Alison Feder
Rapid evolutionary dynamics in viruses, cancer and bacteria. Assistant professor at UW Genome Sciences and Freeman Hrabowski Scholar at HHMI. federlab.github.io
- Are you coming for happy hour, @jrossibarra.bsky.social?
- Reposted by Alison FederPost-doc job alert! Please share with anyone who might be interested! @amersocvirology.bsky.social #virology #virosky #evolution
- Reposted by Alison FederExcited 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
- Reposted by Alison FederIf 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!
- Reposted by Alison FederGrateful 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...
- Reposted by Alison FederVery cool work. 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... - 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 🧪
- 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)
- 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.
- 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.
-
View full threadSo 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...
- Reposted by Alison FederIt 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
- Reposted by Alison FederHi 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 FederThe 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 bit.ly/44JxZ6X
- Reposted by Alison FederWe'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 FederHappy 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!
- 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:
- 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...
- 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...
-
View full threadThere are a bunch of other really exciting projects that aren’t in preprint form yet that I’m looking forward to sharing with the world too, so stay tuned! I'm grateful to get to come to lab each day and work with these brilliant people on interesting problems!
- Reposted by Alison FederStudying cancer evolution needs multi-region or single cell seq for phylogenetics, right? Amazingly (I think!) we found single-sample bulk methylation suffices, via analysis of "fluctuating methylation". In @nature.com today led by brilliant @calumgabbutt.bsky.social www.nature.com/articles/s41...
- Reposted by Alison FederApplying to the NSF-GRFP (or another fellowship) on a tight deadline? We built a 7-week guide + timeline to get you from draft to submission. It’s not too late — you’ve got this! ✨ 🔗 cientificolatino.com/apply-in-7-weeks #NSFGRFP #GradSchool #Fellowship
- Reposted by Alison FederIn these dark times, it comes as a rare pleasure to highlight @natanaels.bsky.social & @marcdemanuel.bsky.social's work on germline and somatic mutations in humans. 1/n www.biorxiv.org/cgi/content/...
- Reposted by Alison FederHelp us give a warm welcome to Dr. Chadi Saad-Roy, who is joining UBC Mathematics this fall as an Assistant Professor, jointly appointed in the Department of Microbiology and Immunology (@ubcmicroimmuno.bsky.social). Full details tinyurl.com/4zwdmr8b
- Amazing new work and video from Pleuni!
- I made a video about my new paper. I hope you enjoy it! vimeo.com/1113132836?s...
- Reposted by Alison FederHow common are frequency dependent fitness effects? New preprint out today 👇 doi.org/10.1101/2025...
- Reposted by Alison FederI'm excited to announce our new biorxiv preprint, wherein we investigate the evolution of the weirdest genetic locus I've ever seen! Behold the tgr genes of the social amoeba, which mediate self/non-self discrimination during facultative multicellularity 🐅 🧵 1/ www.biorxiv.org/content/10.1...
- Reposted by Alison FederThe Mathieson Lab at the University of Pennsylvania is hiring a computational postdoc in machine learning and evolutionary biology. Apply with a CV and references: smathi@sas.upenn.edu. More info: saramathieson.github.io/lab #postdoc
- Reposted by Alison FederI am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!
- Reposted by Alison FederThe Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more. recruit.ap.uci.edu/JPF09601
- Extensive parallelism at the level of font choice suggests avenir is adaptive at the microbial population biology GRC
- Reposted by Alison FederLooking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days! go.bsky.app/GGxRjzCat://did:plc:biu33qzl4taulu3ns5vkitw4/app.bsky.graph.starterpack/3lt3c5yncqg2l
- Reposted by Alison FederThere is one month left to apply for our Simons Graduate Fellowships in Ecology and Evolution! These awards provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in #ecology and #evolution. www.simonsfoundation.org/grant/simons... #science
- Reposted by Alison Feder📣 Applications now open PATH award supports early-career researchers studying the pathogenesis of infectious diseases in humans 💰 $505K over 5 years 🔬 For mid-to-late assistant professors 📅 LOI due: 07/17/25 Apply now 👉 buff.ly/qcSSxbq
- I'm really honored to have received the early career award from @official-smbe.bsky.social, a society that has been an important part of my scientific experience.
- SMBE is delighted to announce our 2025 Faculty Award Winners! Today, we focus on our SMBE Early-Career Excellence Award winner, Alison Feder (@alisonfeder.bsky.social) ⭐ 2025 Winners: members.smbe.org/news/Details... 📄 Information on the Faculty Awards: www.smbe.org/faculty-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.
- I’ve since been back to many SMBEs/regional meetings. SMBE has enabled me to organize symposia, including one with @ksxue.bsky.social when we were only graduate students! I’ve had the opportunity to publish in MBE, and to review for MBE and GBE. academic.oup.com/mbe/article/...
-
View full threadI’m grateful to SMBE for this recognition of the lab’s work, but also much more generally for the important role that they play in our scientific community.
- Reposted by Alison FederPOSTDOC ALERT: Applications now open for SeaBridge postdoc fellowship; opportunity to work on leading-edge biotech w/researchers at the Seattle Hub for Synthetic Biology. brotmanbaty.org/news/new-pos... @marionpepper.bsky.social @jshendure.bsky.social @coletrapnell.bsky.social
- Reposted by Alison Feder[This post could not be retrieved]
- Reposted by Alison FederGet the word out far and wide. New opportunity from the Simons Foundation in the Eco-Evo space. 2026 Simons Graduate Fellowship in Ecology and Evolution Awards, due July 31, 2025, only for incoming PhD students who plan to start their PhDs in Fall 2026. www.simonsfoundation.org/grant/simons...
- Reposted by Alison FederI called my senators about the NIH and NSF cuts this morning (made easy with @5calls.org)! I'll be calling every day this week and encouraging friends & family to do the same
- Reposted by Alison FederOur new big review on Pseudomonas aeruginosa. Hope you enjoy reading it. www.nature.com/articles/s41...
- Reposted by Alison FederHow can one efficiently simulate phylodynamics for populations with billions of individuals, as is typical in many applications, e.g., viral evolution and cancer genomics? In this work with M. Celentano, @wsdewitt.github.io , & S. Prillo, we provide a solution. doi.org/10.1073/pnas... 1/n
- Recasting the perils of phylodynamic non-identifiability as a feature not a bug, we show that a unique forward-equivalent process enables exact and efficient simulation from arbitrarily large populations. With M Celentano, S Prillo, @yun-s-song.bsky.social www.pnas.org/doi/10.1073/pnas.2412978122
- Reposted by Alison FederAnnouncing the 2025 Investigators in the Pathogenesis of Infectious Disease www.bwfund.org/news/announc... #bwfpath
- Really excited about this new work from Sam Hart (and joint with @kelleyharris.bsky.social) trying to disentangle mutational differences between groups of cancers. Check out Kelley's thread with the major results!
- If you’ve ever wondered about the statistical significance of differences among mutational signature profiles, check out our new Aggregate Mutation Spectrum Distance (AMSD) preprint co-led by Sam Hart and @alisonfeder.bsky.social with @nalcala.bsky.social www.biorxiv.org/cgi/content/...
- Reposted by Alison FederYesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab
- Reposted by Alison FederI received a surprising and disturbing request from NIH on Friday. They wrote to cancel a subaward to Hong Kong on one of my grants. (This was disturbing but not surprising.) They also ordered us not to interact with our collaborators in Hong Kong on any work under the award:
- Reposted by Alison FederHearty congratulations to Anurag Agrawal, Amy Angert, and Graham Coop upon their election to the American Academy of Arts & Sciences, for their work illuminating the natural world around us. This recognition is very much deserved.
- Reposted by Alison FederInterested in postdoc opportunities in Seattle, WA? Join us May 6th for Seattle DROP, a virtual event about biomedical research in Seattle. Hear from recruiting faculty, finding the right mentor and enjoy lunch on us via a delivery voucher within the US! Registration: tinyurl.com/seattledrop25
- Reposted by Alison FederAdd R25s to that list. Our NIH funding got straight up cancelled today for the two R25s that my team runs at Columbia for post-bacs and high-school students. I fear for our young scholars, who love learning about the brain and now are losing opportunities to be tomorrow's neuroscientists. 🧪
- Reposted by Alison FederPathogen genomes can provide insights into underlying disease transmission patterns but new methods are needed to analyze large genome datasets. Our work using identical pathogen sequences to characterize fine scale SARS-CoV-2 transmission was just published in @nature.com tinyurl.com/bdzk9xjj 🥳
- Reposted by Alison Feder📣Excited to share my last postdoc paper with @soumya-boston.bsky.social on eQTL mechanisms depending on where the RNA is in the cell! @broadinstitute.org @harvardmed.bsky.social TL;DR:Early RNA eQTL variants in the nucleus and late RNA eQTL variants in the cytosol have distinct molecular mechanism🧵
- Reposted by Alison FederThis is not news to most scientists by now, but others might be interested. Biomedical research is undergoing tremendous damage, even beyond the firings at NIH, CDC, and NSF; the suppression of data sharing; and the attacks on initiatives to improve scientific quality.
- Reposted by Alison FederMeasles infection can cause pneumonia or encephalitis, even death, soon after infection. What most folks don't know is that measles can also kill years later, from SSPE, subacute sclerosing pan-encephalitis. It's brain damage — incurable, irreversible, progressive, and nearly always fatal. 1/13
- Reposted by Alison FederNo job ad yet, but I'll be hiring a postdoc at Purdue in population genetics/quantitative genetics/genomics in plants. DM if you have relevant experience and are potentially interested.
- Reposted by Alison FederIn a new study led by Caelan Radford, we use deep mutational scanning to systematically compare the escape mutations from two broadly neutralizing antibodies in a clade A versus clade B HIV Envelope. www.biorxiv.org/content/10.1...
- Reposted by Alison FederGenome Sciences is looking for a Grants Manager for the Model Organism Genetics labs (which include me!): uwhires.admin.washington.edu/ENG/candidat...
- Reposted by Alison FederHello world! I'm starting out on bluesky with a job posting - we're looking for lab research tech who shares our love of bugs. More info here brownlab.biology.gatech.edu/opportunities/
- Oh yeah?
- Reposted by Alison FederVery excited to have this paper officially out. This one is pretty special... Unfortunately, @kevinwoodum.bsky.social passed away when this paper was in its final stages. He was my biggest supporter, and I miss him deeply as a mentor and friend.
- Reposted by Alison FederI think our preprint on mutation spectra and cancer evolution makes wonderful connections between theory and experiments in asexual bacteria and somatic evolution data from tumors. But we're struggling finding the right target journal. Any suggestions? doi.org/10.1101/2024...
- Reposted by Alison FederIs it “winner-takes all” when the simplest living things compete? Check out my fresh publication on phage coexistence in Science and a thread below🧵 www.science.org/doi/10.1126/...
- Reposted by Alison FederAfter a long and winding odyssey, excited to finally drop anchor in open-access waters. This preprint shows how neutral allele frequency time series can illuminate disease transmission rates between communities— key for epidemic fore- & backcasting. medrxiv.org/content/10.1... 🧵
- Reposted by Alison FederDo mutations that drive evolution improve many traits or few? Does this change over the course of evolution? Excited to share our work in PLOS Biology exploring these questions in the first 2 adaptive steps w/ Yuping Li, @gsherloc.bsky.social, @petrovadmitri.bsky.social 🧵 doi.org/10.1371/jour...
- Reposted by Alison FederA careful dose of ignorance — a story of how my not reading two papers, many years ago, was vital to my career's path. waynemaddison.wordpress.com/2024/12/05/a...
- Reposted by Alison FederNew paper from the Olanrewaju Lab. We showed that we can measure HIV medications, including one used in recently approved long-acting injectable treatments, based on the drugs’ inhibition of viral DNA synthesis. Paper: doi.org/10.1007/s002... Preprint: doi.org/10.1101/2024... 1/5
