I'm excited to share a preprint that's been years in the making: the idea took shape during the COVID pandemic. Anecdotally, people would sometimes spread COVID at work but not at home, and vice versa. Why? One explanation would be if infectiousness is fleeting...

How bursty infectiousness shapes epidemic dynamics

An epidemic’s expected course is determined by the magnitude and timing of a typical person’s infectiousness — captured, in turn, by the basic reproduction number and the generation-time distribution....

medrxiv.org

@alnajifg.bsky.social's long-delayed masterpiece (spanning his time in my and Marco Vignuzzi's labs) on influenza virus WT/DelVG co-evolutionary dynamics is finally out!! Lots of exciting data about how DelVGs evolve and compete within complex populations. www.nature.com/articles/s41...

Fadi Alnaji@alnajifg.bsky.social · 9mo ago

Finally, it's up on bioRxiv! It's been a rewarding journey shaping this story. My deepest gratitude to @vignuzzilab.bsky.social and @christopherbrooke.bsky.social for their incredible support, and to the @mcbillinois.bsky.social & @astar-idlabs.bsky.social for enabling this research

Happy to see @lizthayer.bsky.social's magnum opus published in peer-reviewed form in @cp-cellsystems.bsky.social!! Check it out! www.cell.com/cell-systems...

Single-cell heterogeneity in interferon induction potential is heritable and governed by variation in cell state

Thayer et al. used multiple approaches to uncover why only a few cells in a population express IFN upon RNA stimulation. They found that variation in cell signaling state at the time of stimulation is...

cell.com

Chris Brooke@christopherbrooke.bsky.social · 8mo ago

Check out @lizthayer.bsky.social's new preprint exploring factors that influence cell-to-cell heterogeneity in interferon (IFN) induction potential!

OUR WORK IS NOT DONE. In unusual move, NSF issued a request for information on plan to conform grant policies to the proposed (unfinalized) OMB rule. Plan includes changes to grant termination provisions & disallowing publication costs. Comments due August 24. www.federalregister.gov/documents/20...

Agency Information Collection Activities: Comment Request; National Science Foundation Proposal/Award Information-NSF Guidance on Financial Assistance

The U.S. National Science Foundation (NSF) is announcing plans to renew and revise its collection for its financial assistance policies and procedures. In accordance with the requirements of the Paper...

federalregister.gov

Not too late -- COMMENT! Stop this horrendous, existential threat to USA science. Some resources to write your comment are pinned to my profile.

Jenna Norton@jenna-m-norton.bsky.social · 3w ago

I submitted my comment on the proposed OMB rule. Sharing here to the extent it’s useful. Today is the last day to comment. If you have not yet commented, please do! substack.com/@jennanorton...

Lab account is official! go follow @antigenevo.bsky.social 👇👇👇 research.pasteur.fr/en/team/anti...

Antigen Evolution & Design - Research

Most pathogens have proteins on their surface which are recognised by our immune system and prime it to make antibodies that protect us from future infection. Vaccines contain these proteins to activa...

research.pasteur.fr

Antigen Evolution & Design Lab@antigenevo.bsky.social · 4w ago

Inaugural post! We are a brand new lab @pasteur.fr studying how pathogen antigens evolve and how we can exploit these proteins' evolution to make better vaccines! Read a few words from the currently sole member of the lab @spyroslytras.bsky.social below! 😁 www.pasteur.fr/en/research-...

Jack Dorman, @williambakhache.bsky.social and I wrote a review of #DeepMutationalScanning ( #DMS ) applications in #virology, exploring the ways it’s been used to understand the rules of #virus #evolution and #immunity. We also explore new applications of the technology. Check it out!

Scanning the horizon: deep mutational scanning approaches in virology | Journal of Virology

The development of deep mutational scanning (DMS) approaches has led to a fundamental shift in our ability to connect viral genotype and phenotype (1) and accelerated our understanding of viral evolut...

journals.asm.org

Since the 1960s, the genetic code has been used to predict protein sequences from DNA and mRNA sequences. Our @nature.com article demonstrates that these predictions miss thousands of protein sequences present in human tissues. www.nature.com/articles/s41... 1/

Nikolai Slavov@slavov-n.bsky.social · 2y ago

We report many proteins not predicted by the genetic code. They are stable & abundant O( 10³ ) copies / cell. Generative mechanisms include codon-anticodon mismatches & RNA modifications. Their abundance depends on codon frequency & protein stability. www.biorxiv.org/content/10.1...

Welcome to the Fascist States of America, where the EiC of a leading journal is forcibly removed by police for passing out his own editorial at the annual meeting of the field’s association…because it’s “too political” (read: it calls on scientists to speak out & stand up). We are here. This is it.

This started in 2019 as daydreamy PhD student musings with Tatsuya Araki. We're as excited as ever about germinal centers as a platform for experimental evolution. Many thanks to PIs @victora.bsky.social @matsen.bsky.social, co-1st authors Ashni Vora and Tatsuya, and many other key collaborators!

Replaying germinal center evolution on a quantified affinity landscape

Antibody affinity maturation results from a somatic evolutionary process that takes place in the germinal center. A “parallel replay” experiment on germinal center B cells reveals the evolutionary for...

cell.com

On OMB's proposal to make all grants political: "Speak up! Now’s the time! Standing by the side of the room, glancing around nervously and hoping that somebody else does something will lead us to disaster. These are not normal times, so stop acting as if they are." www.science.org/content/blog...

Action! Action Now.

science.org

Check out our new review with @mfarjo.bsky.social on what we know about the functional and evolutionary consequences of virus-virus interactions within viral populations, out now in @annualreviews.bsky.social: www.annualreviews.org/content/jour... Hope you like it!

Heterogeneity and Collective Interactions Within Viral Populations

The existence of viruses as obligate intracellular parasites with high mutation rates sets them apart from other forms of life in fundamental ways. Frequent errors in replication and assembly processe...

annualreviews.org

Very excited about our recent preprint- @lindashuyingxu.bsky.social and collabs discover that neutrophils repurpose their nucleolus for storage of pre-made IFN-I to be rapidly released via a nucleolar stress response that results in nucleolar extrusion and secretion. www.biorxiv.org/content/10.6...

elizabethginexi.substack.com/p/what-we-ne...

What We Need to do NEXT: OMB’s Proposed Federal Financial Assistance Rule (OMB 2026-10817)

What OMB’s Proposed Federal Financial Assistance Rule Means in Practice

elizabethginexi.substack.com

I'm very excited to share this preprint led by @sorenlouislarsen.bsky.social and Chloe Yand, and made possible by the collaboration with my friend and colleague @ayesha-mahmud.bsky.social. www.medrxiv.org/content/10.6...

Same household, different choices: variation in health behaviors related to respiratory viruses in Illinois

While SARS-CoV-2 and influenza continue to place a significant burden on population health, within-household differences in decisions towards vaccination and seeking care across these two pathogens, a...

medrxiv.org

If you wish to submit a public comment on this, you can do so at www.regulations.gov/commenton/OM.... Public comments regarding the legality of the rule, how arbitrary and capricious the changes are, negative impacts on cities and states, etc can be used as evidence in subsequent lawsuits.

elizabethginexi.bsky.social@elizabethginexi.bsky.social · 2mo ago

Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule. Russell Vought is going destroy American Science. elizabethginexi.substack.com/p/summary-of...

This is bad. Bad for researchers. Bad for science. Bad for universities. Bad for professional associations. For example: 1. Every award would be vetted by political appointees, who could overrule peer reviewers and deny the award if it doesn't advance the president's priorities. 1/🧵

elizabethginexi.bsky.social@elizabethginexi.bsky.social · 2mo ago

Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule. Russell Vought is going destroy American Science. elizabethginexi.substack.com/p/summary-of...

And, here, in much more detail. This is an absolutely critical read for all federally funded scientists and institutions. Now is not the time to sit in the corner, hoping you won't be noticed - now is the time for action. elizabethginexi.substack.com/p/summary-of...

Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule

Russell Vought is going destroy American Science

elizabethginexi.substack.com

Thrilled to announce that the Department of Microbiology at the University of Washington, School of Medicine is hiring at the Assistant Professor level (tenure-track)! The Pacific Northwest is an awesome place to live and do science 🧪🦠. Join us! apply.interfolio.com/185622 Applications due 8/1.

Please share widely! Abstract submissions open for the 2026 Jacques Monod conference: Ecology and evolution of host-parasite interactions in a changing world! Held in beautiful Roscoff France from November 2- 6, 2026. Abstracts submission deadline : June 6 cjm.sb-roscoff.fr/en/conferenc...

Absolutely extraordinary work from Hui Gao, John Briggs and co @mpibiochem.bsky.social on the structure of the influenza matrix protein in situ, particularly in filamentous virions. It's beautiful, and answers questions I've been wondering about for twenty years www.biorxiv.org/content/10.6...

Latent endogenous giant viruses drive active infection and inheritance in a multicellular algal host www.nature.com/articles/s41...

Latent endogenous giant viruses drive active infection and inheritance in a multicellular algal host - Nature Microbiology

Giant endogenous viral elements integrated into the multicellular alga Ectocarpus are reactivated by specific temperature cues, driving productive latent viral infections.

nature.com

Scoop: There has been a massive shakeup at the US National Institute of Allergy and Infectious Diseases (NIAID). Eight of the top ten officials have now been pushed out since President Donald Trump took office. In @nature.com www.nature.com/articles/d41...

Exclusive: NIH ousts infectious-disease leaders as COVID scientists face US charges

Eight of the top ten officials at the US National Institute of Allergy and Infectious Diseases have now been pushed out since President Donald Trump took office.

nature.com

Excited to announce that we are moving the lab to Minneapolis to join the University of Minnesota Department of Microbiology & Immunology and Institute on Infectious Diseases this summer!! We will be hiring so please reach out if interested in viral evolution, viral immunology, etc.!!

“HHS is punishing a world-class scientist who was working to protect people against pandemics, and if he had been listened to more thoroughly, we might have been better prepared for SARS-CoV-2” This might be the most insane thing yet. www.science.org/content/arti...

Virologist accused of starting COVID-19 will fight U.S. ban on funding

HHS memo says Ralph Baric had a “pattern of deception” in describing virus studies long before pandemic

science.org

“The message, very clearly, they’re sending is, do not speak out on behalf of Chinese postdocs. If you do, you’re going to pay a penalty...It seems pretty obvious that this is an attempt by the current administration to silence people that question their activities." — Roger Innes, IU AAUP member

A Professor Defended a Postdoc Who Was Deported. Now His Lab Has Been Suddenly Locked Down.

Work at an Indiana University biology lab was halted amid federal scrutiny, affecting dozens of researchers. “The damage is significant and mounting,” the department chair told The Chronicle.

chronicle.com

www.science.org/content/arti...

Virologist accused of starting COVID-19 will fight U.S. ban on funding

HHS memo says Ralph Baric had a “pattern of deception” in describing virus studies long before pandemic

science.org

With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...

If you want to know what 3′UTRs with long conserved sequence stretches do, check out our BioRxiv preprint doi.org/10.64898/202.... They form functional intermolecular 3′UTR-3′UTR interactions that enable co-folding of proteins to rapidly induce transcriptional programs.

The ISG Atlas: a loss-of-function analysis characterizes antiviral properties of interferon stimulated genes www.nature.com/articles/s41... @natcomms.nature.com