Lightnews — Scholar-powered news

phyloseminar.org @phyloseminar.bsky.social · 16d

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

phyloseminar.org @phyloseminar.bsky.social · 23d

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...

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…

www.youtube.com

3

phyloseminar.org @phyloseminar.bsky.social · 28d

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.

3

phyloseminar.org @phyloseminar.bsky.social · Aug 11

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...

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...

www.youtube.com

1

phyloseminar.org @phyloseminar.bsky.social · Jul 15

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

1

phyloseminar.org @phyloseminar.bsky.social · Jul 14

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...

Phyloseminar #149: Alli Black (Washington State Department of Health)

Practicing the theory: Applying genomic epidemiology to guide public health action

www.youtube.com

1 2

phyloseminar.org @phyloseminar.bsky.social · Jun 20

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.

6

phyloseminar.org @phyloseminar.bsky.social · Jun 16

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...

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...

www.youtube.com

1 2

phyloseminar.org @phyloseminar.bsky.social · May 29

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.

1

phyloseminar.org @phyloseminar.bsky.social · May 26

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

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...

www.youtube.com

2

phyloseminar.org @phyloseminar.bsky.social · May 22

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

phyloseminar.org @phyloseminar.bsky.social · May 19

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...

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...

www.youtube.com

2 4

phyloseminar.org @phyloseminar.bsky.social · May 12

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...

phyloseminar.org @phyloseminar.bsky.social · May 6

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

1

phyloseminar.org @phyloseminar.bsky.social · May 6

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

1

phyloseminar.org @phyloseminar.bsky.social · Apr 28

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_...

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...

www.youtube.com

1

phyloseminar.org @phyloseminar.bsky.social · Mar 27

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

1 1

phyloseminar.org @phyloseminar.bsky.social · Mar 27

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

phyloseminar.org @phyloseminar.bsky.social · Mar 17

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.

1

phyloseminar.org @phyloseminar.bsky.social · Mar 27

This is postponed until May 27th.

phyloseminar.org @phyloseminar.bsky.social · Mar 17

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.

1 2

phyloseminar.org @phyloseminar.bsky.social · Mar 11

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

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 ...

buff.ly

2

phyloseminar.org @phyloseminar.bsky.social · Feb 12

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

3

phyloseminar.org @phyloseminar.bsky.social · Feb 11

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...

buff.ly

2 4

phyloseminar.org @phyloseminar.bsky.social · Feb 10

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

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...

buff.ly

5

phyloseminar.org @phyloseminar.bsky.social · Jan 15

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.

1 1

phyloseminar.org @phyloseminar.bsky.social · Jan 14

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...

Phyloseminar #142: Aaron King (Michigan)

YouTube video by phyloseminar.org

www.youtube.com

2 3