1/ Excited to share the newest tool in the pangenome MUMiverse: Shredtools! Shredtools enables a user to navigate the pangenome coordinate system with multi-MUMs. More in the thread🧵 Code: github.com/vikshiv/shredtools Interactive tool for querying HPRC assemblies: vikshiv.github.io/shredtools

Navigating the pangenome coordinate system with Shredtools

Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...

biorxiv.org

Building chromosome-level genomes no longer needs to be complex or costly. With optimised error correction on Oxford Nanopore long reads, researchers can now achieve near telomere-to-telomere assemblies faster and with fewer resources. Learn more: https://bit.ly/4vzj76A

Colossal Biosciences @itiscolossal.bsky.social will publish all genomic data generated through the US FWS partnership in open-access repositories colossal.com/colossal-bio... 👏

Brilliant session about pangenomes and lots of creative ways for their interpretation today at SMBE2026. Especially enjoyed talk from Davide Bolognini and can’t wait to try Cosigt on my own. Big thanks to @rmwaterhouse.bsky.social for putting it together! #SMBE2026 @official-smbe.bsky.social

Interactive schedule (2.0) for SMBE2026! Enjoy the conference #SMBE2026 moicoll.github.io/SMBE2026_sch...

Looking forward to all the great science discussions at SMBE starting tomorrow. And of course, a nice summer week in Copenhagen! ☀️

Society for Molecular Biology and Evolution@official-smbe.bsky.social · last mo.

We're almost ready for SMBE 2026! While you're preparing, make sure to read the SMBE Code of Conduct, which applies to all SMBE members, including members, volunteers, staff, vendors, and participants in all Society activities. SMBE Code of Conduct 🔗 smbe2026.org/smbe-policies #SMBE2026

BBSRC Early Independence Fellowships had an Outline stage this year to try help with amount of peer review. Turns out they received 586 applications, a 110% increase on 2025, and only typically fund 15 a year. They are cancelling this stage and going straight to full app with an institutional sift.

Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇

The spotlighted work is by @ubechtold.bsky.social @raduzabet.bsky.social @robynemm.bsky.social & co Gene body methylation buffers noise in gene expression in plants in @narjournal.bsky.social academic.oup.com/nar/article/...

Gene body methylation buffers noise in gene expression in plants

Abstract. Non-genetic variability in gene expression is an inevitable consequence of the stochastic nature of processes driving transcription and translati

academic.oup.com

I wanted to share my new Spotlight in @cp-trendsgenetics.bsky.social that highlights a terrific paper linking gene body methylation with noise in gene expression: Silencing the noise with gene body methylation doi.org/10.1016/j.ti...

Plant gene discovery just went single-cell 🧬🔬 New platform PIVOT uses virus delivery+cell-surface markers to screen gene libraries in individual N. benthamiana cells. One leaf=thousands of experiments. Already found new cytokinin regulators from Arabidopsis #plantsci www.nature.com/articles/s41...

A single-cell screening platform accelerates functional genetics in plants - Nature Biotechnology

A pooled, cell-based, genetic screening platform in plants is used for the functional analysis of cytokinin signaling proteins.

nature.com

#ERGAReads | A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species link.springer.com/article/10.1... #pangenomes #TEs #TransposableElements #pipeline #genomes #GenomeBiology @univparissaclay.bsky.social

A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species - Genome Biology

Background The role of transposable elements (TEs) in host adaptation has gained interest in recent years. Individuals of the same species undergo independent TE insertions, providing genetic…

link.springer.com

🆕 A new international network chaired by Dr Rachel Rusholme-Pilcher at the Earlham Institute is looking to overcome computational challenges of generating plant pangenome graphs, through a culture of openness and collaboration. Read more ⤵️ buff.ly/vNi07lz #PlantScience #Pangenomes #CropScience

Breaking the silos: How open collaboration is transforming plant pangenomics

Pangenomes are transforming plant genomic research by capturing the vast genetic diversity that traditional, single reference genomes often miss.

buff.ly

Not all clones are created equal! Our paper quantifying somatic mutation in plant tissue culture is out now in @pnas.org : doi.org/10.1073/pnas... Check out this article for a quick summary, or keep reading: www.plantsciences.ucdavis.edu/news/davis-m...

Post 1/2 Our new preprint is out! 🧬 We’ve extended #Tiberius for accurate ab initio gene prediction across the eukaryotic tree, including Plants, Fungi, Insects, and Diatoms. doi.org/10.64898/202...

🚨 Why can’t mammals regenerate limbs like frog tadpoles or salamanders? In our new paper in @science.org , we show that species-specific oxygen sensing acts as a gatekeeper for initiating limb regeneration 🐭🐸 🔗 www.science.org/doi/10.1126/... #EvoDevo

Heartbroken to hear this news. Philippa was a wonderful and truly inspiring mentor. I really loved working with her.

John Innes Centre@johninnescentre.bsky.social · 4mo ago

We are devastated to announce that our colleague and friend Professor Philippa Borrill died over the Easter weekend following a rare immune system disorder (HLH). She was a fantastic scientist, collaborator and mentor, and a close friend to many: www.jic.ac.uk/news/profess...

🌱 We’re excited to launch the BBSRC-funded UK Plant Epigenetics Network (UK-PEN) with our inaugural workshop (free!): “Plant Epigenetics: From Model to Crop Species” 📅 11–12 June 2026 📍 Uni of Dundee (hybrid) We look forward to welcoming you! Feel free to repost to help us reach the community

Sara Lopez-Gomollon@gomollonsara.bsky.social · 4mo ago

We are pleased to announce the launch of the BBSRC-funded UK Plant Epigenetics Network (UK-PEN) with our inaugural meeting (it is free!): 🌱 “Plant Epigenetics: From Model to Crop Species” 📅 11–12 June 2026 University of Dundee (hybrid event) We look forward to welcoming you!

Hiding in plain sight! 2.3M conserved non-coding sequences traced back 300M years across 284 plant species Ground-breaking study out in First Release @science.org from labs of @madelaineb.bsky.social, @idane.bsky.social & Zach Lippman ▶️ doi.org/10.1126/scie... ▶️ www.slcu.cam.ac.uk/news/hiding-...

BLOG - There is never a right time — how institutional support makes academic careers possible For #IWD2026, Dr Pirita Paajanen, senior scientist, reflects on the support she has received to advance her career, whilst balancing family life www.jic.ac.uk/blog/there-i... @leadersplus.bsky.social

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...

U.S. government has lost more than 10,000 STEM Ph.D.s since Trump took office

A Science analysis reveals how many were fired, retired, or quit across 14 agencies

science.org

📘 @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!

Pangenomics transforms evolutionary biology | Royal Society

This Theo Murphy meeting organised by Dr Joana Meier, Dr Henry North and Dr Charlotte Wright, will showcase cutting-edge pangenome tools, applied uses of pangenomes which are transforming health and a...

royalsociety.org

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/...

Finding balance: the dynamic interplay between H3K27me3 writers and erasers in regulating environmental plasticity and memory

Subject to an ever-changing world, plants must respond to harmful conditions and environmental fluctuations. Their evolutionary success can be attributed to their plasticity in both perceiving and in...

nph.onlinelibrary.wiley.com

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-...

q.e.d: An AI Tool for Smarter Manuscript Review

A team of researchers developed q.e.d, an AI-powered system designed to deliver rigorous and constructive feedback on scientific manuscripts in minutes.

the-scientist.com