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ruiborges23.bsky.social
Rui Borges
@ruiborges23.bsky.social
460 followers 810 following 33 posts
Lecturer in Statistics at the University of St Andrews. Interested in statistical/computational population genetics and phylogenetics. Math enthusiast. He/him. 🇵🇹🇱🇻🇬🇧 https://mrborges23.github.io/mypage/
mrborges23.github.io
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ruiborges23.bsky.social
Rui Borges @ruiborges23.bsky.social · Nov 13
Hi Bluesky! New here and excited to connect with others, especially fellow scientists! I'm a lecturer in Statistics at the University of St Andrews and my research involves merging mathematical models with statistical methods to tackle evolutionary questions.
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ruiborges23.bsky.social
Rui Borges @ruiborges23.bsky.social · Aug 31
If only I wee a candle in the dark.
ruiborges23.bsky.social
Rui Borges @ruiborges23.bsky.social · Aug 22
Glad to share my work on phylogenetic inference for wee, tiny organisms (or highly diverse): the infered topologies seem largely unaffected by unaccounted recurrent mutations, but branch lengths, and mutation-selection usage biases, are significantly impacted.
#eseb #eseb2025
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Rui Borges @ruiborges23.bsky.social · Aug 20
@janekay27.bsky.social presenting her work on merging time scales of evolution to infer adaptive evolution. Great talk! #eseb #fwf
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Rui Borges @ruiborges23.bsky.social · Aug 7
This might sound naive, but I once genuinely believed that the European Union stood firmly for freedom, the rule of law, and human rights.
newseye.bsky.social
News Eye @newseye.bsky.social · Aug 4
This is amongst the most impactful two minutes of broadcasting I’ve ever seen.

By Emma Murphy, International Editor, ITV News. #Gaza
ruiborges23.bsky.social
Rui Borges @ruiborges23.bsky.social · Jul 8
The students absolutely nailed it, and I was genuinely surprised by how financially literate they were in interpreting the simulation results. People often forget how mathematics can be a tremendous help in making better, more informed decisions in everyday life!
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Rui Borges @ruiborges23.bsky.social · Jul 8
In our session today, we wrapped up the activity by simulating the Gambler’s Ruin in R, using a popular scratchcard game as the example. The game costs £5 per card and has a win probability of roughly 1 in 3.3. One of the photos shows one of these simulations.
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ruiborges23.bsky.social
Rui Borges @ruiborges23.bsky.social · Jul 8
I love engaging in outreach activities with math-enthusiastic students, and I always take the opportunity to introduce them to stochastic processes. One process I particularly enjoy teaching is the Gambler’s Ruin.

@uniofstandrews.bsky.social
#standrews #smmb #statistics #maths
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Reposted by Rui Borges
sandra-oliveira.bsky.social
Sandra Oliveira @sandra-oliveira.bsky.social · May 20
Happy to share a PhD opportunity in my new lab at the University of Zurich! Application deadline: June 30. Do not hesitate to contact me for any questions!
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Reposted by Rui Borges
aylwyn-scally.bsky.social
Aylwyn Scally @aylwyn-scally.bsky.social · May 14
Are university lectures on the way out? It seems to me we have to rethink what their purpose is, if any. Because an increasing number of students seem to place relatively little value on them, at least as a real-time experience.

www.varsity.co.uk/comment/29679
Lectures are optional so give us the recordings
Katie Nicholson argues that faculties must make some changes if they expect students to attend lectures regularly
www.varsity.co.uk
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Reposted by Rui Borges
jydutheil.bsky.social
jydutheil.bsky.social @jydutheil.bsky.social · Feb 2
New study from the Lab! Jinyang Liang assesses the possibility of inferring ancestral alleles (aka allele polarization) without outgroup sequence, using the ancestral recombination graph (ARG) alone. Here are some of our findings. (1/5)
biorxiv-evobio.bsky.social
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Feb 2
Polarizing SNPs without outgroup https://www.biorxiv.org/content/10.1101/2025.01.31.635919v1
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Reposted by Rui Borges
chrissuthy.bsky.social
Chris Sutherland @chrissuthy.bsky.social · Jan 29
Now accepting applicants for 25-26 intake of our #StatisticalEcology MSc: bit.ly/3ooHNyc. A unique opportunity to develop skills at the interface of #statistics and #ecology (some partial scholarships available too). Please help me share!
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ruiborges23.bsky.social
Rui Borges @ruiborges23.bsky.social · Jan 27
8/8 This study emphasizes the importance of considering recurrent mutations in highly diverse species for accurate population genetics inference.

(Abstract also available in European Portuguese).
ruiborges23.bsky.social
Rui Borges @ruiborges23.bsky.social · Jan 27
7/8 To illustrate how mutation models can influence the quantification of forces other than drift, we further present a case study showing that the BM model exaggerates the intensity of selective constraints acting on the three codon positions of the bacterium Pseudomonas fluorescens.
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Rui Borges @ruiborges23.bsky.social · Jan 27
6/8 We address these biases by proposing a Bayesian estimator for population size that accounts for recurrent mutations. You can find them here: github.com/mrborges23/m...
GitHub - mrborges23/mutation_models: This repository provides a tutorial along with R scripts for utilizing Bayesian estimators of the effective population size with a boundary mutation and recurrent ...
This repository provides a tutorial along with R scripts for utilizing Bayesian estimators of the effective population size with a boundary mutation and recurrent mutation model. - mrborges23/mutat...
github.com
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Rui Borges @ruiborges23.bsky.social · Jan 27
5/8 Our analyses further reveal that the BM model tends to overestimate the effective population size, particularly in bacteria, where estimated population sizes can be more than five times larger than those expected by the recurrent mutation model.
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Rui Borges @ruiborges23.bsky.social · Jan 27
4/8 By examining mutation rates and effective population sizes across the Tree of Life, we demonstrate that the BM model remains valid for most species but significantly deviates in bacteria.
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Rui Borges @ruiborges23.bsky.social · Jan 27
3/8 However, one can alternatively assume a recurrent mutation model (RM), which additionally considers mutations contributing to shifts in allele frequency.
In this study, we compare these two models.
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ruiborges23.bsky.social
Rui Borges @ruiborges23.bsky.social · Jan 27
2/8 A common assumption is that mutations are infrequent, so when a new mutation arises, the previous one has either become fixed or lost. This assumption implies that mutations occur exclusively at fixed sites and is referred to as the boundary mutation model (BM).
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Rui Borges @ruiborges23.bsky.social · Jan 27
1/8 Mutations are fundamental for evolution, and their mathematical modelling in population genetics heavily relies on our perception of their frequency and the timescale over which they occur.
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Rui Borges @ruiborges23.bsky.social · Jan 27
Glad to see this out today in MEE!
The rarity of mutations and the inflation of bacterial effective population sizes
besjournals.onlinelibrary.wiley.com/doi/10.1111/...

#popgen #populationgenetics #evolution #bacteriagenomics #bacteria #microsky #statsstandrews @uniofstandrews.bsky.social
The rarity of mutations and the inflation of bacterial effective population sizes
Mutations are fundamental for evolution, and their mathematical modelling in population genetics heavily relies on our perception of their frequency and the timescale over which they occur. A comm...
besjournals.onlinelibrary.wiley.com
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ruiborges23.bsky.social
Rui Borges @ruiborges23.bsky.social · Jan 10
Glad to present my work on the implications of different mutation models in #popgen and #phylo inference at #PopGroup58 in Sheffield (even tried my hand at cèilidh dancing). Kudos to the organizers for this excellent meeting! #statsstandrews
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Reposted by Rui Borges
genomebiolevol.bsky.social
Genome Biology and Evolution @genomebiolevol.bsky.social · Oct 26
Genome Biology and Evolution is excited to now be on Bluesky. Please help us by recommending accounts and feeds for us to follow!
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Rui Borges @ruiborges23.bsky.social · Dec 5
Super proud of @janekay27.bsky.social for receiving an OEAW grant to continue their PhD work on codon evolution for another two years 🥳 It was a pity I couldn't be there in person for the award ceremony, but @bio-diogo.bsky.social did a fantastic job stepping in and capturing some great photos:
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Reposted by Rui Borges
larad1010.bsky.social
Lara Radović @larad1010.bsky.social · Nov 20
Update on our latest research featured in PNAS! 🐴 ✨ We used Y chromosome to explain the legacy of Oriental horses, embedded in a 1,500-year-old Crown lineage 👑 spread across continents and centuries! 🌍
Check it out 😊
The global spread of Oriental Horses in the past 1,500 years through the lens of the Y chromosome | PNAS
Since their domestication, horses have accompanied mankind, and humans have constantly shaped horses according to their needs through stallion-cent...
www.pnas.org
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Rui Borges @ruiborges23.bsky.social · Nov 23
A problem for a stormy, rainy day: #maths #mathproblems #OPM
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