Join our department (GEE) as a fellow - Research Career Development Fellowships Program Call: tinyurl.com/2sfpyhsz

GEE invites #ECRs who wish to be sponsored to apply for external fellowships to establish an independent research group. @ucllifesciences.bsky.social

More info: tinyurl.com/mtwhwzjj

New preprint led by Hrushikesh Loya, me, and Simon Myers where we introduce GhostBuster! www.biorxiv.org/content/10.6...

The idea is to find all the different ways a target individual relates to reference groups in genealogies, to "bust the ghosts" in our ancestry.

Wrote a fun little thing on gene tree discordance:

authors.elsevier.com/a/1mzPI3QW8S...

Antimicrobial effectors of plant-associated fungi: multipurpose proteins with fast-evolving surfaces and structurally conserved cores Plants are exposed to a variety of devastating pathogens, causing significant yearly yield losses. In order to facilitate infections, plant pathogens …

So diverse and yet conserved. Check out opinion paper by Leonhard Pachinger @leopach.bsky.social on antimicrobial effectors produced by fungal pathogens: www.sciencedirect.com/science/arti...

Genome–host association mapping reveals wheat pathogen genes involved in host specialization - Nature Plants This study introduces genome–host association (GHA), leveraging natural epidemics to map the genetic landscape of host adaptation in the pathogen Zymoseptoria tritici. Applied to 832 wheat fungal stra...

Thrilled to share our paper now out in Nature Plants 🎉
We developed a genome-host association (GHA) approach to study pathogen adaptation directly from field metadata by using the originating host cultivar as phenotype.

www.nature.com/articles/s41...

TSL Alumnus wins Biochemical Society Award FIRST PUBLISHED: 14.04.26 | THE SAINSBURY LABORATORY

I just published: TSL Alumnus wins Biochemical Society Award

Mauricio Contreras has been recognised as an exceptional Early Career Researcher by the Biochemical Society.

#CelebratingAlumni

medium.com/p/tsl-alumnu...

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - Nature Biotechnology FAMSA2 accurately aligns millions of protein sequences at high speed.

10 years after the first FAMSA paper, its successor is now published in Nat Biotech! We believe that FAMSA2 can enable analyses of large protein collections that were previously unattainable. Thank you, Andrzej and Cedric, for great collaboration
www.nature.com/articles/s41...

Award announcement for Dr. Mauricio P. Contreras from University of Tübingen, Germany, receiving the Early Career Research Award at The Biochemical Society 2027 Awards.

As an emerging leader in plant innate immunity, we're thrilled to present Mauricio Contreras with a 2027 Early Career Research Award! Alongside advocating for Open Science and preprint review, Mauricio's "activation-and-release" and "NLR resurrection" models are already referenced worldwide.

GALBA2 walks into the arena. We rewrote our protein-based genome annotation pipeline in Snakemake.

Give it a genome + proteins from close relatives → get gene predictions. No RNA-Seq, no GeneMark needed.

miniprot → AUGUSTUS, fully containerised, HPC-ready.

github.com/Gaius-Augustus/GALBA2

Publish and Perish: How AI-Accelerated Writing Without Proportional Verification Investment Degrades Scientific Knowledge Artificial intelligence tools are accelerating manuscript production far faster than peer review capacity can expand. Applying the theory of constraints from manufacturing science, we formalize this a...

Interesting piece claiming that the asymmetry between writing acceleration and review acceleration is breaking science. Essentially Brandolini’s law (The amount of energy needed to refute bs is an order of magnitude bigger than that needed to produce it) applied to science publishing >

Preprint alert 🚨 (1/10) 🧵

𝘈𝘶𝘵𝘰𝘱𝘩𝘢𝘨𝘺 𝘪𝘴 𝘢 𝘱𝘢𝘳𝘢𝘥𝘰𝘹 𝘪𝘯 𝘱𝘭𝘢𝘯𝘵 𝘪𝘮𝘮𝘶𝘯𝘪𝘵𝘺:
It can promote resistance, susceptibility, or restrict cell death 🤯

So what is its actual role?

We show it acts as a spatial organizer of immunity across cell types 🌱🦠 #proteostasis

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

Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management Abstract. Microbiomes are increasingly recognized as key to addressing global challenges in health and sustainability, as they can provide emergent biologi

A new paper led by Hiro Toju was published in the ISME Journal @isme-microbes.bsky.social! "Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management" doi.org/10.1093/isme...

Great to see this paper in its final published form!

www.pnas.org/doi/10.1073/...

Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and…

#ERGAReads | Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model 🧬
www.nature.com/articles/s41...
#GenomeAnnotation #Helixer @natmethods.nature.com

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity...

Out now in @newphyt.bsky.social with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social & more! Our high-quality pennycress pangenome is a striking example of genome architecture shaping different kinds of genomic variation, including some surprising centromeric movement

Giorgio Bianchini et al., CC BY 4.0, https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msag097/8650899

Bianchini et al. (2026-04, Molecular Biology and Evolution) (open access)
AliFilter: a Machine Learning Approach to Alignment Filtering
academic.oup.com/mbe/advance-...

Phylogenomic mixture models outperform homogeneous and partitioned models Abstract. Significant advances have been made in resolving the tree of life, but many nodes remain debated. The last two decades saw the emergence of mixtu

From Pisani et al: CAT-GTR is one of the most flexible models in the phylogenomic arsenal.

Phylogenomic mixture models outperform homogeneous and partitioned models

academic.oup.com/mbe/advance-...

Introgression and parental conflict shape repeated occurrences of postzygotic isolation in Mimulus Postzygotic reproductive isolation is often thought to accumulate as a byproduct of neutral divergence. Yet it frequently evolves rapidly, in line wit…

I am SO THRILLED to share our first fully-lab lab paper!!!!!! Led by @hybridzones.bsky.social & @hagarsoliman.bsky.social, w/ a major assist from @pfschwarz.bsky.social!!!!!!!!!!!!! Read more below, if you're curious (you should be- it's AWESOME!!!!!!!)

link: www.sciencedirect.com/science/arti...

7/ One pipeline. To annotate - maybe not all - but many!

1/ BRAKER4 hatched!
The Earth BioGenome Project is on track to sequence ~1.5M eukaryotic species. Every one needs a structural annotation. No Perl monolith was going to survive that. So we rewrote BRAKER from the ground up. github.com/Gaius-August...

Whoa—machine learning strikes again (in a good way)

www.pnas.org/doi/10.1073/...

Coalescent analysis of T2T genomes finds a shared effective population size peak ~3-6 Mya in humans, chimps, and bonobos, but not gorillas or orangutans, suggesting complex, structured speciation at the Homo-Pan split.

www.biorxiv.org/content/10.1101/2024.10....

Welp, didn't realize transparent backgrounds became black when I posted the logo 😅
bsky.app/profile/jlst...

Transposable elements hitchhike on Starships across fungal genomes - Nature Communications Large mobile genetic elements known as Starships act as vehicles for transferring transposable elements (TEs) between fungi. Here, Griem-Krey et al. show that these ‘hitchhiking’ TEs can drive rapid e...

Now out!
We show that TEs can be horizontally transferred between fungal species via Starships. Once transferred, these TEs can become active, changing the genome organization and affecting the lifestyle of the recipient fungus.
www.nature.com/articles/s41...
@oggenfussursula.bsky.social #TEsky

Leaf morphology of Hordeum erectifolium, cultivated (Morex) and wild barley.

A chromosome-scale genome assembly of Hordeum erectifolium: genomic, transcriptomic and anatomical adaptations to drought in a wild barley relative

Haraldsson et al. @plantgen-hhu.bsky.social

nph.onlinelibrary.wiley.com/doi/10.1111/...

Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio Aguilar-Gómez et al. use exome sequencing of 347 strawberry poison frogs to uncover the genetic basis of color variation. They identify that kit, ttc39b, and bco1 underlie blue-red, yellow-red, and gr...

The last chapter of my PhD is finally out !!!! In the same species, on neighboring islands, we see radically different warning colors emerge. Evolution in action:
Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio: Current Biology www.cell.com/current-biol...

It’s time to say farewell to ERC Research Group Leader Thorsten Langner after nearly 3 years at the institute. He reflects on his time here, key milestones, and what’s next: tinyurl.com/2vce2d6k
Congratulations on your new position—we wish you and your team all the best for the future!

Plant cell surface receptors Plant cell surface receptors have evolved to perceive peptides, proteins, glycans, lipids, and small molecules through diverse ectodomains, integrating these inputs into distinct physiological output....

Cell-surface receptors play key roles across many biological processes.
In plants, these receptor families have undergone remarkable expansion. Here, we systematically review these receptors in
@theplantjournal.bsky.social

Happy to see this out!
onlinelibrary.wiley.com/doi/10.1111/...

FERONIA Kinase-Interacting Cell Wall Sensors LRX1/2 Regulate the Plant Rhizosphere Microbiome | Molecular Plant-Microbe Interactions® Plants establish beneficial associations with microbiota, enhancing their resilience to environmental challenges. FERONIA (FER) kinase shapes the microbiome; despite extensive knowledge of FER interac...

Also sharing our recent work on LRX-mediated plant–microbiome interactions.
A big thank you to all Haney lab members for making this possible🙌

doi.org/10.1094/MPMI...

Statistical Rethinking 2026 is done: 20 new lectures emphasizing logical and critical statistical workflow, from basics of probability theory to causal inference to reliable computation to sensitivity. It's all free, made just for you. Lecture list and links: github.com/rmcelreath/s...