Curro Campuzano
@currocam.bsky.social
Bioinformatician. Interested in scientific computing, open source, stats and pop-gen. Doing a PhD in evolutionary ecology at UAntwerpen. Living in Brussels. He/Him
https://currocam.github.io/
https://currocam.github.io/
Reposted by Curro Campuzano
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
Check it out: journals.plos.org/ploscompbiol...
#ScientificWriting #PLOSComputationalBiology
September 24, 2025 at 5:54 PM
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
Check it out: journals.plos.org/ploscompbiol...
#ScientificWriting #PLOSComputationalBiology
Reposted by Curro Campuzano
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 🌍🧪👇
Check out the full paper 🌍🧪👇
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
academic.oup.com
September 22, 2025 at 12:30 PM
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 🌍🧪👇
Check out the full paper 🌍🧪👇
Reposted by Curro Campuzano
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...
🧵
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...
🧵
September 8, 2025 at 1:52 AM
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...
🧵
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...
🧵
Reposted by Curro Campuzano
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/...
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
academic.oup.com
September 1, 2025 at 4:45 PM
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/...
Reposted by Curro Campuzano
#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
snakemake.github.io
August 29, 2025 at 12:54 PM
#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
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)
August 23, 2025 at 11:51 AM
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)
Reposted by Curro Campuzano
Reposted by Curro Campuzano
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
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.
🔗 arxiv.org/abs/2508.03958
1/6
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...
arxiv.org
August 19, 2025 at 2:12 PM
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
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.
🔗 arxiv.org/abs/2508.03958
1/6
Reposted by Curro Campuzano
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. 🧪👇
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.
www.cell.com
August 7, 2025 at 11:10 AM
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. 🧪👇
Reposted by Curro Campuzano
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)](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:ta2whs6wjtpljvpqgs5leu36/bafkreihx6gl7lelgtq6ztc6uwlqxyul4seruddbcrnu2oburmw7daqzx4i@jpeg)
August 14, 2025 at 6:34 AM
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 >
Reposted by Curro Campuzano
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
By @phiejacobs.bsky.social on @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
www.science.org
August 13, 2025 at 1:04 PM
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
By @phiejacobs.bsky.social on @science.org
Reposted by Curro Campuzano
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/...
www.science.org/doi/10.1126/...
July 9, 2025 at 10:34 PM
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/...
www.science.org/doi/10.1126/...
Reposted by Curro Campuzano
Reposted by Curro Campuzano
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).
Available here without a paywall: hdl.handle.net/10067/214834... (click on the ‘Full text (open access)’ link).
June 19, 2025 at 12:23 PM
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).
Available here without a paywall: hdl.handle.net/10067/214834... (click on the ‘Full text (open access)’ link).
Reposted by Curro Campuzano
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/zycRrVS3NLc
Explaining assembly by playing SHENZHEN I/O
YouTube video by Jon Gjengset
youtu.be
May 30, 2025 at 7:57 PM
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/zycRrVS3NLc
Reposted by Curro Campuzano
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:
May 28, 2025 at 5:22 PM
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:
Reposted by Curro Campuzano
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...
You can access it for free using this link:
authors.elsevier.com/a/1l7HM3QW8S...
authors.elsevier.com
May 21, 2025 at 11:06 AM
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...
You can access it for free using this link:
authors.elsevier.com/a/1l7HM3QW8S...
Reposted by Curro Campuzano
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:
This delay is caused by a bug in the compiled #Python extension.
:thread:
May 20, 2025 at 3:46 PM
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:
This delay is caused by a bug in the compiled #Python extension.
:thread:
Reposted by Curro Campuzano
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
Here, we used simulation work + longitudinal GWAS and downstream analyses to explore risks involved in cognitive/physical decline
(1/)🧵🧵
shorturl.at/99gqL
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...
shorturl.at
May 19, 2025 at 12:29 PM
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
Here, we used simulation work + longitudinal GWAS and downstream analyses to explore risks involved in cognitive/physical decline
(1/)🧵🧵
shorturl.at/99gqL
Reposted by Curro Campuzano
Elegant new theory on polygenic adaptation by Will Milligan, Laura Heyward, and Guy Sella.
When should adaptation arise from a polygenic response versus few large effect changes? https://www.biorxiv.org/content/10.1101/2025.05.15.654234v1
May 17, 2025 at 11:55 PM
Elegant new theory on polygenic adaptation by Will Milligan, Laura Heyward, and Guy Sella.
Reposted by Curro Campuzano
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...
Just modify the quarto files (basically plain markdown) and the website will update automatically
github.com/Pakillo/acad...
GitHub - Pakillo/academic-website-template-Quarto
Contribute to Pakillo/academic-website-template-Quarto development by creating an account on GitHub.
github.com
February 1, 2025 at 1:23 PM
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...
Just modify the quarto files (basically plain markdown) and the website will update automatically
github.com/Pakillo/acad...
Reposted by Curro Campuzano
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...
(1) Theory doi.org/10.1007/s112...
(2) Application doi.org/10.48550/arX...
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...
doi.org
January 28, 2025 at 3:01 PM
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...
(1) Theory doi.org/10.1007/s112...
(2) Application doi.org/10.48550/arX...
Reposted by Curro Campuzano
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/10.1093/jeb/voae136
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
doi.org
January 22, 2025 at 1:37 PM
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/10.1093/jeb/voae136
Reposted by Curro Campuzano
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 - pachterlab/fastQpick
Contribute to pachterlab/fastQpick development by creating an account on GitHub.
github.com
January 27, 2025 at 1:11 AM
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...