Physical theory of epigenetic memory and its biological implications www.biorxiv.org/content/10.64898/2026.04...

A computational model for quantifying instability of tandem repeats across the genome www.biorxiv.org/content/10.64898/2026.04...

GitHub - bacpop/ggCaller: Bifrost graph gene caller. Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.

ggCaller v1.5.0 is out! We've removed the integrated clustering to enable users to benefit from new Panaroo features. Now, ggCaller generates GFFs that can be used with any clustering method. But for fans of an integrated ggCaller pangenome workflow read on...

github.com/bacpop/ggCal...

Genome modelling and design across all domains of life with Evo 2 www.nature.com/articles/s41...

What happens when single-author science papers become rare? 🧪

An EMBO Reports Science & Society article explores whether solo publications are being edged out by collaborative #research, and what that means​ for #creativity in #science: link.springer.com/article/10.1038/s44319-0...

Ultima Genomics Solaris 2.0: Greater Version, Smaller Beads, Lose A Box

🧬💻

#AGBTGM26

omicsomics.blogspot.com/2026/03/ulti...

New paper showing that bacteria with more genes for cooperation can live in a broader range of habitats and that genes for cooperation are more more likely to be in the accessory genome www.pnas.org/doi/10.1073/... @lauriebelch.bsky.social

Cool mouse model showing how the gut microbiome is so personalized! A healthy microbiome is NOT one size fits all. Bugs and host are likely co-adapting as we age.

Large-scale online deanonymization with LLMs arxiv.org/abs/2602.16800

Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠

We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵

The visualization of two bacterial genomes, of 50 and 52kb, representing independent instances of extreme genomic reduction in ancient heritable endosymbionts of planthoppers.

Our new paper in @natcomms.nature.com is now online-early!

We describe independent evolution of bacterial genomes of only ~50–52 kb — the smallest known outside cellular organelles — revealing striking convergence toward minimal gene sets.

🔗 doi.org/10.1038/s414...

The "Why Not?" Era of Sequencing Has Begun YouTube video by OMGenomics

We just released a video from our visit to @plasmidsaurus.bsky.social, where we spoke with Mark Budde and team: www.youtube.com/watch?v=nS2o...

Highlights include:
✅ 3D printed magnetic bead contraptions
✅ When sequencing more is easier than sequencing less
✅ Bread machine analogies

Sunrise on Sunday. Today in Chicago.

The Morning Lights. Twilight before sunrise in Chicago on Thursday.

Free deep learning book with ipython notebooks udlbook.github.io/udlbook/

The geometry of cooperation: decoding microbial interactions www.biorxiv.org/content/10.64898/2025.12...

Ep 2: Evolution of Biotech with Keith Robison Lab automation, small molecules, life at Gingko Bioworks, and more

I had fun being interviewed on this podcast

www.legible.bio/p/ep-2-evolu...

CompBio and MIRaS : A Multi-omic Analysis Platform Built on a Memory-Based Intelligence Engine www.biorxiv.org/content/10.64898/2025.12...

We Got Claude to Fine-Tune an Open Source LLM We’re on a journey to advance and democratize artificial intelligence through open source and open science.

hf claude code skills allow you to fine-tune an LLM in natural language. E.g.: "Fine-tune Qwen3-0.6B on the dataset open-r1/codeforces-cots" and it'll validate datasets, choose GPU types, kick off HF Jobs, monitor progress, and publish checkpoints/models
huggingface.co/blog/hf-skil...

Excited to share our final accepted version of the CiFi method out today: www.nature.com/articles/s41...

A genetic platform for a biocementation bacterium Sporosarcina pasteurii is the most widely studied bacterium for microbially-induced calcium carbonate precipitation (MICP), a process of intense interest for materials and construction applications. D...

The #1 organism used to make biocement has never been engineered... until now! Excited to share our work on Sporosarcina pasteurii! Esp. since it's the first project I've contributed to here at Cultivarium :)

www.biorxiv.org/content/10.6...

Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru

🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and
@titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?

doi.org/10.1093/narg...

GlobDB: a comprehensive species-dereplicated microbial genome resource AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...

The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes academic.oup.com/nar/advance-... #jcampubs

What Rosalind Franklin truly contributed to the discovery of DNA’s structure Franklin was no victim in how the DNA double helix was solved. An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player.

Getting Rosalind Franklin’s story right is crucial, because she has become a role model for women going into science

www.nature.com/articles/d41...

🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...

Tracking community change via network coherence www.biorxiv.org/content/10.1101/2025.11....

Nineteen - musings on shrinking the number of amino acids in a proteome

🧬🖥️

omicsomics.blogspot.com/2025/11/nine...

Wednesday's WOW! This morning's spectacular panorama sunrise over Chicago.

Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes Abstract. The classification of living systems presents significant challenges due to the prevalence of gene transfer between genomes. Traditional taxonomi

I've often wondered about what we should call organisms whose similarity might be due to acquired genetic material. It got a little complicated, but I made a stab at it here

Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...