A few months ago, @elena-romero.bsky.social published a paper showing that HIV escape from broadly neutralizing antibody 10-1074 is driven by very recurrent mutation. In her latest, she asks - just how soft are the signatures of these sweeps? www.biorxiv.org/content/10.6...

Haplotype and diversity signatures of ultra-soft selective sweeps in HIV-1

Many urgent medical and agricultural challenges are driven by resistance evolution via soft selective sweeps of multiple simultaneous mutations. Standard approaches to detect these mutations involve g...

biorxiv.org

Applications are open for SFI's 2027 Complexity Postdoctoral Fellowships. SFI is looking for recent Ph.D. graduates with strong quantitative and computational skills who want to pursue independent, transdisciplinary research. Deadline: September 30, 2026 Apply: santafe.edu/sfifellowship

Dear microbiome enthusiasts: I'm excited to be moving my lab to New York University this fall (& the NYU Institute for Engineering Health); with joint-appointment @isbscience.org I'm hiring a postdoc @ NYU to look at diet-driven evolution in the gut: apply.interfolio.com/189980 Please share! 🦠🤓

In new study led by @bdadonaite.bsky.social, we show many influenza HAs (H5, H7, H9, H1, H2, H3) can use avian or human MHC-II to enter cells. We then use novel combo of deep mutational scanning & cryoEM to define how H5 HA binds to avian MHC-II. Preprint: doi.org/10.64898/202...

Michaud, @andrewgoryachev.bsky.social, von Dassow, @xenresearchcenter.bsky.social et al. identify a versatile cortical pattern-forming circuit based on #Rho, F-#actin, Ect2, & RGA-3/4 rupress.org/jcb/article/... 📕 In "Collective Behaviors and Self-Organization in Cells" rupress.org/jcb/collecti...

Fitness Race: Modelling antibody evolution by replaying a monoclonal germinal centre reaction over a 100 times 📷 William DeWitt, Ashni Vora, Tatsuya Araki et al @victora.bsky.social @rockefeller.edu @matsen.bsky.social in @cp-cell.bsky.social ➡️ bpod.org.uk/archive/2026... + John Ankers

Tomorrow is your last chance to comment on the Office of Management and Budget's proposed rule affecting the future of science. These APS leaders are just some of the 2,400+ people who have used our letter-writing portal to share what they think. Submit your comment: https://go.aps.org/4vUO0ST

Fitness flux in SARS-CoV-2 and influenza H3N2 https://www.biorxiv.org/content/10.64898/2026.07.05.736619v1

I am thrilled to share that UC Berkeley and UCSF have launched a joint initiative in Computational Biomedicine! cdss.berkeley.edu/news/uc-berk... We will soon be recruiting new faculty and postdoctoral fellows. Please repost to help spread the word.

UC Berkeley and UCSF Launch Computational Biomedicine Initiative

UC Berkeley and UCSF have launched a joint program called the Bakar Computational Biomedicine Initiative to develop the frontier of AI and biomedicine, tremendously accelerating advances in clinical c...

cdss.berkeley.edu

My department, Neurobiology and Biophysics at the University of Washington (nbio.uw.edu), is hiring a new tenure-track Assistant Professor, application deadline 09/30/26. It's a broad search — molecular to organismal, all of neuroscience/physiology/biophysics welcome. apply.interfolio.com/187735

Scientists, especially younger ones, are going to have to come to terms with the idea that “doing science” is no longer enough. We all have to fight for science: what it means, what are its values, and why it matters.

Bethany Brookshire@beebrookshire.bsky.social · last mo.

Scientific research in the United States might not collapse with a bang, or with a whimper, but with a rule change. And it's not just Science. This rule change hits DOE, DOT, VA, HUD. ALL federal grants are at risk. www.theverge.com/science/9576...

I want to rotate in Phil's lab.

Phil Abitua@ohnolog.bsky.social · last mo.

Annual killifish continue to surprise us: they make neutrophils before almost every other cell type, even before gastrulation. Neutrophils usually arise from the lateral plate mesoderm (forming in cyan), but in killifish they are already patrolling around the embryo in gold. tinyurl.com/killiphil

What if an embryo made immune cells before it finished building the tissue they usually come from? In our new preprint, we show that annual killifish embryos specify neutrophils before germ layers are fully resolved. www.biorxiv.org/content/10.6... Huge thanks to my PI, @ohnolog.bsky.social ! 🧵

Early immune cell development precedes gastrulation in annual killifish

During embryogenesis, cell types arise in a predictable order because developmental regulators act sequentially. But how evolutionary changes in morphogenesis reshape the signaling environments that a...

biorxiv.org

Spectacular preprint led by @sydsat.bsky.social in @ohnolog.bsky.social lab, @uwgenome.bsky.social. Neutrophils precede gastrulation in killifish and rapidly patrol the yolk. (1/2)

Early immune cell development precedes gastrulation in annual killifish

During embryogenesis, cell types arise in a predictable order because developmental regulators act sequentially. But how evolutionary changes in morphogenesis reshape the signaling environments that a...

doi.org

Enjoying those top 1% preeps, thanks @qedscience.bsky.social!

Christophe 🔬 Leterrier@christlet.bsky.social · last mo.

Interesting effect of z҉f҉k҉j҉h҉m҉l҉j҉ on g҉h҉f҉j҉g҉f҉k҉

"The spokesperson went on to describe the platform’s next phase, which seeks to score preprints in real time, reducing the interval between sharing one’s work and feeling terrible about it to under one minute."

In Preparation@inprep.bsky.social · last mo.

Excited to see @jonj-udd.bsky.social's fantastic work out @genetics-gsa.bsky.social. Selection in _heterozygotes_ is the primary force shaping allele frequencies of loss-of-function mutations in humans, even in genes only associated with purely recessive diseases. 🧪🧬 doi.org/10.1093/gene...

Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes

Abstract. The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model pred

doi.org

The human genome is no blueprint or algorithm — it’s something else entirely, something living with promiscuous logic. Can new genomic AI models, such as Evo 2 and AlphaGenome, untangle these tricky knots or will the genome confound them, too? www.quantamagazine.org/why-the-huma...

Why the Human Genome’s Tangled Physicality May Confound AI | Quanta Magazine

Our genetic heritage is not a blueprint or an algorithm, as many biologists have imagined, but something else entirely.

quantamagazine.org

Aggregating many experiments into one zero-shot protein language model score obscures that current models cannot meaningfully rank a set of fit mutations or prioritize new-to-nature functions @clauswilke.com www.biorxiv.org/content/10.6...

I've learned a lot from this community at various meetings since I was a PhD student. I'm looking forward to this one!

John Tsang@tsanglab.bsky.social · 2mo ago

6th iteration of the Physics & Computation in Immunology meeting will be at Yale CSEI @yalecsei.bsky.social Sep 28–30. With Arup Chakraborty, Michael Lässig, @thearmita.bsky.social & Alex Walczak. Speakers from Princeton, Cambridge, Harvard, MSK, UCSF & more. Free. 120 spots. Deadline Sep 6.

Antibody LMs learn what looks antibody-like, but not how selection turns naive germline antibodies into strong binders. @aakarshv1.bsky.social and I are excited to share CoSiNE, a model that learns this germline-to-mature process for variant effect prediction and antibody design. (1/8)

We urge GSA members and the genetics community to submit a public comment on the recently proposed OMB regulations—which pose drastic challenges to the scientific enterprise—by July 13, 2026! Submit your comments here: www.regulations.gov/document/OMB...

Coalition for Life Sciences@c4lifesciences.bsky.social · 2mo ago

This was one of the most complex projects I have ever been involved in. Took us the better part of a decade, but I thoroughly enjoyed every minute of it. Especially the intensive and extensive interactions with @wsdewitt.github.io, @matsen.bsky.social, and @tylernstarr.bsky.social

William DeWitt@wsdewitt.github.io · 2mo ago

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!

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

Barred owlets of Ravenna Park

Barred owlets of Ravenna Park

Out now in Science! Our study challenges long-standing assumptions about transcription factor specificity in eukaryotes. Novel single-molecule measurements of TF behavior in living cells reveal an independence of locus-specific binding from DNA sequence recognition.🧵 www.science.org/doi/10.1126/...

Unstructured transcription factor interactions enable emergent specificity

How intrinsically disordered regions (IDRs) shape chromatin binding and nuclear organization of transcription factors (TFs) remains unclear. We used proximity-assisted photoactivation (PAPA), a single...

science.org

This terrific article by Siobhan Roberts could help elevate the public discussion of AI in mathematics. The interview about the Leiden Declaration is especially helpful. www.nytimes.com/2026/06/02/s...

As A.I. Makes Strides in Mathematics, Mathematicians Urge Caution

nytimes.com