompt-based bioinformatics: a new interface for multi-omics analysis www.nature.com/articles/s41... read free: rdcu.be/eAnf4 Vibeoinformatics... computational vibeology... 🧬🖥️🧪

Oxford Nanopore @nanoporetech.com CEO will leave the company in 2026 after 20 years in the role.

I am opening scientific illustration commissions! Below are some examples of my work. Please contact me via [email protected] if you are interested!

Decoding nature’s grammar with DNA language models. #Genomics #LLMs #AI @pnas.org 🧬 🖥️ www.pnas.org/doi/10.1073/...

We are hiring! If you have experience in plant genomics + AI, or promoter engineering + synthetic biology, check out our two open postdoc positions (computational + wetlab): www.vandepoelelab.be/Jobs please re-share RT #ERC

New Pre-print! A long-standing question for transcription factor biology is how their chromatin context dependency works in plants. In this collaboration with Fred Berger lab, we present some new ideas not only in Arabidopsis but also in Marchantia. www.biorxiv.org/content/10.1...

Are you a PI in a biology field looking for students to join your lab as a PhD student? I made a Starter Pack to help PIs and potential PhD students connect! If you would like to be added to this pack, please let me know! go.bsky.app/EFj87fi

Please share! Our lab is recruiting a PhD student to join us starting fall 2026. Our group is broadly interested in plant molecular evolution and comparative genomics. More info about our lab and grad programs at Colorado St. is available on our lab website. sites.google.com/site/danielb...

Join us Thursday July 17 for a discussion on "Numeracy, Realism & Relevance in Plant Science", featuring Steven Burgess, Samuel Lovat, Jonathan Napier, & Claudia Vickers discussing how to "run the numbers" to identify realistic solutions to today's problems. blog.aspb.org/july-17-plan...

📣 Save the date 📆 Tuesday 7 Oct '25 Get ready for the return of the Norwich Bioscience Institutes Accessible Science Talks! Schools and colleges can join us online to hear directly from our researchers and technical specialists about their science & careers🔬🧬🌿🦠💻

🌾🧬 SPECIAL ISSUE RESEARCH 🌾🧬 📝 Varying gene dosage through mutating DNA methyltransferase 1-1 (MET1-1 ) in polyploid wheat generates quantitative changes to CG methylation without the lethal consequences observed in other crops - Burrows et al. 🔗 doi.org/10.1093/jxb/... #PlantScience 🧪

Multiple Software Updates - RepeatMasker 4.2.0, RepeatModeler 2.0.7, and the newly released RepeatAfterMe tool. See www.repeatmasker.org for details.

If you want to gain skills and experience in #plantsciences and #bioengineering take a look at our 12-month #Internship in the Earlham #Biofoundry:

Shout out to the #rstats {performance} package. Its check_model() function is super helpful for model evaluation. #statistics #STEM

Excited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986

Springer-Nature launched a series of "Discover" journals that closely mimic MDPI titles -- sharing *identical* journal names, and likely similar business model. What is going on, and why researcher will - as always - fall for it? A 🧵 the-strain-on-scientific-publishing.github.io/website/post...