John Barton

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...

Big news! At least for me. I'll start building my own research group at the amazing IMBA in Vienna. Starting from single-cell omics data, we will develop computational tools and theoretical models to understand how single cells make decisions, in particular during development. I think that IMBA is

I’ll spread the word!

Congratulations Daan!

Deadline is approaching (Feb 9) to apply for a PI position at Institut Pasteur. Come join us and contribute to an amazing scientific environment!!!

Microbial Evolution: Impacts on Human Health Call for Papers A defining characteristic of infectious diseases is that they evolve. The consequences of this evolution are among the most pressing medical issues facing humanity, including emerging pandemics, antibiotic resistance, and the success or failure of vaccines. Pathogen evolution profoundly influences virulence, transmission, and responses to a broad array of human interventions. While the evolutionary dynamics of pathogens have historically been challenging to study, large-scale genomic sequencing, novel computational tools, and experimental methods are rapidly changing the field. We encourage submissions on the broad topic of the evolution of infectious diseases. This Special Issue aims to feature research that blends evolutionary approaches to understanding pathogen heterogeneity and ongoing genetic change in clinical samples and models of human infection. It also seeks to highlight opportunities to design treatment and prevention strategies that remain effective in the face of ongoing pathogen evolution. Submission – open until January 31, 2027 Guest editors Robert Woods, MD PhD, University of Michigan Camilo Barbosa, PhD, University of Michigan Silvie Huijben, PhD, Arizona State University

🚨Call for papers🚨
Microbial Evolution: Impacts on Human Health
in the society journal Evolution, Medicine, and Public Health

Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa
EIC: me

This will be great, please submit and share!
academic.oup.com/emph/pages/m...

Postdoc Position in Virology (1yr, renewable) We are launching M+RVL, a new research group dedicated to better understanding the fundamental mechanisms of positive-strand RNA virus replication. Supported by the LabEx NetRNA research cluster, the team is based within the Mosquito Models of Innate Immunity (M3I) unit at the Institute of Molecular and Cellular Biology (IBMC) in Strasbourg, France. Strasbourg is a lively city in northeastern France that offers a high quality of life, a vibrant university system, and a historic city center at the heart of Europe. Research Focus Replication organelles (ROs) are membrane-bound compartments that drive genome replication in positive-strand RNA viruses. Mosquito-borne viruses must assemble ROs in both mosquito and vertebrate hosts, which are separated by hundreds of millions of years of evolution. While structural biology has revealed the architecture of ROs in human cells, structure alone cannot explain their assembly, dynamics, and host-specific interactions, highlighting the need for integrative approaches. To address this gap, M+RVL integrates high-throughput genetics, proteomics, and computational modeling to dissect the mechanisms governing RO formation and function across hosts. Research Leadership The group is led by William Bakhache, Ph.D. Essential Skills: Strong background in virology, molecular biology, and biochemistry techniques. Desired Experience: Experience handling BSL-3 pathogens; expertise in computational biology (e.g., NGS analysis, proteomics data analysis, structural modeling). How to Apply Please send a single PDF containing a cover letter (detailing past and future research interests), a CV, and contact information for two references to williambakhache@hotmail.com.

Post-doc job alert! Please share with anyone who might be interested! @amersocvirology.bsky.social #virology #virosky #evolution

“It’s open season on the unabashedly earnest” feels right lately. In 1967 Brackman called it “the put-on”: ambiguity that makes you question if you're a sucker

I wrote abt how genAI scales put-ons & erodes signs of sincerity, & which I hope stay sacred
statmodeling.stat.columbia.edu/2026/01/07/i...

Launch of new Canada Impact+ Research Training Awards As announced in Budget 2025 -

Interested in the intersection of nonequilibrium thermodynamics and biophysics? Think Canada might be a nice place for your PhD/postdoc? Talk to me! Brand-new funding opportunity has quick deadline (so likely undersubscribed). nserc-crsng.canada.ca/en/news/laun...
SFU internal deadline Feb 11

Diverse bacterial pattern recognition receptors sense the conserved phage proteome Recognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic nucleotide-binding oligomerization domain ...

NLR-like immunity in bacteria

A new study from the Alex Gao lab. The scope of this work is incredible!!!

www.biorxiv.org/content/10.6...

I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful.

andrewcarroll.github.io/2025/12/23/t...

The final piece of my PhD work is now published in Science Translational Medicine! We present a new framework to jointly infer epidemiological and antigenic parameters from multi-pathogen population serological studies🦠

www.science.org/stoken/autho...

PhD position available at the University of Bern in Prof. Claudia Bank's lab. Application deadline: Jan 9, 2026. Ideal for candidates with a strong math and programming background. More info: https://banklab.github.io/positions/ #phd

Replaying evolution to learn about the fitness landscape of affinity maturation A five year collaboration with the Victora lab is bearing fruit for evolutionary biology.

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...

I will never forget and never forgive these actions. And there are so many, with so many people carrying these orders out while others laugh and clap and post excited selfies about it all.

Justice has to be served.

The fitness costs of reproductive specialization scale inversely with organismal size The evolution of reproductive specialization represents a fundamental innovation in multicellular life, yet the conditions favoring its evolution remain poorly understood. Here, we develop a populatio...

1/28 New preprint up, which I think is the best theoretical idea I've ever had. We asked a simple question: what are the costs of investment into non-reproductive somatic cells? Turns out these costs decrease with the *logarithm* of organism size!

www.biorxiv.org/content/10.6...

Screenshot from GRC portal confirming microbial population biology meeting June 27, 2027 in Andover, New Hampshire.

It’s officially happening folks! The Microbial Population Biology Gordon Research Conference is back in Andover, New Hampshire starting June 27th of 2027!
See you there!!

@wcratcliff.bsky.social @ksbakes.bsky.social @surtlab.bsky.social

#microsky #mevosky

Creation of new junior research groups at the Institut Pasteur - Call for applications 2026 - Research The Institut Pasteur is launching an international call to recruit new junior research group leaders leveraging cutting-edge transdisciplinary approaches to exploring infectious diseases, host-microbe...

🔬 Call to create junior research groups at the Institut Pasteur

Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies

📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD

Apply now 📝 research.pasteur.fr/en/call/crea...

#JobOpportunity #Research

The U.S. Is Funding Fewer Grants in Every Area of Science and Medicine (Gift Article) A quiet policy change means the government is making fewer bets on long-term science.

While the administration has said it is cutting “woke programs” that “poison the minds of Americans", it actually funded fewer grants in every area of science and medicine.

“They brought everything to a stop,” said Sarah Kobrin, a branch chief at the N.I.H.’s National Cancer Institute

Early Career Scientist Awards 2026 Application to the UW-Madison Evolution Seminar Series - Early Career Scientist Awards.

Wisconsin Evolution is accepting applications for our Seminar Series' Early Career Scientist Award. Come share your evolution research and visit UW-Madison's evolution community. Open to grad students and postdocs (<5 yrs post PhD) from outside UW-Madison.

Apply by Dec 15th here: shorturl.at/4a4O6

It's been a busy few months for our group so wanted to highlight a few other recent preprints we’ve posted that I haven’t had the chance to share yet... (1/n)

excited that this paper is finally out in @pnas.org :
www.pnas.org/doi/10.1073/...

Led by Gian Marco Visani (effort initiated by Michael Pun), fantastic collaboration with @pgtimmune.bsky.social @asya-minervina.bsky.social and Phil Bradley.

excited to announce that this January we are relocating to Yale to start a theory initiative at the Center for Systems and Engineering Immunology (CSEI): @yalecsei.bsky.social

looking to hire 2 postdocs to join us in this endeavor.

more details can be found here: sites.google.com/uw.edu/statp...

reminder that my (wonderful, diverse, interdisciplinary) department at the University of Oregon is seeking applications for an Associate/Full Professor of Data Science -- deadline 10/31 and only cover letter/CV needed to apply

academicjobsonline.org/ajo/jobs/30328

Graphic announcing that the Center for Systems Immunology and the University of Pittsburgh Department of Immunology are hiring an Assistant Professor in Systems Immunology. To learn more or apply, visit join.pitt.edu and search 24007498 under Faculty Positions

🚨 Faculty position alert! 🚨The Center for Systems Immunology (CSI) and @pitt-immunology.bsky.social are seeking to appoint a tenure-stream Assistant Professor. Learn more and apply: bit.ly/3L42cGS

We'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

We still can’t predict much of anything in biology Biology is hard. Yes, even for AI.

Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...

Reposting, submit soon!