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Marek Glombik

@glombikm.bsky.social
871 followers 519 following 7 posts

postdoc in De Vega lab, Earlham Institute, Norwich, UK. Studying polyploid crops, evolution and improvement.

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Reposted by Marek Glombik
Vikram Shivakumar @vikramshivakumar.bsky.social · 15/07/2026
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
biorxiv.org
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...
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Oxford Nanopore @nanoporetech.com · 03/07/2026
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: bit.ly/4vzj76A
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Stephen Turner @stephenturner.us · 01/07/2026
Colossal Biosciences @itiscolossal.bsky.social will publish all genomic data generated through the US FWS partnership in open-access repositories colossal.com/colossal-bio... 👏
colossal.com
Colossal Biosciences Will Make Its BioVault Endangered-Species Genomic Data Free and Public - Colossal
Colossal Biosciences BioVault open-access genomic data will be made free to researchers and conservationists worldwide, the company announced through a […]
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Marek Glombik @glombikm.bsky.social · 01/07/2026
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
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moicoll.bsky.social @moicoll.bsky.social · 30/06/2026
Interactive schedule (2.0) for SMBE2026! Enjoy the conference #SMBE2026 moicoll.github.io/SMBE2026_sch...
moicoll.github.io
SMBE 2026 — Program & Posters
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Marek Glombik @glombikm.bsky.social · 27/06/2026
Looking forward to all the great science discussions at SMBE starting tomorrow. And of course, a nice summer week in Copenhagen! ☀️
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Daniel Padfield @padpadpadpad.bsky.social · 14/05/2026
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.
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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 13/05/2026
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 🧪 🧵👇
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James Lloyd 🧬 @jamespblloyd.bsky.social · 24/04/2026
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/...
academic.oup.com
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
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James Lloyd 🧬 @jamespblloyd.bsky.social · 24/04/2026
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...
Figure from journal article with graphic showing that genes with methylation in the body have lower noise (variation in expression) than when methylation is removed.
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Plant Science Spotlight @plant-sci.bsky.social · 06/05/2026
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...
nature.com
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.
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ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 06/05/2026
#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
link.springer.com
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…
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Earlham Institute @earlhaminst.bsky.social · 05/05/2026
🆕 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
buff.ly
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.
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Matt Davis @davismw.bsky.social · 02/05/2026
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...
An image of a developing somatic embryo emerging from a cotyledon. Photo credit: Hannah McCurry
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Katharina Hoff @katharinahoff.bsky.social · 29/04/2026
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...
doi.org
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canaztekin.bsky.social @canaztekin.bsky.social · 10/04/2026
🚨 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
science.org
Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration
Why mammals cannot regenerate limbs like amphibians do presents a long-standing puzzle in biology. To uncover the underlying differences, we compared amputation responses of embryonic mouse (Mus musculus) and Xenopus laevis tadpole limbs. Lowering ...
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Marek Glombik @glombikm.bsky.social · 08/04/2026
Heartbroken to hear this news. Philippa was a wonderful and truly inspiring mentor. I really loved working with her.
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Claudia Martinho @cssmartinho.bsky.social · 26/03/2026
🌱 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
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Sainsbury Laboratory Cambridge University (SLCU) @slcuplants.bsky.social · 12/03/2026
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-...
Phylogeny of the 284 species of plants included in Conservatory data set. Conservatory uncovered ~2.3 million conserved non-coding DNA sequences across 284 plant species from 72 families including eudicots, monocots, gymnosperms, and algae. Illustrations by Professor Madelaine Bartlett.
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John Innes Centre @johninnescentre.bsky.social · 08/03/2026
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
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Ali Raza @aliraza6.bsky.social · 04/02/2026
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
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.
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Prof Mike Yearworth @mikeyearworth.bsky.social · 27/01/2026
“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...
science.org
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
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Physalia-courses@ONLINE @physaliacourses.bsky.social · 27/01/2026
📘 @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 🚀 🧵
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Vandepoele lab @vandepoelelab.bsky.social · 23/12/2025
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
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Charlotte Wright @charlottewright.bsky.social · 10/12/2025
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!
royalsociety.org
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...
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Neal Agarwal @neal.fun · 10/12/2025
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/
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Michael D. Barton @darwinsbulldog.bsky.social · 10/12/2025
Now on Bluesky: @darwin-online.bsky.social. Give 'em a follow! #HPS #histsci
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Sjon Hartman @hartman-plantlab.com · 04/12/2025
Lovely new review on H3K27me3 dynamics and potential functions in #plantscience by @drosborneplantsci.bsky.social nph.onlinelibrary.wiley.com/doi/10.1111/...
nph.onlinelibrary.wiley.com
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...
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Nick Desnoyer @nickdesnoyer.bsky.social · 01/12/2025
The hidden danger of Biorender (& the death of scientific illustration) A short thread 🧵
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Oded Rechavi @odedrechavi.bsky.social · 19/11/2025
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-...
the-scientist.com
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.
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James Davies @jojdavies.bsky.social · 05/11/2025
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.
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Joel Sharbrough @jsharbro.bsky.social · 03/11/2025
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!
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Mike Barker @barkerms.bsky.social · 24/10/2025
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! 🧬🌵🤖
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.
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Nature Biotechnology @natbiotech.nature.com · 30/10/2025
Chromatin organization is measured in single cells using droplet microfluidics go.nature.com/3NCqwO1 rdcu.be/eNah5
go.nature.com
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.
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Ksenia Krasileva @kseniakrasileva.bsky.social · 29/10/2025
🚀 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
biorxiv.org
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...
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Kentaro K. Shimizu @kkshimizu1.bsky.social · 28/10/2025
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.
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Marek Glombik @glombikm.bsky.social · 27/10/2025
Please spread the word to anyone who might be interested! #PhD available in our group
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Javier Santoyo @jsantoyo.bsky.social · 25/10/2025
Pre-phasing long reads improves structural variant genotyping. #LongReads #Sequencing #ReadsPhasing #StructuralVariants #Genotyping #Genomics #Bioinformatics academic.oup.com/bioinformati...
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Niels G. Mede @nielsmede.bsky.social · 21/10/2025
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
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 21/10/2025
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...
github.com
GitHub - RILAB/statements: Successful Job Applications and Grants
Successful Job Applications and Grants. Contribute to RILAB/statements development by creating an account on GitHub.
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The Royal Society @royalsociety.org · 21/10/2025
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...
royalsociety.org
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.
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Oded Rechavi @odedrechavi.bsky.social · 15/10/2025
Here's the link to the system, try it! qedscience.com @qedscience.bsky.social
qedscience.com
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
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Dr Radu Zabet @raduzabet.bsky.social · 14/10/2025
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.
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Stephen Turner @stephenturner.us · 25/09/2025
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...
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Rebecca R Helm @rebeccarhelm.bsky.social · 24/09/2025
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 🧵)
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ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 23/09/2025
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
erga-biodiversity.eu
Efficient evidence-based genome annotation with EviAnn
This month's ERGA BioGenome Analysis & Applications Seminar will feature a talk by speaker Aleksey V. Zimin about EviAnn (Evidence-based Annotator), a novel evidence-based eukaryotic gene annotation s...
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Stephen Turner @stephenturner.us · 16/09/2025
StackOverflow AI stackoverflow.ai
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Germán Martínez @german-martinez.bsky.social · 16/09/2025
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/...
biomedcentral.com
Call for papers - Plant epigenetic regulation
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Rayan Chikhi @rayanchikhi.bsky.social · 03/09/2025
🌎👩‍🔬 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...
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Sam Yeaman @samyeaman.bsky.social · 20/08/2025
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/...
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