Fibo

<sigh>

One reviewer used AI to review our manuscript.

How do we know?

Suggested papers to cite that do not exist. Some titles correct, but everything else is wrong or just fabricated out of whole cloth.

Requested citations for things I’ve said in review papers that were citing other papers.

New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/
www.biorxiv.org/content/10.6...

What do you mean that the goal is to my conclusions be proven false in the future?

Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating).

A brief 🧵 (carried over from the old place)

Paralog interference contributes to the preservation of genetic redundancy Duplicated self-interacting proteins can interact and interfere with each other’s function. Cisneros, Mattenberger, et al. show that selection against interfering loss-of-function alleles extends the ...

New paper alert: Paralog interference contributes to the preservation of genetic redundancy www.cell.com/current-biol...

Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs - Nature Structural & Molecular Biology METALoci, a new three-dimensional genome computational tool, reveals a major rewiring of regulatory interactions during sex determination. By combining this method with transgenic models, the authors ...

🔊💥 How is sex determined? How is it encoded in the #3Dgenome?

Read all about it in our last paper!
www.nature.com/articles/s41...

It’s been looong but feels satisfying to see this finally out.

(With CapelLab, @dariloops.bsky.social Lab and @mamartirenom.bsky.social Lab)

🧵👇

So excited to share this manuscript led by the inimitable Cara Brand, who discovered that Topoisomerase II evolution causes hybrid female lethality in Drosophila.

Congrats to Cara, @nickbr0wn.bsky.social, Anirban, and
@buszczaklab.bsky.social!

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

Ancestry and somatic profile indicate acral melanoma origin and prognosis - Nature Analysis of the somatic and transcriptomic profile of 123 acral melanoma samples from Mexican patients helps understand tumour origins and prognosis, and highlights the importance of including samples...

We are very happy to see our study finally appear online @nature.com! This has been work of nearly 10 years in collaboration with the National Institute of Genome Medicine 🇲🇽, the National Cancer Institute 🇲🇽, the @sangerinstitute.bsky.social and others ⬇️

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

Rodrigo Pérez Ortega, On the Rewards of Reporting Between Two Worlds “Editors were hungry for these stories from the Global South,” said the biomedical researcher-turned-science journalist, who has found a niche filling that gap.

"I hope I’ve been successful at building bridges, trying to blur the line between science journalism in the U.S. and Latin America." Thanks to Laura for this great Q&A, in which share a bit of my particular views on doing science journalism between two worlds. ksj.mit.edu/news/2026/02...

I had a similar experience. It still fails to challenge any biases even if needed, one had to pivot directly. It was particularly good at explaining similarities and differences in concepts and processes.

Job alert! Assistant professor position in the Department of Molecular Genetics (University of Toronto). Amazing department and city. jobs.utoronto.ca/job/Toronto-... Please share.

Are you an early-stage graduate student (2nd or 3rd year) or early-stage postdoc based in the US or Canada, working primarily in Drosophila? Would you like to help improve the experience of all trainees working in Drosophila research? If so, read on.

(Please repost to reach a broad audience.)

Lethal epistasis maintains strong linkage disequilibrium between unlinked supergenes https://www.biorxiv.org/content/10.64898/2026.01.08.698410v1

A dark stain on a bow with the shape on some sort of embryo. You can see a head, the trunk, limb buds

This is the equivalent of Jesus on a toast for developmental biologists 🧪

reconcILS: A gene tree-species tree reconciliation algorithm that allows for incomplete lineage sorting Reconciliation algorithms infer the evolutionary history of individual gene trees given a species tree. Many reconciliation algorithms consider only duplication and loss events (and sometimes horizont...

While our updated paper is fast approaching book-length, the results remain the same: our method (reconcILS) is still highly accurate.

So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!

www.biorxiv.org/content/10.1...

New preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life

I saw Arya's work on GRC last June. This is really exciting. Congratulations!

Looking to start your lab in generative biology / AI?
Come join us at the @sangerinstitute.bsky.social
Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways!
pls RT
tinyurl.com/GenGenFaculty

I am very excited to announce that a fully funded PhD position is available in my group.

Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia

Please RT or forward this information to interested candidates.

Deadline: 11.01.26

More info:

shorturl.at/f1TuF

Postdoctoral Researcher in Theoretical Evolutionary Biology Postdoctoral Researcher in Theoretical Evolutionary Biology

📢 I'm hiring! 3-year postdoc in theoretical evolutionary ecology at University of Helsinki 🇫🇮 Apply: jobs.helsinki.fi/job/Helsinki-Postdoctoral-Researcher-in-Theoretical-Evolutionary-Biology/1348955157/
#AcademicJobs #Postdoc #EvolutionaryEcology #TheoreticalEcology #ScienceJobs #AcademicChatter

de cuyo nombre no quiero acordarme.

The 2025 Headline of the Year Nominees

🧵

What sets the mutation rate of a cell type in an animal species? Germline mutation rates per generation are strikingly similar across animals, despite vast differences in life histories. Analogously, in at least one somatic cell type, mutation rates at the end of l...

Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social,
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n

Any time you come to Chi, let me know.

Congratulations Dr. Killian Campbell! It's awesome you are going to @annaselmecki.bsky.social's lab. Cheers!

Context Widows or, of GPUs, LPUs, and Goal Displacement

Absolutely essential piece by @kevinbaker.bsky.social critiquing AI automation of science by pulling back the curtain on what modern science actually is. LLMs already replicate and accelerate its irrational bureaucratic structure.

Learned today that “Galápagos” comes from a Spanish word for tortoise, meaning that “Galápagos Tortoise” is,

in fact,

a tortology

Have you had a reaction of the class yet? I am curious to hear what they thought of it.

Causal modelling of gene effects from regulators to programs to traits - Nature Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.

Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:

1/2 🚨New paper

In a collab b/w my group + @nathangrubaugh.bsky.social, led by a fabulous doctoral student, we synthesize the data on epistasis across several viral pathogen systems (e.g., influenza, HIV, SARS-CoV-2, tobacco etch virus, etc).

academic.oup.com/ve/article/1...