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Alexei Drummond

@alexeidrummond.bsky.social

Professor of Computational Biology, University of Auckland. Atheist, Rock climber, Trail runner. Co-creator of BEAST1 and BEAST2. Founder of Geneious.

14 Posts2190 Follower2122 Folgt
Alexei Drummond@alexeidrummond.bsky.social · last wk.

Get excited :) PhyloSpec is coming! A shared standard + modelling language for phylogenetic models. Write a model once, run it across engines like BEAST X, BEAST 2.8 & RevBayes. Easy and reproducible. Built by @tochsner.bsky.social & collaborators (ETH Zürich, Auckland, LMU). phylospec.com

PhyloSpec

A standardized way to describe phylogenetic model components, common assumptions, and best practices in the field of phylogenetics.

phylospec.com

Molecular Biology and Evolution@molbioevol.bsky.social · 4w ago

Klawitter & @alexeidrummond.bsky.social introduce novel and efficient methods for estimating the credible level of individual tree topologies using tractable tree distributions, specifically conditional clade distribution (CCD). 🔗 doi.org/10.1093/molbev/msag141 #societyjournal #compbio

Bayesian credible sets for phylogenetic tree topologies with applications to coverage analysis and cross-model comparison

Abstract. Credible intervals and credible sets, such as highest posterior density intervals, form an integral statistical tool in Bayesian phylogenetics, b

doi.org

Molecular Biology and Evolution@molbioevol.bsky.social · last yr.

Vaughan & @tanjastadler.bsky.social develop a method to infer multitype population trajectories and apply it to MERS-CoV, revealing transmission patterns between camels and humans. 🔗 doi.org/10.1093/molbev/msaf130 #evobio #molbio #virus

Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data

Abstract. Phylodynamic methods provide a coherent framework for the inference of population parameters directly from genetic data. They are an important to

doi.org

Alexei Drummond@alexeidrummond.bsky.social · last yr.

Check out our new method for summarising BEAST trees. The CCD0-MAP tree gives much more accurate results than MCC tree. It returns the tree that maximises the product of sampled clade probabilities regardless of whether that tree was sampled. Highly recommend :) journals.plos.org/ploscompbiol...

Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities

Author summary Our research introduces novel methods to analyse a set of phylogenetic tree topologies, such as those generated by Bayesian Markov Chain Monte Carlo algorithms. We define a new model fo...

journals.plos.org

Alex Mackintosh@thymelicus.bsky.social · 2y ago

My and Derek Setter's work on gene flow is now published in the latest issue of Genetics. We show that it is possible to detect past gene flow between two populations by summarising the asymmetry in pop-specific external branch lengths. 1/2 tinyurl.com/5ff8ch9e

Genealogical asymmetry under the isolation with migration model and a two-taxon test for gene flow

Abstract. Methods for detecting gene flow between populations often rely on asymmetry in the average length of particular genealogical branches, with the A

tinyurl.com

Nicola Gaston@nicgaston.bsky.social · 2y ago

My slightly more considered take on the Marsden fund changes is now here. This govt is focused on the impacts of funding — I don’t mind that — but they don’t seem to have thought for a second about the impact of the lack of it. On people; on society; on academic freedom.

Funding research for economic return sounds good – but that’s not how science really works

The Marsden Fund was set up to support pure research. Diverting half of it to fund applied research undermines New Zealand’s potential to generate ideas that underpin commercial success.

theconversation.com

Paul Gardner@ppgardne.bsky.social · 2y ago

Is this the shortest term thinking government NZ has ever had? Cut hospitals, cut ferries, cut R&D, cut universities, ... Is it all ignorance + arrogance, or do they think their rapture is coming? What is going on???

Altmetric@altmetric.com · 2y ago

One of the reasons Bluesky is seeing more engagement: other platforms have adopted the behaviour of de-prioritising external links (like, say, to research papers) due to Ad models. See this: bsky.app/profile/alt... Here links can be freely shared without being drowned out or de-emphasized

@altmetric.com on Bluesky

We’re no experts but this sounds like it might be suboptimal for disseminating research. [contains quote post or other embedded content]

bsky.app

Altmetric@altmetric.com · 2y ago

There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research. A Place of Joy.

‘A place of joy’: why scientists are joining the rush to Bluesky Researchers say the social-media platform — an alternative to X — offers more control over the content they see and the people they engage with.: https://www.nature.com/articles/d41586-024-03784-6
Rob Lanfear@roblanfear.bsky.social · 2y ago

My experience (in phylogenetics, not deep learning) is almost the opposite. When I ask colleagues I know well to look at something, most are polite and encouraging but not *all that critical or useful*. But when I get peer reviews back, they are _almost_ always critical, constructive, and useful.

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Jonathan Pritchard@jkpritch.bsky.social · 2y ago

In a new preprint led by @TheNikhilMilind, we explored a fascinating paradox: For many traits the number of duplications or loss-of-function (LoF) mutations is correlated with phenotype. Curiously, for most traits, the AVERAGE direction of LoFs and Dups is the SAME. Why?

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Deon de Jager@ddj-sa.bsky.social · 2y ago

Today is the 40th anniversary of the first #ancientDNA paper, ever! "DNA sequences from the quagga, an extinct member of the horse family" www.nature.com/articles/312.... The quagga was a subspecies of plains zebra endemic to #SouthAfrica (where I'm from)! #SciSky @aarc-community.bsky.social

DNA sequences from the quagga, an extinct member of the horse family - Nature

Nature - DNA sequences from the quagga, an extinct member of the horse family

nature.com

Alexei Drummond@alexeidrummond.bsky.social · 2y ago

Have ideas about how AI/deep-learning can augment Bayesian model-based (phylogenetic) inference in scientific software like BEAST2? I would love to hear from you. We are embarking on some exploratory work in this direction and there is a lot to learn :)