Marek Glombik

Super-pangenomes expand species-level pan-genomes to genus-wide frameworks, which integrate cultivated and wild genomes to capture hidden diversity. Super-pangenomes reduce reference bias, discover structural variations, rare alleles, and regulatory elements which drive stress adaptation and trait evolution. By leveraging QTL/GWAS and panomics, super-pangenomes fast-track breeding of stress-smart and high-yielding crops. This review highlights advances, challenges, and prospects, which position super-pangenomes as a “surprise package” for sustainable, food-secure agriculture.

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

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

“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

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...

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

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...

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 🧵

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.

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!

The allotetraploid lycophyte Selaginella rupincola growing among the boulders at Cochise Stronghold in the Dragoon Mountains southeast of Tucson, Arizona.

Xanthisma spinulosum growing outside a gym in Tucson, Arizona.

Selaginella arizonica X eremophila hybrid zone at Alamo Canyon in Organ Pipe National Monument.

A Dieteria sp. being visited by a skipper in the White Mountains of Arizona.

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! 🧬🌵🤖

Droplet Hi-C enables scalable, single-cell profiling of chromatin architecture in heterogeneous tissues - Nature Biotechnology Chromatin organization is measured in single cells using droplet microfluidics.

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

Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes Understanding the genetic code of cis-regulatory elements (CREs) is essential for engineering gene expression and modulating agronomic traits in crops. In plants, CREs underlying rapid evolution of ge...

🚀 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

@pavlahubalkova.bsky.social mozny tip do newsletteru jak si stoji CR

GitHub - RILAB/statements: Successful Job Applications and Grants Successful Job Applications and Grants. Contribute to RILAB/statements development by creating an account on GitHub.

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...

UK immigration costs: an international comparison of skilled worker, researcher and student visas in 2025 | Royal Society 2025 update to the Royal Society's analyses of upfront immigration costs in the UK and 17 other leading science nations.

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...

q.e.d Science Critical Thinking AI for constructive criticism and science evaluation

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...