Next talk: Cedric Chauve (Simon Fraser University) on "Handling uncertainty in ancestral gene orders reconstruction" Monday, April 27, 2026 at 9:00 AM PDT

Phyloseminar #155: Darrin Schultz (Stanford University) Understanding animal evolution through multi-scale synteny Animal genomes record evolutionary history across multiple scales, from local gene neighborhoods to chromosome-wide architectures, but most…

Darrin Schultz (Stanford University) will be speaking in 24 hours on "Understanding animal evolution through multi-scale synteny" www.youtube.com/watch?v=714Z...

Next talk: Darrin Schultz (Stanford University) on "Understanding animal evolution through multi-scale synteny" Monday, March 16, 2026 at 9:00 AM PDT

Phyloseminar #154: Nadia El-Mabrouk (Université de Montréal) Reconstructing the evolution of homologous genomic regions through gain and loss events Several biological systems rely on sets of colocalized genes sharing a common evolutionary history, and…

Nadia El-Mabrouk (Université de Montréal) will be speaking in 24 hours on "Reconstructing the evolution of homologous genomic regions through gain and loss events" www.youtube.com/watch?v=VuvN...

Our next three talks will be on genomic evolution and synteny. First talk: Nadia El-Mabrouk
(Université de Montréal) on "Reconstructing the evolution of homologous genomic regions through gain and loss events" pn Thursday, March 5 at 9:00 AM PST.

Phyloseminar #153: Trevor Graham (Institute for Cancer Research, London) Quantitative measurement of cancer evolutionary history from single-sample bulk DNA methylation data Cancers evolve. Current methods to measure evolutionary dynamics rely on genome sequencing of…

Trevor Graham (Institute for Cancer Research, London) will be speaking in 24 hours on "Quantitative measurement of cancer evolutionary history from single-sample bulk DNA methylation data" www.youtube.com/watch?v=8shM...

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.

Phyloseminar #152: Ben Raphael (Princeton) 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…

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.

Phyloseminar #151: Niko Beerenwinkel (ETH Zurich) 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…

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.

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

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

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

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.

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

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.

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

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

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

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

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

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!