Curro Campuzano

Just published in JOSS: 'ArviZ: a modular and flexible library for exploratory analysis of Bayesian models' https://doi.org/10.21105/joss.09889

Newly expanded version of my guide to scientific writing -- known as the “15 steps” -- published in PLOS Computational Biology. Special thanks to Éric Marty for creating a fantastic visualization.

Check it out: journals.plos.org/ploscompbiol...

#ScientificWriting #PLOSComputationalBiology

Ecological speciation in sympatric palms: 5. Evidence for pleiotropic speciation genes using gene knockout and high-throughput phenotyping Abstract. Theoretical models predict that sympatric, ecological speciation may be facilitated more readily when so-called ‘magic traits’ are present, linki

Magic traits may assist sympatric #Ecological speciation, but few examples exist & evidence for their role is rare. Yet, this study found #pleiotropy affected soil preference & flowering time in #Hawea, consistent with speciation!

Check out the full paper 🌍🧪👇

Blog post: github.com/sophieehill/...

TL;DR: There are a LOT of errors/inconsistencies in the results reported in this paper (estimates outside CIs, sign errors, duplicates, asymmetric CIs). Even in the abstract itself!

This suggests manual editing of results tables.

Which is not good...

🧵

Infinite Mixture Models for Improved Modeling of Across-Site Evolutionary Variation Abstract. Scientific studies in many areas of biology routinely employ evolutionary analyses based on inference of phylogenetic trees from molecular sequen

Infinite Mixture Models for Improved Modeling of Across-Site Evolutionary Variation by Mandev Gill, @guybaele.bsky.social, @msuchard.bsky.social, and @lemeylab.bsky.social academic.oup.com/mbe/article/...

#Snakemake 9.10 has been released. The major change is that it now supports scheduling plugins. By that your scheduling algorithm research becomes immediately usable with thousands of workflows by thousands of users. snakemake.github.io

We can (and should) do better by incorporating biological knowledge about species invasions and recent advances in population genetics in our models. If you want to see the poster (or try it out), contact me and check it out! (2/2)

currocam.github.io/eseb_barcelo...

Thank you everyone who came to my poster at #ESEB2025 to hear about inferring (very) recent Ne under invasion scenarios using LD data in a coalescent framework with a Bayesian flavor. (1/2)

If you like adaptive radiation and the effect of gene-flow on diversification, come have a look at my poster 03.340 at #eseb2025

tskit_arg_visualizer: interactive plotting of ancestral recombination graphs Summary: Ancestral recombination graphs (ARGs) are a complete representation of the genetic relationships between recombining lineages and are of central importance in population genetics. Recent brea...

Excited to share our new preprint for the tskit_arg_visualizer Python package! ARGs can sometimes feel like a black box, so
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.

🔗 arxiv.org/abs/2508.03958

1/6

Notes from Beethoven’s genome Wesseldijk et al. compare the genomic information collected from Ludwig van Beethoven with population-based datasets used to quantify musical achievement.

If someone you know buys into claims about "genetic optimization" of embryos using polygenic scores of cognition, just send them our 2024 paper on Beethoven & musicality. We wrote it to help communicate limits of individual-level genetic predictions & complexity of links between DNA & behaviour. 🧪👇

################################ probdata[which(probdata == 0)] <- 0.001 # small but not 0 if (length(which(is.na(probdata))) != 0) { stop("NAs in probdata matrix!!!") } L <- (-1) * sum(log(probdata), na.rm = T)

Rounding to zero is often a problem in machine learning, which is why we do computations on log scale and use various composition functions. This below (from materials in a paper I am reading) is not how to do it. If you are getting zeros in your prob vector, back up and do the calculations right >

‘Sex reversal’ is surprisingly common in birds, new study suggests Survey of five Australian avians finds numerous discordant individuals, including a genetically male bird that had laid an egg

Sex-reversal in birds (genetically male/female but appear female/male) is surprisingly common. Best detail: A genetically male bird called a laughing kookaburra had recently laid an egg. (1/2)

By @phiejacobs.bsky.social on @science.org

This is a good time to remember that Moas, Emus, and the other ratites diverged so long ago, they FLEW to different continents, and then lost the ability to fly and became giants independently. You can't just sprinkle a few variants to make one into the other.

www.science.org/doi/10.1126/...

Coalescence and Translation: A Language Model for Population Genetics Probabilistic models such as the sequentially Markovian coalescent (SMC) have long provided a powerful framework for population genetic inference, enabling reconstruction of demographic history and an...

Cool new paper on pop gen and machine learning:

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

A circular phylogeny of Malawi cichlids with inversion frequencies indicated for different taxa as rings around the tree.

Check out our new paper about chromosomal inversions in Malawi cichlids! 🐟🧬

Available here without a paywall: hdl.handle.net/10067/214834... (click on the ‘Full text (open access)’ link).

Explaining assembly by playing SHENZHEN I/O YouTube video by Jon Gjengset

SHENZHEN I/O stream where I try to teach some assembly by playing an assembly-inspired game is now up! This is very much an experiment, so please let me know if this format was still entertaining + educational :)

youtu.be/zycRrVS3NLc

Fitting a generalized mixed model with a gamma distribution log link and random slopes to reaction time data to arrive at precisely the same point estimate as the authors did by simply averaging and conducting a t-test:

I wrote a Dispatch for Current Biology on the neat new paper by @princessquatris.bsky.social et al., highlighting why occupancy modelling is an exciting tool for understanding sampling bias in palaeontology 🦕
You can access it for free using this link:
authors.elsevier.com/a/1l7HM3QW8S...

A code block labeled "A Common Bug (in compiled extension modules)." The code shows an attempt to exit a calculation of a large array of random numbers, and then indicates that a Ctrl+C interrupt takes 3.5 seconds to return, rather than returning immediately as is probably the desired and expected behavior.

Have you ever started a Python process, realized that you made a mistake, immediately hit Ctrl+C to interrupt it and then waited a surprisingly long time to get the command line back?

This delay is caused by a bug in the compiled #Python extension.

:thread:

Combining cross-sectional and longitudinal genomic approaches to identify determinants of cognitive and physical decline - Nature Communications Large-scale genomic studies focusing on the genetic contribution to human aging have mostly relied on cross-sectional data. With the release of longitudinally curated aging phenotypes by the UK Bioban...

Happy to share our new study on genetic & environmental contributors to age-related decline in ~100K UK Biobank participants!

Here, we used simulation work + longitudinal GWAS and downstream analyses to explore risks involved in cognitive/physical decline
(1/)🧵🧵

shorturl.at/99gqL

Elegant new theory on polygenic adaptation by Will Milligan, Laura Heyward, and Guy Sella.

GitHub - Pakillo/academic-website-template-Quarto Contribute to Pakillo/academic-website-template-Quarto development by creating an account on GitHub.

Here's a template to make an academic website using #Quarto_pub hosted for free on GitHub

Just modify the quarto files (basically plain markdown) and the website will update automatically

github.com/Pakillo/acad...

Hilbert space methods for reduced-rank Gaussian process regression - Statistics and Computing This paper proposes a novel scheme for reduced-rank Gaussian process regression. The method is based on an approximate series expansion of the covariance function in terms of an eigenfunction expansio...

A colleague today asked about Gaussian Processes on a sphere. Like spatial autocorrelation on the globe. I asked @avehtari.bsky.social. There are papers! This problem common enough to be worth having a case study I think?
(1) Theory doi.org/10.1007/s112...
(2) Application doi.org/10.48550/arX...

The joint evolution of separate sexes and sexual dimorphism Abstract. Dioecious plants are frequently sexually dimorphic. Such dimorphism, which reflects responses to selection acting in opposite directions for male

1/7 Very happy to share our latest paper on the joint evolution of separate sexes and sexual dimorphism in @jevbio.bsky.social, led by @thomaslesaffre.bsky.social and in collaboration with John Pannell at @dee-unil.bsky.social

🔗 doi.org/10.1093/jeb/voae136

GitHub - pachterlab/fastQpick Contribute to pachterlab/fastQpick development by creating an account on GitHub.

If you need to sample reads (with or without replacement) from FASTQ files you may find the fastQpick utility by Joseph Rich super useful: github.com/pachterlab/f...