Alison Feder
@alisonfeder.bsky.social
Rapid evolutionary dynamics in viruses, cancer and bacteria. Assistant professor at UW Genome Sciences. federlab.github.io
Hunter Colegrove extends a model of epithelial homoeostasis to investigate how mucosal gene therapy could be used to prevent the spread of pathogenic mutations in people with Fanconi anemia (with Ray Monnat)!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 10, 2025 at 4:46 PM
Hunter Colegrove extends a model of epithelial homoeostasis to investigate how mucosal gene therapy could be used to prevent the spread of pathogenic mutations in people with Fanconi anemia (with Ray Monnat)!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Yingnan Gao has a major overhaul on his paper investigating how to detect selection in lineage tracing data using tree balance statistics! #evoSky
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 10, 2025 at 4:46 PM
Yingnan Gao has a major overhaul on his paper investigating how to detect selection in lineage tracing data using tree balance statistics! #evoSky
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Sam Hart describes and applies a method to distinguish differences in mutational processes between groups of cancers without signature decomposition (joint work with @kelleyharris.bsky.social and in collaboration with @nalcala.bsky.social )! #Genomics 🖥️ 🧬
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 10, 2025 at 4:46 PM
Sam Hart describes and applies a method to distinguish differences in mutational processes between groups of cancers without signature decomposition (joint work with @kelleyharris.bsky.social and in collaboration with @nalcala.bsky.social )! #Genomics 🖥️ 🧬
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Alex Robertson @alexrob.bsky.social has some very exciting new results describing when and how intracellular interactions among polioviruses can slow resistance evolution (with Ben Kerr)!: #VirEvol #evoSky
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 10, 2025 at 4:46 PM
Alex Robertson @alexrob.bsky.social has some very exciting new results describing when and how intracellular interactions among polioviruses can slow resistance evolution (with Ben Kerr)!: #VirEvol #evoSky
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Elena Romero led a new preprint detailing joint work with Lillian Cohn's lab at Fred Hutch describing really crazy parallelism in in vivo HIV escape from broadly neutralizing antibodies! #VirEvol #evoSky
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 10, 2025 at 4:46 PM
Elena Romero led a new preprint detailing joint work with Lillian Cohn's lab at Fred Hutch describing really crazy parallelism in in vivo HIV escape from broadly neutralizing antibodies! #VirEvol #evoSky
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
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:
September 10, 2025 at 4:46 PM
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:
Since starting my lab, I’ve been back to meetings with several of my graduate students. Elena Romero got to go to SMBE 2023 enabled by one of SMBE's Young Investigator Travel Awards.
June 27, 2025 at 3:40 PM
Since starting my lab, I’ve been back to meetings with several of my graduate students. Elena Romero got to go to SMBE 2023 enabled by one of SMBE's Young Investigator Travel Awards.
SMBE was my first real conference. I went as an undergrad in 2011 (with many thanks to @jplotkin.bsky.social). It was a completely mind-blowing experience to get to go to Kyoto and talk about science for four days. It solidified my decision to go to graduate school in this field.
June 27, 2025 at 3:40 PM
SMBE was my first real conference. I went as an undergrad in 2011 (with many thanks to @jplotkin.bsky.social). It was a completely mind-blowing experience to get to go to Kyoto and talk about science for four days. It solidified my decision to go to graduate school in this field.
April 2, 2024 at 8:17 PM
Does anyone know of an earlier map of spatial genetic variation than this one for chr 3 inversions in D. pseudoobscura from Dobzhansky from 1939? Maybe @gcbias.bsky.social?
February 20, 2024 at 9:45 PM
Does anyone know of an earlier map of spatial genetic variation than this one for chr 3 inversions in D. pseudoobscura from Dobzhansky from 1939? Maybe @gcbias.bsky.social?
Wow... joint spatial, lineage tracing and cell state capture 👀 www.biorxiv.org/content/10.1...
January 4, 2024 at 5:33 PM
Wow... joint spatial, lineage tracing and cell state capture 👀 www.biorxiv.org/content/10.1...
We also present our best guess of the chronology of how MeV comes to take over the brain. 13/
January 3, 2024 at 5:50 PM
We also present our best guess of the chronology of how MeV comes to take over the brain. 13/
À la Novembre et al, we also checked if viral genes mirror geography in the brain. They sort of do? 12/
January 3, 2024 at 5:49 PM
À la Novembre et al, we also checked if viral genes mirror geography in the brain. They sort of do? 12/
This doesn’t even include lots of other cool stuff in the paper. For example, inspired by approaches from cancer genomics, Will turned short reads with minimal linkage info into a phylogenetic tree, then into a map of MeV “sub-clones” across the brain. 11/
January 3, 2024 at 5:49 PM
This doesn’t even include lots of other cool stuff in the paper. For example, inspired by approaches from cancer genomics, Will turned short reads with minimal linkage info into a phylogenetic tree, then into a map of MeV “sub-clones” across the brain. 11/
We hypothesized that an intermediate frequency driver mut truncating the F tail might be on G1 or G2, and could be cooperating with the other lineage to not “overshoot” optimal fusogenicity. But when we checked, the mut was on both G1 and G2 backgrounds but fixed on neither! 7/
January 3, 2024 at 5:48 PM
We hypothesized that an intermediate frequency driver mut truncating the F tail might be on G1 or G2, and could be cooperating with the other lineage to not “overshoot” optimal fusogenicity. But when we checked, the mut was on both G1 and G2 backgrounds but fixed on neither! 7/
Through ampFISH, Iris was able to observe this co-localization even more clearly. The G1 and G2 viruses not only share a brain region, but frequently the exact same cell. Could they be cooperating? 5/
January 3, 2024 at 5:47 PM
Through ampFISH, Iris was able to observe this co-localization even more clearly. The G1 and G2 viruses not only share a brain region, but frequently the exact same cell. Could they be cooperating? 5/
Second, we saw two clusters of mutations that appeared at similar freqs across regions. The cluster freqs were complementary within a region (i.e., f_A + f_B = 1), suggesting the coexistence of two distinct viral lineages. Both lineages (G1 and G2) were seen in all locations. 4/
January 3, 2024 at 5:47 PM
Second, we saw two clusters of mutations that appeared at similar freqs across regions. The cluster freqs were complementary within a region (i.e., f_A + f_B = 1), suggesting the coexistence of two distinct viral lineages. Both lineages (G1 and G2) were seen in all locations. 4/
To do this, we performed extensive spatial RNA sequencing on a frozen brain specimen of an individual who succumbed to SSPE. All sequenced regions contained MeV, and in certain parts of the brain, 1 in 5 reads mapped to the MeV genome! 2/
January 3, 2024 at 5:45 PM
To do this, we performed extensive spatial RNA sequencing on a frozen brain specimen of an individual who succumbed to SSPE. All sequenced regions contained MeV, and in certain parts of the brain, 1 in 5 reads mapped to the MeV genome! 2/
Excited to share a new collaborative paper exploring how measles can come to infect the brain: journals.plos.org/plospathogen...
I'll write a thread after the break, but for now - really fun to collaborate with the recently defended Will Hannon, and the Cattaneo lab. Lots left to understand here!
I'll write a thread after the break, but for now - really fun to collaborate with the recently defended Will Hannon, and the Cattaneo lab. Lots left to understand here!
December 21, 2023 at 9:03 PM
Excited to share a new collaborative paper exploring how measles can come to infect the brain: journals.plos.org/plospathogen...
I'll write a thread after the break, but for now - really fun to collaborate with the recently defended Will Hannon, and the Cattaneo lab. Lots left to understand here!
I'll write a thread after the break, but for now - really fun to collaborate with the recently defended Will Hannon, and the Cattaneo lab. Lots left to understand here!
Are you an early career scientist who wants to pursue a research project in the lab of a Fred Hutch Computational Biologist mentor? If yes, then the Mahan Fellowship is for you. Apply by Dec. 1, 2023! Learn more: bit.ly/3YWS2e8
November 15, 2023 at 8:27 PM
Are you an early career scientist who wants to pursue a research project in the lab of a Fred Hutch Computational Biologist mentor? If yes, then the Mahan Fellowship is for you. Apply by Dec. 1, 2023! Learn more: bit.ly/3YWS2e8
So fun to sneak into @nanditagarud.bsky.social's seminar today, where she shared many ridiculously cool things her lab has discovered over the past few years!
I wanted to include @mharris.bsky.social and (longer!) @jonmah.bsky.social results, but my whiteboard was too small!
I wanted to include @mharris.bsky.social and (longer!) @jonmah.bsky.social results, but my whiteboard was too small!
October 18, 2023 at 8:01 PM
So fun to sneak into @nanditagarud.bsky.social's seminar today, where she shared many ridiculously cool things her lab has discovered over the past few years!
I wanted to include @mharris.bsky.social and (longer!) @jonmah.bsky.social results, but my whiteboard was too small!
I wanted to include @mharris.bsky.social and (longer!) @jonmah.bsky.social results, but my whiteboard was too small!
Google scholar once again finds me extremely non-diverse giant shoulders on which to stand.
October 13, 2023 at 1:32 AM
Google scholar once again finds me extremely non-diverse giant shoulders on which to stand.