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phyloseminar.bsky.social
phyloseminar.org
@phyloseminar.bsky.social
370 followers 4 following 30 posts
A free online seminar about phylogenetics.
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phyloseminar.bsky.social
Next talk: Trevor Graham (Institute for Cancer Research, London) on "Quantitative measurement of cancer evolutionary history from single-sample bulk DNA methylation data" Monday, November 24 at 9:00 AM PST.
October 22, 2025 at 1:23 PM
phyloseminar.bsky.social
Next talk: Ben Raphael (Princeton) on "Tumor Evolution over Space and Time" Monday, October 20 at 9:00 AM PDT.
September 22, 2025 at 4:49 PM
phyloseminar.bsky.social
The next 3 talks will be on the intersection of phylogenetics and cancer research. First talk: Niko Beerenwinkel (ETH Zurich) on "Modeling tumor progression from single-cell sequencing data." Tuesday, September 16 at 9:00 AM PDT.
September 10, 2025 at 1:14 AM
phyloseminar.bsky.social
Next talk: Arianna Miles-Jay (Michigan Department of Health and Human Services) on "Applying phylogenetics in public health: Past, present, and potential for the future." Tuesday, August 12, 2025 at 9:00 AM PDT
July 15, 2025 at 7:55 PM
phyloseminar.bsky.social
Next talk: Alli Black (Washington State Department of Health) on "Practicing the theory: Applying genomic epidemiology to guide public health action." Tuesday, July 15 at 9:00 AM PDT.
June 20, 2025 at 7:04 PM
phyloseminar.bsky.social
Next we will have a trio of talks on public heath. Henry Kunerth (Minnesota Department of Health) will start things off with a talk on "Genomic Surveillance of Human Respiratory Syncytial Virus in Minnesota – Statewide Efforts, Global Impacts" Tuesday, June 17 at 9:00 AM PDT.
May 29, 2025 at 11:09 PM
phyloseminar.bsky.social
Next talk: Antoine Koehl (UC Berkeley) on "Deep Models of Protein Evolution" Tuesday, May 27 at 9:00 AM PDT
May 22, 2025 at 7:04 PM
phyloseminar.bsky.social
Next talk: Pierre Barrat-Charlaix (Politecnico di Torino) on "Reconstruction of ancestral protein sequences using autoregressive generative models" Tuesday, May 20 at 9:00 AM PDT
May 6, 2025 at 11:46 PM
phyloseminar.bsky.social
Next talk: Faruck Morcos (UT Dallas) on "Modeling sequence evolution by learning epistatic terms from protein families" Tuesday, April 29, 2025 at 9:00 AM PDT
March 27, 2025 at 12:39 AM
phyloseminar.bsky.social
Next we will have a trio of talks on next-generation sequence evolution models. Antoine Koehl @antoinekoehl.bsky.social (UC Berkeley) will start things off with a talk "Deep Models of Protein Evolution" on Tuesday, April 1 at 9:00 AM PDT.
Models of protein evolution seek to quantify how proteins evolve over time while experiencing intricate constraints and adapting new functions. These models are the engine of phylogenetics, enabling, amongst other applications, phylogenetic tree reconstruction and ancestral sequence inference. Classic and contemporary work in protein sequence modeling incompletely address each others’ shortcomings - the gold standard classical models (e.g. WAG, LG) are limited by a need to consider sites in protein sequences as evolving independently, and while deep protein language models are able to account for interactions between sites, they lack an explicit time component. Here, we tackle this challenge by introducing a framework for training deep evolutionary models on protein family trees. By constructing comprehensive training datasets, we are able to train a deep generative model that bridges this methodological gap to model evolutionary transitions on unaligned sequence pairs, capturing the full spectrum of evolutionary forces including insertions and deletions. Our model, termed PEINT (Protein Evolution IN Time) significantly outperforms classical evolutionary approaches and enables realistic simulations of evolutionary trajectories. This advance opens new possibilities to understand and harness evolution for protein design, variant effect prediction, viral evolution forecasting, and statistical phylogenetics.
March 17, 2025 at 10:59 PM
phyloseminar.bsky.social
Next talk: Qianying Lin (Los Alamos) on "Segment trees can not identify viral genomic reassortment" Wednesday, March 12 at 9:00 AM PDT
February 12, 2025 at 9:55 PM
phyloseminar.bsky.social
Aaron King (Michigan) will be giving the second of two talks on "Phylodynamics via Markov genealogy processes" on Tuesday, February 11, 2025 at 9:00 AM PST.
Phylodynamic inference allows us to extract information on determinants of epidemic dynamics from sampled pathogen genomes. Specifically, phylodynamics seeks to infer the structure and parameterization of dynamic population models from patterns of shared ancestry. A key problem in phylodynamics has been a mismatch between inference methodology and epidemiological models: the approximations that must be made to perform inference conflict with questions of great interest. I will describe recent work in which we have obtained exact expressions for phylodynamic likelihoods associated with population models of (almost) arbitrary complexity. These results unify and strictly extend existing approaches and broaden the scope of phylodynamic inference methods. In the second talk, I will deduce an exact expression for the likelihood of an observed genealogy, as the solution to a well-defined filter equation, which can be solved numerically using standard Monte Carlo techniques. I will conclude by highlighting the need for improved algorithms and indicating some open questions.
January 15, 2025 at 10:50 PM
phyloseminar.bsky.social
Next, Aaron King (Michigan) will be giving two talks on "Phylodynamics via Markov genealogy processes". The first will be on Tuesday, January 14, 2025 at 9:00 AM PST.
Abstract: Phylodynamic inference allows us to extract information on determinants of epidemic dynamics from sampled pathogen genomes. Specifically, phylodynamics seeks to infer the structure and parameterization of dynamic population models from patterns of shared ancestry. A key problem in phylodynamics has been a mismatch between inference methodology and epidemiological models: the approximations that must be made to perform inference conflict with questions of great interest. I will describe recent work in which we have obtained exact expressions for phylodynamic likelihoods associated with population models of (almost) arbitrary complexity. These results unify and strictly extend existing approaches and broaden the scope of phylodynamic inference methods.
December 19, 2024 at 10:50 AM