@willfreyman

computational biologist. phylogenetics, population genetics. No longer active on twitter, find me at https://xitter.cf/t.co/c9VJRDZJ6R

willfreyman.org
Joined November 2017
  • Tweets497
  • Following124
  • Followers202
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Check out this website ibd.la/ that summarizes the phenotypic and genetic characteristics of around 300+ genetic clusters identified in the UCLA biobank. @ChristaCaggiano gave an interesting talk on this fascinating work #ASHG22 #DRIFT22
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Relatedness inference with low-coverage ancient DNA data is still a hard problem. Today, we posted a preprint presenting a new method called KIN that identifies close relatives up to 3rd-degree while differentiating parent-child from siblings: biorxiv.org/content/10.1101/… (1/3)

KIN: A method to infer relatedness from low-coverage ancient DNA

Genetic kinship of ancient individuals can provide insights into their culture and social hierarchy, and is relevant for downstream genetic analyses. However, estimating relatedness from ancient DNA...

biorxiv.org
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1/8 25 years ago, today (Oct 24, 1997), 'Gattaca' was released. Me & @DocEdge85 chose to commemorate the event w/ a technical perspective recently published in GENETICS @GeneticsGSA Here I'll just post several items related to the broader project. academic.oup.com/genetics/ad…

Gattaca as a lens on contemporary genetics: marking 25 years into the film’s “not-too-distant”...

In this article, Ogbunugafor and Edge commemorate the 25th anniversary of the release of the film Gattaca, using the moment as an opportunity to examine co

academic.oup.com
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New version of SHAPEIT is released (v5). It phases rare variants in the UK Biobank whole-genome and whole-exome sequencing data with great accuracy. Thanks to all co-authors @Rbn_Hfmstr @Diogo_M_Ribeiro @simrubk @ODelaneau ! @DelaneauGroup @dbc_unil biorxiv.org/content/10.1101/…

Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank

The UK Biobank performed whole-genome sequencing (WGS) and whole-exome sequencing (WES) across hundreds of thousands of individuals, allowing researchers to study the effects of both common and rare...

biorxiv.org
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Improving polygenic risk prediction in admixed populations by explicitly modeling ancestral-specific effects via GAUDI biorxiv.org/content/10.1101/…

Improving polygenic risk prediction in admixed populations by explicitly modeling ancestral-speci...

Polygenic risk scores (PRS) have shown successes in clinics, but most PRS methods have focused only on individuals with one primary continental ancestry, thus poorly accommodating recently-admixed...

biorxiv.org
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Summary of the #Bayesian #phylogenetic framework and conceptualization of a variety of methods to improve posterior approximations via Markov chain Monte Carlo sampling. #inference [Review co-authored by EVBC members @suchard_group @LemeyLab] doi.org/10.1098/rstb.2021.02…

Scalable Bayesian phylogenetics

Abstract. Recent advances in Bayesian phylogenetics offer substantial computational savings to accommodate increased genomic sampling that challenges tradi

royalsocietypublishing.org
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The race/genetics discordance is like nails on the blackboard for me. A reminder - race/ethnicity is selected from societal pre-defined boxes, 1 dimension, ~30 choices. Genetics is measuring someone's DNA over ~300,000 (ish) dimensions of their DNA. They are *not* the same.
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MAST: Phylogenetic Inference with Mixtures Across Sites and Trees dlvr.it/SZlMhY
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Fast computation of principal components of genomic similarity matrices biorxiv.org/cgi/content/shor… #bioRxiv
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I really love this paper by @nhcooper123 et al. Small amounts of measurement error can lead to 100% rejection of the simpler (correct) model. onlinelibrary.wiley.com/doi/…

A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies

Phylogenetic comparative methods are increasingly used to give new insights into the dynamics of trait evolution in deep time. For continuous traits the core of these methods is a suite of models...

onlinelibrary.wiley.com
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New preprint! We demonstrate that PGS accuracy varies continuously cross individuals within and across genetic ancestry clusters and highlight that PGS should be interpreted through the lens of continuous genetic ancestries. 🧵 biorxiv.org/content/10.1101/…

Polygenic scoring accuracy varies across the genetic ancestry continuum in all human populations

Polygenic scores (PGS) have limited portability across different groupings of individuals (e.g., by genetic ancestries and/or social determinants of health), preventing their equitable use. PGS...

biorxiv.org
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The virtual symposium "Using Ancestral Recombination Graphs (ARGs) to Infer Evolutionary Processes" will take place on Friday September 30. You can find the program here: virtual.oxfordabstracts.com/…"
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Now published in Methods in Ecology and Evolution! besjournals.onlinelibrary.wi…

Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with...

The availability of population genomic data through new sequencing technologies gives unprecedented opportunities for estimating important evolutionary forces such as genetic drift, selection and ...

besjournals.onlinelibrary.wiley.com
Rui Borges@RBorges2317 Dec 2021
Glad to announce that the polymorphism-aware phylogenetic models have met RevBayes. Our implementations permit the joint estimation of species trees and forces (mutation and selection biases) responsible for the molecular evolution of genomic sequences. 1/4
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Deciphering the genetic structure of the Quebec founder population using genealogies biorxiv.org/content/10.1101/…

Deciphering the genetic structure of the Quebec founder population using genealogies

Using genealogy to study the demographic history of a population makes it possible to overcome the models and assumptions often used in population genetics. The Quebec founder population is one of...

biorxiv.org
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Excited to share a revision of the preprint “Nested Rhat: Assessing the convergence of Markov chain Monte Carlo when running many short chains”, with Matt Hoffman, Pavel Sountsov, Lionel Riou-Durand, @avehtari, and Andrew Gelman. arxiv.org/abs/2110.13017

Nested $\hat R$: Assessing the convergence of Markov chain Monte...

Recent developments in parallel Markov chain Monte Carlo (MCMC) algorithms allow us to run thousands of chains almost as quickly as a single chain, using hardware accelerators such as GPUs. While...

arxiv.org
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Demographic History Inference and the Polyploid Continuum biorxiv.org/cgi/content/shor… #bioRxiv
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This population doesn't exist: learning the distribution of evolutionary histories with generative adversarial networks biorxiv.org/cgi/content/shor… #biorxiv_evobio
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We are officially announcing the Fall 2022 Bay Area Population Genomics (BAPG) conference to be held at UC Berkeley on October 15! Check out our website: sites.google.com/berkeley.ed… where you'll find logistics info + link to registration. Contact me or @YunDeng5 with any questions.

BAPG Fall 2022

We are very excited to announce the 20th Bay Area Population Genomics (BAPG) Conference at UC Berkeley! Thank you to everyone who has signed up to present either a talk or a poster. We have posted...

sites.google.com
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#PLOSCompBio: Recombination-aware phylogeographic inference using the structured coalescent with ancestral re ... dx.plos.org/10.1371/journal.…
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