Alison Feder
@alisonfeder.bsky.social
Rapid evolutionary dynamics in viruses, cancer and bacteria. Assistant professor at UW Genome Sciences and Freeman Hrabowski Scholar at HHMI. federlab.github.io
Pinned
Alison Feder
@alisonfeder.bsky.social
· Sep 10
The constant barrage of terrible news on bluesky has made me feel weird about promoting papers, but people in the lab have been doing so much amazing work over the past few months that I want to share a few brief teasers/links:
Are you coming for happy hour, @jrossibarra.bsky.social?
January 23, 2026 at 1:10 AM
Are you coming for happy hour, @jrossibarra.bsky.social?
Reposted by Alison Feder
Post-doc job alert! Please share with anyone who might be interested! @amersocvirology.bsky.social #virology #virosky #evolution
January 8, 2026 at 10:56 PM
Post-doc job alert! Please share with anyone who might be interested! @amersocvirology.bsky.social #virology #virosky #evolution
Reposted by Alison Feder
Excited that SpaceBar is now out in Nature Methods!🥳
We combined clone tracing with spatial transcriptomics to untangle what drives gene expression in tumors: a cell's identity or its neighborhood?
Most genes were driven by location, but some showed strong clonal patterns.
rdcu.be/eVhpc
We combined clone tracing with spatial transcriptomics to untangle what drives gene expression in tumors: a cell's identity or its neighborhood?
Most genes were driven by location, but some showed strong clonal patterns.
rdcu.be/eVhpc
SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics
Nature Methods - SpaceBar is a cellular barcoding strategy for simultaneous analysis of cell clonal and spatial identities.
rdcu.be
December 18, 2025 at 7:55 PM
Excited that SpaceBar is now out in Nature Methods!🥳
We combined clone tracing with spatial transcriptomics to untangle what drives gene expression in tumors: a cell's identity or its neighborhood?
Most genes were driven by location, but some showed strong clonal patterns.
rdcu.be/eVhpc
We combined clone tracing with spatial transcriptomics to untangle what drives gene expression in tumors: a cell's identity or its neighborhood?
Most genes were driven by location, but some showed strong clonal patterns.
rdcu.be/eVhpc
Amazing work, Ricky!!
December 17, 2025 at 9:22 PM
Amazing work, Ricky!!
Reposted by Alison Feder
If you are interested in this work and are looking for a postdoc position, please get in touch -- we are actively looking for someone to join our group at UCLA!
December 17, 2025 at 6:53 PM
If you are interested in this work and are looking for a postdoc position, please get in touch -- we are actively looking for someone to join our group at UCLA!
Amazing work, @rwolff.bsky.social and @nanditagarud.bsky.social!!!
December 17, 2025 at 9:14 PM
Amazing work, @rwolff.bsky.social and @nanditagarud.bsky.social!!!
Reposted by Alison Feder
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
www.nature.com
December 17, 2025 at 6:53 PM
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Thanks so much, Asher! The project was much enriched by conversations I had at your sociovirology meeting in Puerto Rico!
December 15, 2025 at 5:07 PM
Thanks so much, Asher! The project was much enriched by conversations I had at your sociovirology meeting in Puerto Rico!
Reposted by Alison Feder
Very cool work.
Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback
www.nature.com/articles/s41...
Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback
www.nature.com/articles/s41...
Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback - Nature Ecology & Evolution
A model of intrahost poliovirus replication shows that, after several rounds of replication, pocapavir, a poliovirus capsid inhibitor, collapses viral density, preventing intracellular interactions th...
www.nature.com
December 10, 2025 at 9:55 PM
Very cool work.
Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback
www.nature.com/articles/s41...
Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback
www.nature.com/articles/s41...
Reposted by Alison Feder
Over the past 5+ years I've had the honor of working with @wsdewitt.github.io @victora.bsky.social and many others on a project to "replay" affinity maturation evolution from a fixed starting point.
matsen.group/general/2025...
matsen.group/general/2025...
Replaying evolution to learn about the fitness landscape of affinity maturation
A five year collaboration with the Victora lab is bearing fruit for evolutionary biology.
matsen.group
December 11, 2025 at 5:36 PM
Over the past 5+ years I've had the honor of working with @wsdewitt.github.io @victora.bsky.social and many others on a project to "replay" affinity maturation evolution from a fixed starting point.
matsen.group/general/2025...
matsen.group/general/2025...
So much fun to work with Alex and Ben Kerr on this project, and to wade deeper into this exciting field of sociovirology. #socialviruses
We're also grateful for great suggestions from two anonymous reviewers during peer review.
www.nature.com/articles/s41...
We're also grateful for great suggestions from two anonymous reviewers during peer review.
www.nature.com/articles/s41...
Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback - Nature Ecology & Evolution
A model of intrahost poliovirus replication shows that, after several rounds of replication, pocapavir, a poliovirus capsid inhibitor, collapses viral density, preventing intracellular interactions th...
www.nature.com
December 10, 2025 at 9:07 PM
So much fun to work with Alex and Ben Kerr on this project, and to wade deeper into this exciting field of sociovirology. #socialviruses
We're also grateful for great suggestions from two anonymous reviewers during peer review.
www.nature.com/articles/s41...
We're also grateful for great suggestions from two anonymous reviewers during peer review.
www.nature.com/articles/s41...
Please check out the paper for our full results, and this nice press release put out by @uwnews.uw.edu!
newsroom.uw.edu/news-release...
newsroom.uw.edu/news-release...
Social lives of viruses affect antiviral effectiveness - UW Medicine | Newsroom
newsroom.uw.edu
December 10, 2025 at 9:07 PM
Please check out the paper for our full results, and this nice press release put out by @uwnews.uw.edu!
newsroom.uw.edu/news-release...
newsroom.uw.edu/news-release...
This parallels ongoing work in the treatment of cancers and bacteria showing that competitive inhibition and ecological interaction mediated by drug dosing can improve population control.
December 10, 2025 at 9:07 PM
This parallels ongoing work in the treatment of cancers and bacteria showing that competitive inhibition and ecological interaction mediated by drug dosing can improve population control.
Understanding this feedback could allow us to design more evolution-proof therapies by maintaining therapeutically useful social interactions over time.
@alexrob.bsky.social finds that neutralizing fewer viruses with weaker drugs can paradoxically lead to less resistance and lower viral loads.
@alexrob.bsky.social finds that neutralizing fewer viruses with weaker drugs can paradoxically lead to less resistance and lower viral loads.
December 10, 2025 at 9:07 PM
Understanding this feedback could allow us to design more evolution-proof therapies by maintaining therapeutically useful social interactions over time.
@alexrob.bsky.social finds that neutralizing fewer viruses with weaker drugs can paradoxically lead to less resistance and lower viral loads.
@alexrob.bsky.social finds that neutralizing fewer viruses with weaker drugs can paradoxically lead to less resistance and lower viral loads.
The point is much broader than poliovirus and pocapavir: if we're trying to design therapeutics that exploit social interactions between viruses, we need to account for the effects of therapeutic success in diminishing those interactions.
bsky.app/profile/alex...
bsky.app/profile/alex...
Big picture: the feedback loop between viral density leading to social interaction, which leads to realized phenotype, which alters fitness, leading to new viral densities, should be considered when designing optimal treatments.
December 10, 2025 at 9:07 PM
The point is much broader than poliovirus and pocapavir: if we're trying to design therapeutics that exploit social interactions between viruses, we need to account for the effects of therapeutic success in diminishing those interactions.
bsky.app/profile/alex...
bsky.app/profile/alex...
The answer? Sometimes! The key variable is the density of the viral population. When viruses coinfect often, interference is effective at arresting resistance evolution.
BUT, if the drug works well, it reduces viral density, ultimately allowing resistance to escape this interference.
BUT, if the drug works well, it reduces viral density, ultimately allowing resistance to escape this interference.
December 10, 2025 at 9:07 PM
The answer? Sometimes! The key variable is the density of the viral population. When viruses coinfect often, interference is effective at arresting resistance evolution.
BUT, if the drug works well, it reduces viral density, ultimately allowing resistance to escape this interference.
BUT, if the drug works well, it reduces viral density, ultimately allowing resistance to escape this interference.
In theory, this means that sus viruses should prevent resistance from spreading intra-host while it's rare.
Does it work? @alexrob.bsky.social built a poliovirus replication model to probe the impact of intra-cellular resource sharing, and validated it against experimental and clinical data.
Does it work? @alexrob.bsky.social built a poliovirus replication model to probe the impact of intra-cellular resource sharing, and validated it against experimental and clinical data.
December 10, 2025 at 9:07 PM
In theory, this means that sus viruses should prevent resistance from spreading intra-host while it's rare.
Does it work? @alexrob.bsky.social built a poliovirus replication model to probe the impact of intra-cellular resource sharing, and validated it against experimental and clinical data.
Does it work? @alexrob.bsky.social built a poliovirus replication model to probe the impact of intra-cellular resource sharing, and validated it against experimental and clinical data.
Pocapavir binds an oligomeric poliovirus capsid composed of 60 subunits.
Mutations can change this subunit's shape and prevent binding. However, if capsids contain both susceptible AND resistant subunits, drug can bind anyway.
As a result, sus viruses can sensitize res ones when they share a cell.
Mutations can change this subunit's shape and prevent binding. However, if capsids contain both susceptible AND resistant subunits, drug can bind anyway.
As a result, sus viruses can sensitize res ones when they share a cell.
December 10, 2025 at 9:07 PM
Pocapavir binds an oligomeric poliovirus capsid composed of 60 subunits.
Mutations can change this subunit's shape and prevent binding. However, if capsids contain both susceptible AND resistant subunits, drug can bind anyway.
As a result, sus viruses can sensitize res ones when they share a cell.
Mutations can change this subunit's shape and prevent binding. However, if capsids contain both susceptible AND resistant subunits, drug can bind anyway.
As a result, sus viruses can sensitize res ones when they share a cell.
So excited to share this work led by @alexrob.bsky.social with Ben Kerr!
We investigated a poliovirus capsid inhibitor that exploits a breakdown in the genotype-phenotype map to prevent drug resistance evolution. Or does it?
See Alex's thread, but a few extras:
#socialviruses #evosky #virosky 🧪
We investigated a poliovirus capsid inhibitor that exploits a breakdown in the genotype-phenotype map to prevent drug resistance evolution. Or does it?
See Alex's thread, but a few extras:
#socialviruses #evosky #virosky 🧪
My first lead author paper is out with Ben Kerr and @alisonfeder.bsky.social! We found that making an antiviral too strong can sometimes make resistance easier to evolve. This has implications for how we design drugs, choose doses, and think about viral evolution in the face of treatment. (1/n)
Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback - Nature Ecology & Evolution
A model of intrahost poliovirus replication shows that, after several rounds of replication, pocapavir, a poliovirus capsid inhibitor, collapses viral density, preventing intracellular interactions th...
www.nature.com
December 10, 2025 at 9:07 PM
So excited to share this work led by @alexrob.bsky.social with Ben Kerr!
We investigated a poliovirus capsid inhibitor that exploits a breakdown in the genotype-phenotype map to prevent drug resistance evolution. Or does it?
See Alex's thread, but a few extras:
#socialviruses #evosky #virosky 🧪
We investigated a poliovirus capsid inhibitor that exploits a breakdown in the genotype-phenotype map to prevent drug resistance evolution. Or does it?
See Alex's thread, but a few extras:
#socialviruses #evosky #virosky 🧪
Reposted by Alison Feder
It was great to write a brief commentary with @sociovirology.bsky.social on @nanamikubota.bsky.social and @vscooper.micropopbio.org's recent discovery of cheat-driven cycles in Pseudomonas (www.cell.com/current-biol... - amazing example of the tragedy of the commons!
🧪 #socialviruses #evosky
🧪 #socialviruses #evosky
Phage–bacteria dynamics: The tragedy of the commons at hyperspeed
A recent study found that apparently stable coexistence between a clinically important
pathogen, Pseudomonas aeruginosa, and its integrated prophages can break down, setting
off an evolutionary cycle ...
www.cell.com
December 4, 2025 at 8:56 PM
It was great to write a brief commentary with @sociovirology.bsky.social on @nanamikubota.bsky.social and @vscooper.micropopbio.org's recent discovery of cheat-driven cycles in Pseudomonas (www.cell.com/current-biol... - amazing example of the tragedy of the commons!
🧪 #socialviruses #evosky
🧪 #socialviruses #evosky
Reposted by Alison Feder
Hi everyone! I'm co-organizing this retreat/workshop June 15-19 for those looking to get started in mathematical/computational modeling of biological processes. Location is a beautiful farm in NC. Please share with students and others who want to build modeling skills. Interdisciplinarity welcome!
December 2, 2025 at 7:00 PM
Hi everyone! I'm co-organizing this retreat/workshop June 15-19 for those looking to get started in mathematical/computational modeling of biological processes. Location is a beautiful farm in NC. Please share with students and others who want to build modeling skills. Interdisciplinarity welcome!
Reposted by Alison Feder
The world is a few steps closer to a cure for #HIV, a hopeful sign illuminated by two studies published Monday featuring work from Fred Hutch's Lillian Cohn, Daniel Reeves and others. #WorldAIDSDay https://bit.ly/44JxZ6X
Path to HIV cure includes Seattle scientists
Two new studies provide insights into a possible cure for HIV, and feature the work of researchers from the UW and Fred Hutchinson Cancer Center.
bit.ly
December 1, 2025 at 11:34 PM
The world is a few steps closer to a cure for #HIV, a hopeful sign illuminated by two studies published Monday featuring work from Fred Hutch's Lillian Cohn, Daniel Reeves and others. #WorldAIDSDay https://bit.ly/44JxZ6X
Really enjoying reading your updates/highlights from the meeting! Thanks for posting!
October 29, 2025 at 9:53 PM
Really enjoying reading your updates/highlights from the meeting! Thanks for posting!
Reposted by Alison Feder
We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT
October 15, 2025 at 3:53 PM
We're excited to be recruiting an NIH funded postdoc to work in the Coop lab at UC Davis. We're specifically interested in candidates who are want to work at the intersection of human genetics, GWAS, and population genetics modeling. Please RT
Reposted by Alison Feder
Happy to have started as an @hhmi.org Freeman Hrabowski Scholar! Incredibly grateful for this opportunity and am excited for some very cool new directions! We are *HIRING*, especially postdocs! Please reach out if you’re interested in uterine and pregnancy biology. Please repost!
October 9, 2025 at 7:42 PM
Happy to have started as an @hhmi.org Freeman Hrabowski Scholar! Incredibly grateful for this opportunity and am excited for some very cool new directions! We are *HIRING*, especially postdocs! Please reach out if you’re interested in uterine and pregnancy biology. Please repost!