Dan Weinberger and I @yalesph.bsky.social are hiring multiple research positions in microbial/virus sequencing and bioinformatics workflows with respiratory pathogens, including Streptococcus pneumoniae, Mycobacterium tuberculosis, RSV, and/or hMPV.

See 👉 forms.gle/xpmzTtNqHFqK...

Excited to share our latest work in Nature. Applying single-molecule and single-cell DNA sequencing methods, we uncover an extraordinary landscape of somatic mutations in immune checkpoint genes in autoimmune B cells, suggesting that somatic mutations may be key to autoimmunity [1/n] rdcu.be/fdqbr

We are recruiting 1-2 postdoctoral fellows to investigate the specificity of human anti-influenza virus antibodies, and to determine how these antibodies impact global antigenic drift of influenza viruses.

Join our lab at Penn in Philly. Reach out if you are interested in applying! Please repost!

It looks like there will be an open postdoc position in my lab soon. I'll be looking for someone with substantial wet-lab experience in microbiology / microbial ecology / evolution / physiology. If everything goes well, an ad will be coming. But if you know someone, ask them to reach out already.

I was frustrated that CDC no longer issues many health alert network (HAN) alerts, so I started my own. Weekly outbreak updates + as needed info for clinicians. As seen on Medscape, NPR. Most recent alert on extended RSV season. www.foiclinical.com

My lab at Pitt is looking for a Research Scientist to help us make phage therapy for patients with antibiotic-resistant infections. Please share and apply! cfopitt.taleo.net/careersectio...

One month until London Q-Immuno Day 2026! 🧬💻

Join us on May 8th for interdisciplinary discussions at the intersection of theory, computation and immunology. More details and free registration at: qimmuno.com/ldnday/

A star scientist showed that better genetics lessons could reduce racism. It was the death knell for his career

The loss of Brian Donovan’s grants and job speak volumes about federal funding priorities — and academia

www.statnews.com/2026/04/07/b...

NEE Focus issue on "Evolution in medicine", including a comment article from @alisonfeder.bsky.social and me.

With @saramitri.bsky.social, @sonjalehtinen.bsky.social and L. Lehmann we’ve launched the UNIL Center for Theory in Ecology and Evolution @unil.bsky.social🇨🇭

To kick things off, we’re offering short visiting fellowships for theorists in ecology & evolution. Apply & pls RP 😀

tinyurl.com/2wem36zz

Call for applications, pls share!

2026 Evolutionary Medicine Summer Institute (EMSI) advances research in a frontier of evolutionary medicine. They provide training in methods needed to address cutting edge questions in that frontier.

2026 focus: Climate Change and Health

sites.duke.edu/emsi/

Comparative analysis of deep mutational scanning datasets in enteroviruses A and B identifies functional divergence and therapeutic targets - Nature Ecology & Evolution A comparison of proteome-wide mutational scanning datasets from enterovirus A and B species reveals evolutionary constraints shared by these viral species that localize to core functional regions, as ...

www.nature.com/articles/s41...

Excited to have this collaboration from #QVEU and @rongellerlab.bsky.social lab out in the world! After publishing our own #DeepMutationalScanning studies on two related viruses, we asked what we learn from comparisons of such datasets. The answer is a lot!

Antibody-mediated feedback modulates interclonal competition in the germinal center Antibodies generated by prior immune responses regulate B cell responses upon recall immunization. Barbulescu et al. examine whether antibodies produced by an ongoing immune response influence the out...

One more trick pulled off by antibody-mediated feedback

www.cell.com/immunity/ful...

You know that annoying NSF form "List every coauthor/co-PI from the last 4y" ?

At @cevianlabs.io we built a free tool that drafts the COI form from your PDF CV in minutes. Check it out 👇

Mapping the specificity of H3N2 strain-specific and cross-reactive human neutralizing antibodies elicited by the 2025-2026 influenza vaccine An H3N2 variant, named subclade K, continues to circulate widely during the 2025-2026 influenza season. This virus possesses a hemagglutinin (HA) protein that has eleven substitutions relative to the ...

Our preprint examining the specificity of human antibodies that cross-react with subclade K H3N2 viruses was posted this morning on medRxiv. These studies have implications on what vaccine strains should be selected for next year’s influenza season. 1/
www.medrxiv.org/content/10.6...

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n
doi.org/10.64898/202...

We have posted data providing real-time measurement of human neutralizing antibody landscape to seasonal influenza.

Data explain spread of subclades K (H3N2) & D.3.1.1 (H1N1), identify subclade K subvariants w reduced neutralization, & can inform choice of strains for next vaccine.

Assistant Professor (Tenure Track) of Computational Immunology

We have an open Assistant Professor position (tenure track) @ethz.ch in Computational Immunology - ethz.ch/en/the-eth-z... Please apply / share!

Learning the Principles of T Cell Antigen Discernment T cells are central to the adaptive immune response, capable of detecting pathogenic antigens while ignoring healthy tissues with remarkable specificity and sensitivity. Quantitatively understanding h...

Happy to share our latest review article, “Learning the Principles of T Cell Antigen Discernment.” www.annualreviews.org/content/jour...
with @fxpbourassa.bsky.social , Sooraj Achar and Grégoire Altan-Bonnet ! 1/4

From Pankaj’s Mehta group www.biorxiv.org/content/10.6... “Our findings highlight the need for rigorous benchmarking and suggest that the biology of cell identity can be captured by simple linear representations of single cell gene expression data.” 🔥🔥🔥

🧵 New preprint! Our 4-lab team evolved Streptococcus pneumoniae in antibiotic-treated mice of varying immune states and discovered something surprising: bacteria rarely evolved resistance. Instead, they found a different way to survive — by rewiring RNA turnover.
🔗 www.biorxiv.org/content/10.6...

Demographic and genetic factors shape the epitope specificity of the human antibody repertoire against viruses - Nature Immunology Patin and colleagues present a mineable Resource database for identifying demographic and genetic factors that impact antiviral antibody repertoires in humans.

🤯
*PhiPseq of 108 health/envt variables + human genetic variation maps antibody repertoire in 1,212 adults.
*Age, sex, birth continent affect specific viral epitopes
*Abs vs variable flu epitopes decrease w/age
*Viral Abs & host genetics affect autoimmune disease risk www.nature.com/articles/s41...

How AI assistance impacts the formation of coding skills Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.

"We found that using AI assistance led to a statistically significant decrease in mastery. On a quiz that covered concepts they’d used just a few minutes before, participants in the AI group scored 17% lower than those who coded by hand, or the equivalent of nearly two letter grades."

Exciting new Research Fellow position in modelling infectious diseases to reduce inequities in health outcomes in Africa! Join a multidisciplinary 4 year project with me at UCL and partners in Zimbabwe, Zambia, The Gambia, South Africa, Kenya and the UK. www.ucl.ac.uk/work-at-ucl/...

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

Strategy to generate a DMS plasmid library for Your Favorite Gene (YFG) using short, degenerate libraries. 1. Segmentation of YFG into sub-fragments, each fragment corresponding to a DNA region to be synthesized. The same approach can be applied to promoter and terminator regions, if desired. 2. Example of a pool of degenerate oligonucleotides (oPool) derived from one YFG fragment associated with DNA barcodes. Each oPool contains: (i) ~40 bp of homology upstream of the YFG fragment of interest, (ii) the YFG fragment sequence with a single NNK codon, (iii) BsaI cloning sites, (iv) a DNA barcode composed of codon-position specific regions and six degenerate nucleotides (N), and (v) a conserved i7 primer binding site (PBS_i7) present in all oPools and used for rapid and efficient sequencing library preparation. Current oligonucleotide synthesis technologies allow for a total of nine degenerate positions per fragment: three are used for the degenerate codon (NNK), and six for the barcode. A complete list of all oPool sequences and their detailed composition is provided in S1 Table. 3. Protocol for constructing YFG DMS plasmid library from oPools using two cloning steps that maintain the physical barcode-mutation association. The libraries of oPools are cloned into the plasmid template by Gibson cloning. Following this step, for each fragment, a necessary short-read sequencing using PBS_i5 (included in the 5′ sequencing primer) and PBS_i7 is performed to associate each barcode with its corresponding mutation and to assess both barcode diversity per mutation and mutation coverage for the whole fragment. The ultimate step consists in Golden Gate cloning of the missing 3′ gene fragment between the degenerate fragment and the barcode. An additional short-read sequencing step of the barcodes can be performed to make sure that coverage and diversity have been maintained. Figure created in BioRender.

#DeepMutationalScanning (DMS) experiments are limited by gene size due to library complexity & costs. @christianlandry.bsky.social &co develop an efficient & cost-effective barcoded cloning strategy for plasmid-based DMS libraries that enables study of large genes @plosbiology.org 🧪 plos.io/4abhyUf

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)

Improving atlas-scale single-cell annotation models with hierarchical cross-entropy loss - Nature Computational Science A hierarchical cross-entropy loss is presented, which incorporates ontology structure into training and improves the out-of-distribution performance of large-scale single-cell annotation models withou...

Excited to see our hierarchical cross-entropy strategy for improved cell type annotation out today in @natcomputsci.nature.com! Congratulations to the team! Try out the HCE loss with your own models and datasets:
📄: www.nature.com/articles/s43...
💻: github.com/microsoft/hc...

Registration is open for the inaugural GRC conference in the Function of Evolving Systems. Aug 9-14, 2026, Waterville Valley. Truly stellar speaker lineup. Student/postdoc fellowships are available! Please come join us! www.grc.org/function-of-... @joybergelson.bsky.social

Postdoctoral position - Synthetic Biology / Bacterial Immunity - Research The Bikard lab at Institut Pasteur in Paris is seeking to hire postdoctoral researchers. We are investigating bacteria / bacteriophages interactions, and the genetic innovation that happens at this in...

🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...