phyloseminar.org

Tumor Evolution over Space and Time Cancer is the result of an evolutionary process where genomic mutations and epigenetic alterations accumulate in cells that form a tumor. Modern single-cell and… Phyloseminar #152: Ben Raphael (Princeton)

Ben Raphael (Princeton) will be speaking in 24 hours on "Tumor Evolution over Space and Time" www.youtube.com/watch?v=j19t...

Next talk: Ben Raphael (Princeton) on "Tumor Evolution over Space and Time" Monday, October 20 at 9:00 AM PDT.

Modeling tumor progression from single-cell sequencing data Cancer progression is a somatic evolutionary process characterized by the accumulation of genetic alterations and responsible for tumor… Phyloseminar #151: Niko Beerenwinkel (ETH Zurich)

Niko Beerenwinkel (ETH Zurich) will be speaking in 24 hours on "Modeling tumor progression from single-cell sequencing data." Link: www.youtube.com/watch?v=IVR7...

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.

Applying phylogenetics in public health: Past, present, and potential for the futureWith the rapid growth of pathogen genomics in public health comes the inc... Phyloseminar #150: Arianna Miles-Jay (Michigan Department of Health and Human Services)

Arianna Miles-Jay (Michigan Department of Health and Human Services) will be speaking in 24 hours on "Applying phylogenetics in public health: Past, present, and potential for the future." Link: www.youtube.com/watch?v=bMqj...

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

Practicing the theory: Applying genomic epidemiology to guide public health action Phyloseminar #149: Alli Black (Washington State Department of Health)

Alli Black (Washington State Department of Health) will be speaking in 24 hours on "Practicing the theory: Applying genomic epidemiology to guide public health action" Link: www.youtube.com/watch?v=D__w...

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.

Genomic Surveillance of Human Respiratory Syncytial Virus in Minnesota – Statewide Efforts, Global ImpactsOver the past two respiratory seasons, we’ve succes... Phyloseminar #148: Henry Kunerth (Minnesota Department of Health)

Henry Kunerth (Minnesota Department of Health) will be speaking in 24 hours on "Genomic Surveillance of Human Respiratory Syncytial Virus in Minnesota – Statewide Efforts, Global Impacts." Link: www.youtube.com/watch?v=e97k...

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.

Deep Models of Protein EvolutionModels of protein evolution seek to quantify how proteins evolve over time while experiencing intricate constraints and adapt... Phyloseminar #147: Antoine Koehl (UC Berkeley)

Antoine Koehl (UC Berkeley) will be speaking on "Deep Models of Protein Evolution" in 24 hours. Link: www.youtube.com/watch?v=SgZv...

Next talk: Antoine Koehl (UC Berkeley) on "Deep Models of Protein Evolution" Tuesday, May 27 at 9:00 AM PDT

Reconstruction of ancestral protein sequences using autoregressive generative modelsAncestral sequence reconstruction (ASR) is an important tool to understan... Phyloseminar #146: Pierre Barrat-Charlaix (Politecnico di Torino)

Pierre Barrat-Charlaix (Politecnico di Torino) will be speaking on "Reconstruction of ancestral protein sequences using autoregressive generative models" in 24 hours. Link: www.youtube.com/watch?v=-wqg...

This talk has been moved 24 hours and 30 minutes later, to Wednesday, May 21, 2025 at 9:30 AM PDT.

bsky.app/profile/phyl...

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

Modeling sequence evolution by learning epistatic terms from protein familiesThe use of coevolutionary information, i.e. the knowledge of amino acid or nucle... Phyloseminar #145: Faruck Morcos (UT Dallas)

Faruck Morcos (UT Dallas) will be speaking on "Modeling sequence evolution by learning epistatic terms from protein families" in 24 hours. Link: www.youtube.com/watch?v=gpZ_...

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

This talk has been postponed until May 27th. bsky.app/profile/did:...

This is postponed until May 27th.

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.

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.

Phyloseminar #144: Qianying Lin (Los Alamos) Segment trees can not identify viral genomic reassortmentReassortment is an evolutionary process common in viruses with segmented genomes. These viruses can ...

Qianying Lin (Los Alamos) will be speaking on "Segment trees can not identify viral genomic reassortment" in 24 hours. buff.ly/4hV1WFh

Next talk: Qianying Lin (Los Alamos) on "Segment trees can not identify viral genomic reassortment" Wednesday, March 12 at 9:00 AM PDT

Phyloseminar #143: Aaron King (Michigan) Phylodynamics via Markov genealogy processes (2/2)Phylodynamic inference allows us to extract information on determinants of epidemic dynamics from sampled p...

Our site appears to be down, but we are casting Aaron King's seminar at https://buff.ly/3QeJb3Z now!

Phyloseminar #143: Aaron King (Michigan) Phylodynamics via Markov genealogy processes (2/2)Phylodynamic inference allows us to extract information on determinants of epidemic dynamics from sampled p...

The second talk from Aaron King (Michigan) on "Phylodynamics via Markov genealogy processes" will be starting in 24 hours.

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.

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.

YouTube video by phyloseminar.org Phyloseminar #142: Aaron King (Michigan)

The first talk from Aaron King (Michigan) on "Phylodynamics via Markov genealogy processes" will be starting in 10 minutes.

www.youtube.com/watch?v=AQLr...

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.

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.

We passed the 15 year mark! Planning the 141st seminar now.

Thanks to all the speakers, and all of you for getting the word out!

We are here! All future seminar announcements will be posted here.