sgravel.bsky.social
@sgravel.bsky.social
94 followers 61 following 29 posts
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sgravel.bsky.social @sgravel.bsky.social · 16d
An ever-slightly non-PSD matrix allows your favourite algorithm to find loophole states with negative errors. Ulises shows how to efficiently restore the PSD condition with no cost to algorithm performance, little to no approximation cost, and a large potential bonus to stability.
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sgravel.bsky.social @sgravel.bsky.social · 16d
Because LD matrices are large, efficient methods take shortcuts, for example by neglecting LD between distant SNPS. These shortcuts seem benign, but sometimes cause the LD matrix to lose a mathematical property called positive semi-definiteness (PSD). This is a problem.
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sgravel.bsky.social @sgravel.bsky.social · 16d
To analyze millions of genetic variants, we need tools that are fast and memory efficient. Some of the most efficient tools have problems with numerical instability on dense sets of snps. Bercovich et al. figured out how to overcome a common source of instability: www.biorxiv.org/content/10.1...
LD Matrix Approximations for Scalable Analysis of High-dimensional Genetic Data
Linkage disequilibrium (LD) matrices are an essential part of many statistical genetics methods. However, their high dimensionality makes their computation and storage impractical for large genomic da...
www.biorxiv.org
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Reposted by sgravel.bsky.social
biorxiv-genetic.bsky.social
bioRxiv Genetics @biorxiv-genetic.bsky.social · 19d
Sex differences in transcription-associated mutagenesis in the human germline https://www.biorxiv.org/content/10.1101/2025.09.18.677082v1
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sgravel.bsky.social @sgravel.bsky.social · 16d
Finally, it shows that integrating multiple sources of heterogeneity does not need to be complicated. The work was inspired by excellent previous work by Màrquez-Luna t al (pubmed.ncbi.nlm.nih.gov/29110330/) and Mostafavi et al (pubmed.ncbi.nlm.nih.gov/29110330/).
Multiethnic polygenic risk scores improve risk prediction in diverse populations - PubMed
Methods for genetic risk prediction have been widely investigated in recent years. However, most available training data involves European samples, and it is currently unclear how to accurately predic...
pubmed.ncbi.nlm.nih.gov
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sgravel.bsky.social @sgravel.bsky.social · 16d
The bottom line: The increase in prediction accuracy is modest, but fairly robust. The approach does away with the awkward task of finding a "matching" cohort, which often does not exist for a given individual. It can also reveal unexpected gene-by-something interactions.
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sgravel.bsky.social @sgravel.bsky.social · 16d
Each individual gets assigned a weighted mixture of scores based on age, ancestry, sex, and other information. This typically favours scores learned in groups of matched sex and ancestry, but not always. Age effects tend to be important, reflecting e.g. differences in medication use.
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sgravel.bsky.social @sgravel.bsky.social · 16d
To predict genetic risk for an individual, which score should you use? The one learned from a cohort that best matches by ancestry? Or by sex, or age, or environment? Shadi Zabad proposes to combine scores taking all these into account. www.biorxiv.org/content/10.1...
Personalized polygenic risk prediction and assessment with a Mixture-of-Experts framework
With the increasing availability of high quality genomic data from diverse cohorts, polygenic scores (PRS) have become a mainstay of genetic analyses of complex traits and diseases. Despite their prol...
www.biorxiv.org
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sgravel.bsky.social @sgravel.bsky.social · Jul 11
Testing of a suspect's DNA against crime scene DNA is fine. Screening existing databases in search of relatives is debatable. Indiscriminate collection of new genetic data on individuals with no link to the crime scene is fucked up and should not be tolerated.
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sgravel.bsky.social @sgravel.bsky.social · Jul 11
The RCMP surreptitiously collected DNA from random individuals at a Kurdish festival based on the inferred Kurdish ancestry of a suspect, in search of a relative. www.theglobeandmail.com/canada/artic...
RCMP: "Police will use all tools available."
Let's make this tool unavailable.
Ontario privacy commissioner urges guardrails on police gravitating toward ‘unbridled genetic surveillance’
Watchdog’s report warns new era of DNA-based criminal investigations calls for clearer rules and more transparency
www.theglobeandmail.com
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sgravel.bsky.social @sgravel.bsky.social · May 16
Preprint out: A multi-ancestry genetic reference for the Quebec population.

2173 WGS and 29k genotyping arrays in a longitudinal biobank.

www.medrxiv.org/content/10.1...
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Reposted by sgravel.bsky.social
aylwyn-scally.bsky.social
Aylwyn Scally @aylwyn-scally.bsky.social · May 16
Delighted to see this paper out, investigating factors affecting human germline mutation in a cohort of 10,000 families from the UK 100k Genomes Project.

www.nature.com/articles/s41...
The impact of ancestral, genetic, and environmental influences on germline de novo mutation rates and spectra - Nature Communications
Here the authors analyze de novo mutations in >10,000 parent-offspring trios and find that ancestry and smoking independently associate with mutation rate, but that common genetic variants likely c...
www.nature.com
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Reposted by sgravel.bsky.social
martinsauvageau.bsky.social
Martin Sauvageau @martinsauvageau.bsky.social · Apr 2
If you’re interested in moving your lab to beautiful Montreal Canada, this program offers chairholders funding of up to 1M$ a year for 8 years. See link for details.
www.nature.com/naturecareer...
Canada Excellence Research Chairs (CERC) - Montréal, Quebec (CA) job with University of Montreal (UdeM) | 12838461
Canada Excellence Research Chairs (CERC)
www.nature.com
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sgravel.bsky.social @sgravel.bsky.social · Mar 31
My sister Élise will get her doctorate without a single peer reviewed paper! She'll be getting a doctorate, honoris causa, from @uqam.ca for her contributions to children's literature. Her books are often engaged, often silly, and always good reads. Very well-deserved ❤️🍉!
elisegravel.bsky.social
Elise Gravel @elisegravel.bsky.social · Mar 29
❤️
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sgravel.bsky.social @sgravel.bsky.social · Mar 28
This is so outlandish that I had to go and read the original to see if there was any context I was missing. But no, you summed it up perfectly. I guess they singled those out as "things an antiracist would say", and therefore verboten?
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sgravel.bsky.social @sgravel.bsky.social · Mar 28
Une présentation de la Dre Liu à NYU annulée pour faits dérangeants. Son commentaire plein de nuance ici
www.ledevoir.com/opinion/idee....

A conference by Dr Liu at NYU cancelled for including unpleasant facts. Her thoughtful commentary (in French):
www.ledevoir.com/opinion/idee....
Ma présentation a été annulée par l’Université de New York
Mon «alma mater» a préféré jouer de surobéissance préventive pour ne pas froisser le gouvernement Trump.
www.ledevoir.com
sgravel.bsky.social @sgravel.bsky.social · Mar 28
Methods like this can help geneticists find unexpected patterns in their models of human history. However, it will also be tempting to over-interpret them (because they are so pretty and detailed!). Expecting heated arguments in the near future about how these should be interpreted!
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sgravel.bsky.social @sgravel.bsky.social · Mar 28
It creates detailed illustrations of possible routes followed by our ancestors. We spent a lot of time looking at such maps from recent historical records in www.science.org/doi/10.1126/.... Impressive to see this done with from genetic data and going back thousands of years!
A map of human migrations
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sgravel.bsky.social @sgravel.bsky.social · Mar 28
Grundler et al propose a new method to infer the geographic position of all our genetic ancestors www.science.org/doi/10.1126/...
building on a method by Wohns et al www.science.org/doi/10.1126/....

My thoughts on the approach: www.science.org/doi/epdf/10.....
A geographic history of human genetic ancestry
Describing the distribution of genetic variation across individuals is a fundamental goal of population genetics. We present a method that capitalizes on the rich genealogical information encoded in g...
www.science.org
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sgravel.bsky.social @sgravel.bsky.social · Mar 17
Ancestral Recombination Graphs are an amazing tool to study genetic variation. In this preprint, Alejandro Mejia-Garcia shows that ARGs are surprisingly good at identifying founder variants, and help us pick apart their geographic distribution and phenotypic effect.

www.biorxiv.org/content/10.1...
Using the ancestral recombination graph to study the history of rare variants in founder populations
Gene genealogies represent the ancestry of a sample and are often encoded as ancestral recombination graphs (ARG). It has recently become possible to infer these gene genealogies from sequencing or ge...
www.biorxiv.org
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sgravel.bsky.social @sgravel.bsky.social · Mar 5
A faculty position in Synthetic biology at Concordia University in Montreal, with possibility of funding from a Canada Research Chair: www.concordia.ca/artsci/about... .
Canada Research Chair (CRC) Tier II in Synthetic Biology and Biomanufacturing - Concordia University
The department of Biology in the Faculty of Arts and Science at Concordia University invites applications for a tenure-track faculty position with the opportunity to apply for a Tier II Canada Researc...
www.concordia.ca
sgravel.bsky.social @sgravel.bsky.social · Feb 28
Faculty position opening in bioinformatics at the University of Montreal! There is a great bioinfo and comp bio community in Montreal.

www.umontreal.ca/carrieres/pr...
Professeurs
www.umontreal.ca
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sgravel.bsky.social @sgravel.bsky.social · Feb 7
Bizarrement ça me dit que je veins de Laval :) Je ne sais pas si d'autres Québécois sont aussi assignés à l'ouest de la France, ce qui serait cool.
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ajhgnews.bsky.social
The American Journal of Human Genetics @ajhgnews.bsky.social · Jan 29
📢New Perspective from Hatchell et al.
📰Experience using conventional compared to ancestry-based population descriptors in clinical genomics laboratories
www.cell.com/ajhg/fulltex...
Experience using conventional compared to ancestry-based population descriptors in clinical genomics laboratories
While the use of genetically defined population descriptors in human research studies has been proposed to reduce inaccuracies and harms associated with the use of conventional, non-biologically based...
www.cell.com
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Reposted by sgravel.bsky.social
jkpritch.bsky.social
Jonathan Pritchard @jkpritch.bsky.social · Jan 27
I posted a couple days ago about our new paper on building causal graphs from genetic associations + Perturb-seq.

Here I want to expand on the value of using DIRECTIONAL information contained in LoF burden tests.🧵
[work led by @minetoota.bsky.social ]

bsky.app/profile/jkpr...
jkpritch.bsky.social
Jonathan Pritchard @jkpritch.bsky.social · Jan 26
GWAS provides a unique tool in human biology as it can establish causal links from variants to trait.

But interpretation is difficult as most effects flow through (unobserved) gene regulatory networks. Can we gain insight by linking to modern Perturb-seq data?

www.biorxiv.org/content/10.1...
Causal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq
Genetic association studies provide a unique tool for identifying causal links from genes to human traits and diseases. However, it is challenging to determine the biological mechanisms underlying mos...
www.biorxiv.org
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