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.
Pinned
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
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...
journals.plos.org/ploscompbiol...
Reposted by Alexei Drummond
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
🔗 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
June 17, 2025 at 2:29 PM
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
🔗 doi.org/10.1093/molbev/msaf130
#evobio #molbio #virus
Reposted by Alexei Drummond
BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be...
Details and instructions for installing on the BEAST website: beast.community
Details and instructions for installing on the BEAST website: beast.community
July 2, 2025 at 8:32 PM
BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be...
Details and instructions for installing on the BEAST website: beast.community
Details and instructions for installing on the BEAST website: beast.community
Reposted by Alexei Drummond
@alexeidrummond.bsky.social gave a wonderful keynote at @geneticsaus.bsky.social about how Bayesian/MCMC #models can be used on #cancer cells to determine when they originated and updates on #LPhy for all those #evolutionary #biologists out there.
July 9, 2025 at 9:43 PM
@alexeidrummond.bsky.social gave a wonderful keynote at @geneticsaus.bsky.social about how Bayesian/MCMC #models can be used on #cancer cells to determine when they originated and updates on #LPhy for all those #evolutionary #biologists out there.
Taming the BEAST Beijing!
July 14th-18th 2025
Register now :) Application deadline 25th April.
taming-the-beast.org/workshops/Ta...
July 14th-18th 2025
Register now :) Application deadline 25th April.
taming-the-beast.org/workshops/Ta...
Taming the BEAST Beijing
taming-the-beast.org
April 23, 2025 at 3:02 AM
Taming the BEAST Beijing!
July 14th-18th 2025
Register now :) Application deadline 25th April.
taming-the-beast.org/workshops/Ta...
July 14th-18th 2025
Register now :) Application deadline 25th April.
taming-the-beast.org/workshops/Ta...
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...
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
February 14, 2025 at 5:53 AM
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...
journals.plos.org/ploscompbiol...
Reposted by Alexei Drummond
Looks like another nice example of convergence helping to identify (not so nice for us) adaptation.
cattle B3.13 genotype H5N1 viruses rapidly accumulated adaptations in polymerase genes = better replication in bovine cells, + other mammalian species including humans and pigs: PB2 M631L, PA K497R and PB2 D740N
👉 www.biorxiv.org/content/10.1...
👉 www.biorxiv.org/content/10.1...
January 10, 2025 at 12:36 AM
Looks like another nice example of convergence helping to identify (not so nice for us) adaptation.
Reposted by Alexei Drummond
If you've never donated to Wikipedia, now's the time. Elon Musk is attacking it because it's one of the only sources of honest, curated information that he can't control.
www.newsweek.com/elon-musk-ta...
www.newsweek.com/elon-musk-ta...
Elon Musk takes aim at Wikipedia
The billionaire has become one of the most prominent supporters of President-elect Donald Trump.
www.newsweek.com
December 25, 2024 at 3:54 AM
If you've never donated to Wikipedia, now's the time. Elon Musk is attacking it because it's one of the only sources of honest, curated information that he can't control.
www.newsweek.com/elon-musk-ta...
www.newsweek.com/elon-musk-ta...
Reposted by Alexei Drummond
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
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
December 12, 2024 at 2:17 PM
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
tinyurl.com/5ff8ch9e
Reposted by Alexei Drummond
HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X https://www.biorxiv.org/content/10.1101/2024.12.08.627395v1
December 10, 2024 at 9:48 AM
HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X https://www.biorxiv.org/content/10.1101/2024.12.08.627395v1
Reposted by Alexei Drummond
20%, under $15m, of Marsden funding went to social sciences while just under $60m went to hard sciences.
Total govt research funding in year to March 2023 was ~$1.1b (0.29% of GDP).
Cutting the humanities out of Marsden is just spite.
Total govt research funding in year to March 2023 was ~$1.1b (0.29% of GDP).
Cutting the humanities out of Marsden is just spite.
www.nzherald.co.nz/nz/rod-emmer... Rod Emmerson’s cartoons: Week of December 2 - 8
December 5, 2024 at 7:53 PM
20%, under $15m, of Marsden funding went to social sciences while just under $60m went to hard sciences.
Total govt research funding in year to March 2023 was ~$1.1b (0.29% of GDP).
Cutting the humanities out of Marsden is just spite.
Total govt research funding in year to March 2023 was ~$1.1b (0.29% of GDP).
Cutting the humanities out of Marsden is just spite.
Reposted by Alexei Drummond
How fast are viruses spreading in the wild? Check out our latest study now published in @plosbiology.bsky.social: doi.org/10.1371/jour.... A study performed with Paul Bastide, Pauline Rocu, Denis Fargette, Olivier Hardy, @msuchard.bsky.social, @stephaneguindon.bsky.social, and Philippe Lemey (1/7)
December 4, 2024 at 8:49 AM
How fast are viruses spreading in the wild? Check out our latest study now published in @plosbiology.bsky.social: doi.org/10.1371/jour.... A study performed with Paul Bastide, Pauline Rocu, Denis Fargette, Olivier Hardy, @msuchard.bsky.social, @stephaneguindon.bsky.social, and Philippe Lemey (1/7)
Reposted by Alexei Drummond
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???
December 5, 2024 at 3:28 AM
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???
Reposted by Alexei Drummond
PhD opportunity in computational population genetics at @MPI_EVA_Leipzig:
Join our fully funded project to develop IBD-segment tools, connecting high-quality genomes from 500 Black Death victims to modern Europeans. 🌍💻🧬
Please spread the word! 📢🙌 #aDNA #PopGen
www.eva.mpg.de/de/karriere/...
Join our fully funded project to develop IBD-segment tools, connecting high-quality genomes from 500 Black Death victims to modern Europeans. 🌍💻🧬
Please spread the word! 📢🙌 #aDNA #PopGen
www.eva.mpg.de/de/karriere/...
December 3, 2024 at 12:52 PM
PhD opportunity in computational population genetics at @MPI_EVA_Leipzig:
Join our fully funded project to develop IBD-segment tools, connecting high-quality genomes from 500 Black Death victims to modern Europeans. 🌍💻🧬
Please spread the word! 📢🙌 #aDNA #PopGen
www.eva.mpg.de/de/karriere/...
Join our fully funded project to develop IBD-segment tools, connecting high-quality genomes from 500 Black Death victims to modern Europeans. 🌍💻🧬
Please spread the word! 📢🙌 #aDNA #PopGen
www.eva.mpg.de/de/karriere/...
Reposted by Alexei Drummond
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
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
December 3, 2024 at 2:01 PM
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
See this: bsky.app/profile/alt...
Here links can be freely shared without being drowned out or de-emphasized
Reposted by Alexei Drummond
Don't forget to submit your abstract for "Probabilistic Modeling in Genomics 2025". Deadline: January 10th, 2025. meetings.cshl.edu/meetings.asp...
Probabilistic Modeling in Genomics
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
meetings.cshl.edu
December 2, 2024 at 5:27 PM
Don't forget to submit your abstract for "Probabilistic Modeling in Genomics 2025". Deadline: January 10th, 2025. meetings.cshl.edu/meetings.asp...
Reposted by Alexei Drummond
Modeling the velocity of evolving lineages and predicting dispersal patterns
www.pnas.org/doi/10.1073/...
www.pnas.org
December 2, 2024 at 9:43 AM
Modeling the velocity of evolving lineages and predicting dispersal patterns
www.pnas.org/doi/10.1073/...
Reposted by Alexei Drummond
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.
December 3, 2024 at 2:00 PM
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.
Reposted by Alexei Drummond
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.
November 26, 2024 at 12:32 AM
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.
Reposted by Alexei Drummond
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?
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?
November 22, 2024 at 4:45 PM
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?
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?
Reposted by Alexei Drummond
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
@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
www.nature.com
November 15, 2024 at 3:08 PM
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
@aarc-community.bsky.social
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 :)
We are embarking on some exploratory work in this direction and there is a lot to learn :)
November 12, 2024 at 6:42 PM
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 :)
We are embarking on some exploratory work in this direction and there is a lot to learn :)
Today I was reminded that I am living in a simulation. The postdoc running things seems to be testing what happens when mendacity is turned up to maximum.
November 6, 2024 at 7:46 AM
Today I was reminded that I am living in a simulation. The postdoc running things seems to be testing what happens when mendacity is turned up to maximum.
Last chance to fill in our survey! Have your say while you can :) Thanks for all those of you that already have!
Want to have your say about BEAST2 future developments?
Fill in our BEAST2 user and developer survey :)
forms.gle/mTWvaXHZAA12...
Fill in our BEAST2 user and developer survey :)
forms.gle/mTWvaXHZAA12...
BEAST 2 user and developer experience and future development survey
This survey aims to gather feedback from the BEAST2 user and developer community to inform the development of future versions of BEAST. Your insights will help us prioritise features, address pain poi...
forms.gle
October 21, 2024 at 3:46 AM
Last chance to fill in our survey! Have your say while you can :) Thanks for all those of you that already have!
Want to have your say about BEAST2 future developments?
Fill in our BEAST2 user and developer survey :)
forms.gle/mTWvaXHZAA12...
Fill in our BEAST2 user and developer survey :)
forms.gle/mTWvaXHZAA12...
BEAST 2 user and developer experience and future development survey
This survey aims to gather feedback from the BEAST2 user and developer community to inform the development of future versions of BEAST. Your insights will help us prioritise features, address pain poi...
forms.gle
September 20, 2024 at 5:24 PM
Want to have your say about BEAST2 future developments?
Fill in our BEAST2 user and developer survey :)
forms.gle/mTWvaXHZAA12...
Fill in our BEAST2 user and developer survey :)
forms.gle/mTWvaXHZAA12...