Interested in the effects of diets on B cell repertoires ? Have a look at our new publication: "Diet-derived LPS determines intestinal IgA induction and repertoire characteristics independently of the microbiota" www.cell.com/immunity/ful... This work was done at @unibe.ch. Share if you like it.

It's an exciting moment for immune repertoire research! At the end of December in Cell Systems, we shared our perspective on recent advances in ML for immune repertoire interpretation: www.sciencedirect.com/science/arti...

Beyond advancing impactful science, Imprint offers a unique culture as a Focused Research Organization (FRO). FROs are non-profit, impact-driven moonshot initiatives, combining philanthropic support with startup-like agility to tackle humanity's biggest challenges. Learn more about Imprint:

Looking for a job in immunology or biotech research? ✨IMPRINT is #hiring! ✨ Join us to help revolutionize how we decode the body’s immune memory, uncover the causes of chronic diseases, and drive breakthroughs in autoimmunity and neuropsychiatric research. #BiotechJobs #Immunology #sciencejobs

The AIRR Community Meeting VII #AIRRC7 is starting this Monday, June 3rd, at the University of Porto! A huge thank you to our sponsors. Your support is invaluable! Check out the full agenda and more details on the meeting page: tinyurl.com/airrcmeeting7 #Immunology

A new variety of reverse transcriptase discovered in bacteria “reads RNA as a template to make completely new genes written in DNA. These genes are then transcribed back into RNA, which is translated into protective proteins when a bacterium is infected by a virus.” 🐋🌱🧪🦋🦫 #EvoBio

Register for the AIRR-C 7 meeting! Once registered, remember to sign up for the workshops and tutorials through the meeting app!. Also, if you haven’t already be sure to sign up for the fabulous Cálem Port Wine Cellars Tour & Group Dinner. www.antibodysociety.org/the-airr-com... #AIRRC7 #Immunology

Our bit for PLOS Bio’s special on symbiosis thinking about the (under-appreciated) role of fitness trade-offs in the origins of endosymbiosis journals.plos.org/plosbiology/...

In new study led by Andrea Loes, we develop sequencing-based neutralization assay that measures replicate curves for hundreds of virus-serum pairs per 96-well plate (see image below) www.biorxiv.org/content/10.1...   We apply assay to characterize response to repeat influenza vaccination

Addressing technical pitfalls in pursuit of molecular factors that mediate immunoglobulin gene regulation biorxiv.org/cgi/content/... #biorxiv_genomic

Review: Single-cell genomics meets human genetics www.nature.com/articles/s41... 🧬🖥️

Bioframe: operations on genomic intervals in Pandas dataframes academic.oup.com/bioinformati... 🧬🖥️ github.com/open2c/biofr...

An optimized culturomics strategy for isolation of human milk microbiota www.frontiersin.org/journals/mic... #jcampubs

The Hallmarks of Cancer Research 🧪

Thrilled to share our latest paper on commensal colonization during early life! This study explores how human milk oligosaccharides trigger the colonization program in Bacteroides fragilis. 🦠🧫🧪 www.sciencedirect.com/science/arti...

A nice summary by Jon Cohen 'COVID'S COLD COUSINS' www.science.org/content/arti...

Stochastic Models and Experiments in Ecology and Biology (SMEEB) 2024 L'Aquila, Italy from May 28th to 31st, 2024 Theory, experiment and data in microbial ecology, evolution and systems biology! Featuring @saramitri.bsky.social and @seppekuehnlab.bsky.social #evosky #livingmatter

In new study led by Frances Welsh, we map how mutations to influenza affect neutralization by antibodies from humans of various ages   We find differences in mutation effects among age groups   Virus seems to evolve especially to escape antibodies of teenagers   www.biorxiv.org/content/10.1...

Closing out the year with a fresh preprint! 🤓🧪

A very nice method for detection of sweeps in gut microbial populations:

New paper on statistical predictions of bacterial traits from genomes. This is a deep technical dive into the intricacies of how to perform these predictions, when and how they work, and when they can reveal underlying mechanisms. journals.plos.org/ploscompbiol...

Extremely excited to share that our effort to identify and characterize novel gene families exclusive of uncultivated taxa is now published in Nature! www.nature.com/articles/s41...

Multistability driven by cooperative growth in microbial communities www.biorxiv.org/content/10.1... #jcampubs

Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies www.biorxiv.org/content/10.1... #jcampubs

A big step forward in the science of aging: organ-specific tracking via plasma proteins www.nature.com/articles/s41... 20% of people assessed had accelerated aging in 1 organ, 1.7% multi-organ

Gaining life expectancy up to a decade longer with a healthy diet nature.com/articles/s43...

I’m so proud of @juanquintana.bsky.social for his latest paper & to have played a (very) small part in it! Interested in the brain, autoimmunity, B cells & parasitic infection? Then this is the pajar for you! 🧪🧬🔭 #LGBTQSTEM #Immunosky

On the 10 years anniversary of bioRxiv, John and I discuss the birth of bioRxiv, embedding sci comm within CSHL, the the pandemic, and career options for young scientists in a new podcast ebrcintranslation.buzzsprout.com/1581817/1390...

EMBO|EMBL Symposium AI and Biology 12-15 March 2024 in Heidelberg with an exciting line-up of invited speakers and interactive sessions. Submit your contributed talk before 5 Dec. www.embl.org/about/info/c...

Influenza virus RNA genome segments undergo a full cycle of replication in a test tube in the presence of viral RNA polymerase, viral nucleoprotein and human ANP32B, an essential host factor for influenza virus genome replication. journals.plos.org/plosbiology/...

Reactivity of complex communities can be more important than stability @NatureComms by Yuguang Yang, @coytelab.bsky.social, Kevin R. Foster & Aming Li www.nature.com/articles/s41...

“TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering” has been updated 🧪🧶🧬 Provides a framework to integrate PLMs, backbone diffusion, docking, inverse folding, etc www.biorxiv.org/content/10.1... trill.readthedocs.io/en/latest/ho...

B cells and plasma cells 1/ Where do I start? Is it at Von Behring and Kitasato who were the first to discover that immunization of animals with diptheria and tetanus toxins resulted in soluble substances in the serum that neutralize these same toxins making them harmless? bit.ly/VonBehring1890

I'm excited to give the last SFI Community Lecture of 2023: "The Future of AI" (because we AI folks are so good at predicting the future of our field ☺️) Wed. Nov. 15, 7:30pm Mountain Time. And yes, it will be livestreamed on SFI's YouTube channel! lensic.org/events/the-f...

Hadn't seen this before: Identification of bacteria-derived HLA-bound peptides in melanoma www.nature.com/articles/s41... Curious what you all think of it

Towards broad neutralizing antibodies that could take down the family of sarbecoviruses, and serve as a template for a universal coronarvirus vaccine cell.com/immunity/ful...

This is really cool - using the distribution of cells in a pipette tip for CFU quantification: www.nature.com/articles/s41...

A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity https://www.biorxiv.org/content/10.1101/2023.11.02.565382v1

Really excited that our work on the plasticity of antibody developability is out www.biorxiv.org/content/10.1.... A fantastic collaborative effort led by Habib Bashour, @evasmorodina.bsky.social, Matteo Pariset, and @jahnzhong.bsky.social. All details are in the thread below.

Our work on antibody developability is out! We present a cartography of the developability landscapes of native and human-engineered antibodies. This study was a team effort of Habib Bashour, @evasmorodina.bsky.social, Matteo Pariset, and @jahnzhong.bsky.social from @victorgreiff.bsky.social, UiO

Targeting intracellular oncoproteins with dimeric IgA promotes expulsion from the cytoplasm and immune-mediated control of epithelial cancers

Our latest work, out today in PLOSBiology suggests that not only do mammalian cells absorb bacteriophages, but they appear to use them as a resource to enhance growth! journals.plos.org/plosbiology/... This work was led by PhD Marion Bichet and is out on World Phage Week! #WorldPhageWeek

Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry https://www.biorxiv.org/content/10.1101/2023.10.23.563321v1

“Pre-Training on Large-Scale Generated Docking Conformations with HelixDock to Unlock the Potential of Protein-ligand Structure Prediction Models” 🧪🧶🧬 A case where the scaling hypothesis is true only if the small molecule docking model is pre-trained arxiv.org/abs/2310.13913

www.pnas.org/doi/full/10.... The immune cell census in the human body! These ~2 trillion cells collectively weigh ~1.2 kg, 40% are lymphocytes, 10% macrophages

🎉 Happy to share my new preprint in which we present LIgO — a powerful tool to simulate adaptive immune receptor (AIR) and repertoire (AIRR) data for the development and benchmarking of AIRR-based ML www.biorxiv.org/content/10.1... Try LIgO now! 🚀 github.com/uio-bmi/ligo

Machine learning on immune receptors/repertoires is an exponentially expanding field, but labeled data to benchmark ML methods are missing. We address this need with our new simulation framework LIgO. www.biorxiv.org/content/10.1... Led by @mchernigovskaya.bsky.social and Milena Pavlović.

Identification and cultivation of anaerobic bacterial scavengers of dead cells www.nature.com/articles/s41... #jcampubs

New comment on paper by Andreas Wagner on “evolvability-enhancing mutations.” I talk about the paper, and bigger issues in the study of evolvability. https://www.nature.com/articles/s41467-023-41914-2

Proud supervisor as PhD student Matt Thomas submits his first first-author publication, collab with Mike Brockhurst exploring what makes a temperate phage an effective bacterial weapon www.biorxiv.org/content/10.1...