Sign in

Curro Campuzano

@currocam.bsky.social
135 followers 347 following 3 posts

Bioinformatician. Interested in scientific computing, open source, stats and pop-gen. Doing a PhD in evolutionary ecology at UAntwerpen. Living in Brussels. He/Him currocam.github.io

PostsRepliesMedia
Reposted by Curro Campuzano
Alex Mackintosh @thymelicus.bsky.social · 19/07/2026
New preprint on the effect of ancient admixture / structure on genealogical trees. I introduce a new way of summarising reconstructed genealogies that captures a clear signal of ancient gene flow into the ancestors of modern humans. Feedback welcome!
13314
Reposted by Curro Campuzano
Madeline G. Eppley, PhD @madeline-eppley.bsky.social · 06/03/2026
New paper out in ecology letters! with @andylee.bsky.social @allydefduf.bsky.social We synthesized the active debate on how scientists define sex, including limitations and assumptions. We believe this discussion will lead to more accurate science. onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
There is No Consensus on Biological Sex
At this critical moment when misinformation about sex is being applied to policy globally, scientific clarification on the definition of biological sex is valuable. Here, we evaluate the primary appr...
317684
Reposted by Curro Campuzano
Cichlid Science 2026 @cichlidscience2026.bsky.social · 25/04/2026
🐟 CALL FOR ABSTRACTS 🐟 Abstract submission for Cichlid Science 2026 is open until May 31st - spread the word! We look forward to welcoming you to Antwerp!
1119
Reposted by Curro Campuzano
Journal of Open Source Software @joss-openjournals.bsky.social · 06/03/2026
Just published in JOSS: 'ArviZ: a modular and flexible library for exploratory analysis of Bayesian models' doi.org/10.21105/joss.09889
0132
Reposted by Curro Campuzano
John M. Drake @jdrakephd.bsky.social · 24/09/2025
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
14326
Reposted by Curro Campuzano
Evolutionary Journal of the Linnean Society @evojlinnsoc.bsky.social · 22/09/2025
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 🌍🧪👇
academic.oup.com
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
073
Reposted by Curro Campuzano
Sophie E. Hill @sophieehill.bsky.social · 08/09/2025
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... 🧵
Summary
Unfortunately, this example is not an isolated issue.

Across 9 appendix tables with 256 regression coefficients, I find:

5 cases of estimates outside their reported confidence interval
46 duplicates (i.e. estimate/CI combinations with an identical match in the same table)
At least 20 cases of asymmetric confidence intervals, which cannot be explained as rounding errors
17 values rounded to 4 decimal places (all others to 3 decimal places), indicating manual editing of tables
Over 50% of all estimates and confidence intervals are multiples of 0.008
It is difficult to diagnose exactly what is going on without access to the underlying data and code.

However, two broad conclusions can be drawn:

There are many errors and inconsistencies in the results which appear to be the result of manual editing.
There are strange patterns in the results which, if genuine, should have been noted and explained by the authors.
29430
Reposted by Curro Campuzano
Joseph W. Brown @josephwb.bsky.social · 01/09/2025
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/...
academic.oup.com
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
043
Reposted by Curro Campuzano
Johannes Köster @johanneskoester.bsky.social · 29/08/2025
#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
snakemake.github.io
Snakemake
075
Curro Campuzano @currocam.bsky.social · 23/08/2025
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)
140
Reposted by Curro Campuzano
Els De Keyzer @elsdekeyzer.bsky.social · 21/08/2025
If you like adaptive radiation and the effect of gene-flow on diversification, come have a look at my poster 03.340 at #eseb2025
071
Reposted by Curro Campuzano
James Kitchens @kitchensjn.bsky.social · 19/08/2025
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
arxiv.org
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...
26335
Reposted by Curro Campuzano
Simon Fisher @profsimonfisher.bsky.social · 07/08/2025
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. 🧪👇
cell.com
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.
720494
Reposted by Curro Campuzano
Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 14/08/2025
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 >
  ################################
  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)
1503
Reposted by Curro Campuzano
Laura Helmuth @laurahelmuth.bsky.social · 13/08/2025
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
science.org
‘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
521980664
Reposted by Curro Campuzano
Fernando Villanea @fervillanea.bsky.social · 09/07/2025
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/...
Maps of continents breaking apart does not match the order in which flightless birds speciate, which indicates they flew over water rather than walk across a mega continent.
13441166
Reposted by Curro Campuzano
Matthew Hahn @3rdreviewer.bsky.social · 28/06/2025
Cool new paper on pop gen and machine learning: www.biorxiv.org/content/10.1...
biorxiv.org
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...
04520
Reposted by Curro Campuzano
Moritz Blumer @moritzblumer.bsky.social · 19/06/2025
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).
A circular phylogeny of Malawi cichlids with inversion frequencies indicated for different taxa as rings around the tree.
22011
Reposted by Curro Campuzano
Jon Gjengset @jonhoo.eu · 30/05/2025
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
youtu.be
Explaining assembly by playing SHENZHEN I/O
YouTube video by Jon Gjengset
1224
Reposted by Curro Campuzano
Julia M. Rohrer @dingdingpeng.the100.ci · 28/05/2025
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:
1828832
Reposted by Curro Campuzano
Dr. Bethany Allen @bethanyjallen.bsky.social · 21/05/2025
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...
authors.elsevier.com
23817
Reposted by Curro Campuzano
Chase Million @millionconcepts.com · 20/05/2025
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:
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.
2157
Reposted by Curro Campuzano
Tabea Schoeler @tabeasch.bsky.social · 19/05/2025
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
shorturl.at
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...
32913
Reposted by Curro Campuzano
Jonathan Pritchard @jkpritch.bsky.social · 18/05/2025
Elegant new theory on polygenic adaptation by Will Milligan, Laura Heyward, and Guy Sella.
05326
Reposted by Curro Campuzano
Francisco Rodriguez-Sanchez @frodsan.bsky.social · 01/02/2025
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...
github.com
GitHub - Pakillo/academic-website-template-Quarto
Contribute to Pakillo/academic-website-template-Quarto development by creating an account on GitHub.
23910
Reposted by Curro Campuzano
Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 28/01/2025
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...
doi.org
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...
6478
Reposted by Curro Campuzano
Charles Mullon @charlesmullon.bsky.social · 22/01/2025
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
doi.org
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
34626
Reposted by Curro Campuzano
Lior Pachter @lpachter.bsky.social · 27/01/2025
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...
github.com
GitHub - pachterlab/fastQpick
Contribute to pachterlab/fastQpick development by creating an account on GitHub.
18225