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Marek Glombik

@glombikm.bsky.social

600 followers 450 following 2 posts

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

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Marek Glombik @glombikm.bsky.social · May 29

Happy to share that our study of inheritance of homoeolog expression bias in wheat biparental populations is out in @biomedcentral.bsky.social Genome Biology! 🧬

Many thanks to all co-authors and @philippaborrill.bsky.social for great leadership on the project!
#PlantScience #Botany

rdcu.be/eokf2

Rapid reprogramming and stabilization of homoeolog expression bias in hexaploid wheat biparental populations

rdcu.be

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Reposted by Marek Glombik

Stephen Turner @stephenturner.us · 14d

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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Reposted by Marek Glombik

Rebecca R Helm @rebeccarhelm.bsky.social · 14d

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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Reposted by Marek Glombik

ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 16d

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

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Stephen Turner @stephenturner.us · 22d

StackOverflow AI stackoverflow.ai

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Reposted by Marek Glombik

Germán Martínez @german-martinez.bsky.social · 22d

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/...

Call for papers - Plant epigenetic regulation

www.biomedcentral.com

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Reposted by Marek Glombik

Rayan Chikhi @rayanchikhi.bsky.social · Sep 3

🌎👩‍🔬 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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Reposted by Marek Glombik

Sam Yeaman @samyeaman.bsky.social · Aug 20

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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Axel Visel @axelvisel.bsky.social · Aug 21

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

Graphic announcing a Computational Postdoctoral Fellow position. Text: Computational Postdoctoral Fellow – Plant Genomic Language Models (gLMs). JGI is seeking a Computational Postdoctoral Fellow to join a funded project at Berkeley Lab’s Joint Genome Institute applying genomic language models (gLMs) to unlock new biological insights in plants. Join one of the world’s leading genomics facilities to pioneer AI applications in plant biology, with access to cutting-edge computational resources and diverse genomic datasets. This project will focus on developing and exploring applications of gLMs to plant genomes, from identifying novel regulatory elements to revealing evolutionary patterns across species, with particular interest in cross-species and data-limited scenarios. In this role, you will design tasks and datasets to test and extend gLM capabilities, apply models to generate new biological hypotheses, and share findings through high-impact publications and presentations.

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K.D. Murray @kdm9.bsky.social · Aug 14

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

Pangenomic context reveals the extent of intraspecific plant NLR evolution

Individual- and population-level diversity is required for pathogen defense by nucleotide-binding site leucine-rich repeat (NLR) proteins. Teasdale et al. leverage annotated, divergent A. thaliana gen...

www.cell.com

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Reposted by Marek Glombik

Stephen Turner @stephenturner.us · Aug 14

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

Vibeoinformatics... computational vibeology... 🧬🖥️🧪

Prompt-based bioinformatics: a new interface for multi-omics analysis - Nature Reviews Genetics

Prompt-based methods, which involve the careful design of inputs to guide large language model (LLM) outputs, are beginning to reshape bioinformatic analytical workflows. The authors compare prompt-dr...

www.nature.com

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Albert Vilella, PhD. @albertvilella.bsky.social · Aug 11

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

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Brooke Fitzwater, PhD (she/her) 🐟🪱🏳️‍🌈♾️ @oceanfilly.bsky.social · Aug 7

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

Watercolor illustration of male and hermaphrodite rivulus fish

Watercolor illustration of a sea otter in kelp

Pen and colored pencil illustration of a green sea turtle

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Reposted by Marek Glombik

Javier Santoyo @jsantoyo.bsky.social · Aug 6

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

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Vandepoele lab @vandepoelelab.bsky.social · Jul 16

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

Jobs | Vandepoele Lab

www.vandepoelelab.be

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Facundo Romani @fromani.bsky.social · Jul 21

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...

Conservation of chromatin states and their association with transcription factors in land plants

The complexity of varied modifications of chromatin composition is integrated in archetypal combinations called chromatin states that predict the local potential for transcription. The degree of conse...

www.biorxiv.org

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Brooke Fitzwater, PhD (she/her) 🐟🪱🏳️‍🌈♾️ @oceanfilly.bsky.social · Jul 17

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

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Dan Sloan @sloanevolab.bsky.social · Jul 14

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...

Sloan Lab

Welcome! Our research focuses on the evolutionary process at the molecular level. In particular, we investigate how a mixture of natural selection and non-adaptive forces create and maintain the amazi...

sites.google.com

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Mary Williams @PlantTeaching @plantteaching.bsky.social · Jul 14

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...

July 17: Plant Physiology panel discussion on Numeracy, Realism, and Relevance in Plant Science | Plant Science Today

Plant Physiology webinar Numeracy, Realism, and Relevance in Plant Science When: Thursday July 17, 2025 at Noon UTC | 8 AM EDT | 1 PM UK | 3 PM Israel | 10 PM Brisbane, Australia About this panel…

blog.aspb.org

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The Sainsbury Laboratory @thesainsburylab.bsky.social · Jul 9

📣 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🔬🧬🌿🦠💻

graphic with text stating Accessible Science with the Norwich Bioscience Institutes. Logos from Earlham, John Innes Centre, Quadram and TSL

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Journal of Experimental Botany @jxbotany.bsky.social · Jul 4

🌾🧬 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 🧪

Fig. 1. (short legend see paper for full description): Null met1-1 mutants cannot be produced by crossing TILLING lines with disruptions in the three MET1-1 homoeologues. (A) Evolutionary relationships between MET1 homologues in Arabidopsis (AtMET1), rice (OsMET1a and OsMET1b), and wheat (homoeologue groups TaMET1-1, TaMET1-2, and TaMET1-3). (B) Crossing schematic showing the generation of the hexaploid MET1-1 populations: the C0465×C0884 population (top) and the C0451×C2028×C1292 population (bottom). (C) Structure of the three MET1-1 homoeologues. Filled rectangles represent exons, open rectangles represent untranslated regions, and lines represent introns. Triangles indicate the positions of the premature termination codon mutations in the TILLING lines used to produce the two hexaploid F2 populations (C0465×C0884, orange; C0451×C2028×C1292, purple). The green box signifies the Bromo adjacent homology domain (BAH) and the blue box signifies the C-5 cytosine methyltransferase domain.

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RepeatMasker Project @repeatmasker.bsky.social · Jul 1

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

RepeatMasker Home Page

www.repeatmasker.org

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Earlham Institute @earlhaminst.bsky.social · Jun 26

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

John Innes Foundation Internship in Plant Science

buff.ly

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Ian Henderson @hendersi.bsky.social · Jun 26

deepmind.google/discover/blo...

AlphaGenome: AI for better understanding the genome

Introducing a new, unifying DNA sequence model that advances regulatory variant-effect prediction and promises to shed new light on genome function — now available via API.

deepmind.google

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Uriel Menalled @urielmenalled.bsky.social · Jun 23

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

#statistics #STEM

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Reposted by Marek Glombik

Vikram Shivakumar @vikramshivakumar.bsky.social · Jan 6

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.

Mumemto: efficient maximal matching across pangenomes

Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts ...

www.biorxiv.org

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