Sign in

Julien Limenitakis

@jlimenitakis.bsky.social
99 followers 140 following 1 posts

Senior computational immunologist at IMPRINT @imprintlabs.bsky.social‬

PostsRepliesMedia
Reposted by Julien Limenitakis
Journal of Experimental Medicine @jem.org · 04/05/2026
IgD from atypical-like memory #Bcells and #plasmacells targets commensal and environmental antigens. New study by @rosertp.bsky.social, Bashour, Filipska, and colleagues from the @victorgreiff.bsky.social & Cerutti labs at the Uni of Oslo & @researchmar.bsky.social: rupress.org/jem/article-...
054
Reposted by Julien Limenitakis
IMPRINT @imprintlabs.bsky.social · 30/10/2025
A recent @natmachintell.nature.com paper by our cofounder-CTO @victorgreiff.bsky.social shows models trained on harder antibody binding tasks learned better, boosting antibody ML generation. At IMPRINT, this mindset drives our push for robust AI-based mapping of adaptive immunity. #Immunology #AI
nature.com
Training data composition determines machine learning generalization and biological rule discovery - Nature Machine Intelligence
Negative data composition critically shapes machine learning robustness in sequence-based biological tasks. Training data composition and its implications are investigated on biological rule discoveri...
031
Julien Limenitakis @jlimenitakis.bsky.social · 27/06/2025
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.
cell.com
Diet-derived LPS determines intestinal IgA induction and repertoire characteristics independently of the microbiota
The microbiota’s impact on immune development is well appreciated. Mooser et al. show now that dietary LPS promotes intestinal germinal center reactions and IgA production independently of the microbi...
020
Reposted by Julien Limenitakis
IMPRINT @imprintlabs.bsky.social · 09/01/2025
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...
143
Reposted by Julien Limenitakis
IMPRINT @imprintlabs.bsky.social · 01/05/2025
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:
imprint.org
Imprint FRO
IMPRINT is developing tools to read and analyze immune memory signatures, providing a new approach to identify hidden causes of chronic disease.
142
Reposted by Julien Limenitakis
IMPRINT @imprintlabs.bsky.social · 01/05/2025
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
imprint.org
Jobs — Imprint FRO
Join our team—current openings at Imprint
179
Reposted by Julien Limenitakis
AIRR-Community @airr-community.bsky.social · 31/05/2024
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
021
Reposted by Julien Limenitakis
Greg Priest @gregpriest.bsky.social · 22/05/2024
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
nature.com
Bizarre bacteria defy textbooks by writing new genes
Bacterial defensive systems scramble the standard workflow of life. Bacterial defensive systems scramble the standard workflow of life.
12612
Reposted by Julien Limenitakis
AIRR-Community @airr-community.bsky.social · 07/05/2024
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
antibodysociety.org
AIRR Community Meeting VII - Learnings and Perspectives - The Antibody Society
15 years after the first AIRR-seq sequencing, what have we learned in the basic and biomedical research fields? What is next? Join us at the AIRR-C Meeting in Porto this June, the premiere event for g...
011
Reposted by Julien Limenitakis
Michael Brockhurst @brockhurstlab.bsky.social · 18/04/2024
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/...
0156
Reposted by Julien Limenitakis
Bloom lab @jbloomlab.bsky.social · 10/03/2024
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
21613
Reposted by Julien Limenitakis
Corey Watson @cdubsig.bsky.social · 09/03/2024
Addressing technical pitfalls in pursuit of molecular factors that mediate immunoglobulin gene regulation biorxiv.org/cgi/content/... #biorxiv_genomic
021
Reposted by Julien Limenitakis
Stephen Turner @stephenturner.us · 01/03/2024
Review: Single-cell genomics meets human genetics www.nature.com/articles/s41... 🧬🖥️
nature.com
Single-cell genomics meets human genetics - Nature Reviews Genetics
In this Review, the authors describe the emerging field of single-cell genetics, which lies at the intersection of single-cell genomics and human genetics. They review the first single-cell expression...
024
Reposted by Julien Limenitakis
Stephen Turner @stephenturner.us · 01/03/2024
Bioframe: operations on genomic intervals in Pandas dataframes academic.oup.com/bioinformati... 🧬🖥️ github.com/open2c/biofr...
academic.oup.com
Bioframe: operations on genomic intervals in Pandas dataframes
AbstractMotivation. Genomic intervals are one of the most prevalent data structures in computational genome biology, and used to represent features ranging from
074
Reposted by Julien Limenitakis
Cameron Thrash @jcamthrash.bsky.social · 01/03/2024
An optimized culturomics strategy for isolation of human milk microbiota www.frontiersin.org/journals/mic... #jcampubs
frontiersin.org
Frontiers | An optimized culturomics strategy for isolation of human milk microbiota
<p>Viable microorganisms and a diverse microbial ecosystem found in human milk play a crucial role in promoting healthy immune system and shaping the microbi...
011
Reposted by Julien Limenitakis
Michael Hoffman @michaelhoffman.bsky.social · 01/03/2024
The Hallmarks of Cancer Research 🧪
A diagram titled 'Hallmarks of Cancer Research', designed in a clean, academic style, including funding, trend chasing, glam papers, and big data.
53011
Reposted by Julien Limenitakis
Hiutung Chu @chulab.bsky.social · 15/01/2024
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...
167
Reposted by Julien Limenitakis
Ian M. Mackay, PhD (he/him) 🦠🤧🧬📑🦟🧀 @mackayim.bsky.social · 16/01/2024
A nice summary by Jon Cohen 'COVID'S COLD COUSINS' www.science.org/content/arti...
2177
Reposted by Julien Limenitakis
Living Physics Lab @livingphysics.org · 15/01/2024
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
Stochastic Models and Experiments in Ecology and Biology (SMEEB) 2024 L'Aquila, Italy from May 28th to 31st, 2024 poster
1910
Reposted by Julien Limenitakis
Bloom lab @jbloomlab.bsky.social · 17/12/2023
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...
biorxiv.org
Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
23919
Reposted by Julien Limenitakis
Erin Stephenson @erinstephenson.bsky.social · 24/12/2023
Closing out the year with a fresh preprint! 🤓🧪
183
Reposted by Julien Limenitakis
Alex Crits-Christoph @acritschristoph.bsky.social · 24/12/2023
A very nice method for detection of sweeps in gut microbial populations:
13013
Reposted by Julien Limenitakis
SeppeKuehnLab @seppekuehnlab.bsky.social · 20/12/2023
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...
11914
Reposted by Julien Limenitakis
Alvaro Rodriguez del Rio 🍉 @alvarordr.bsky.social · 19/12/2023
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...
nature.com
Functional and evolutionary significance of unknown genes from uncultivated taxa - Nature
Nature - Functional and evolutionary significance of unknown genes from uncultivated taxa
12514
Reposted by Julien Limenitakis
Cameron Thrash @jcamthrash.bsky.social · 14/12/2023
Multistability driven by cooperative growth in microbial communities www.biorxiv.org/content/10.1... #jcampubs
biorxiv.org
Multistability driven by cooperative growth in microbial communities
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
052
Reposted by Julien Limenitakis
Cameron Thrash @jcamthrash.bsky.social · 14/12/2023
Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies www.biorxiv.org/content/10.1... #jcampubs
biorxiv.org
Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
032
Reposted by Julien Limenitakis
Eric Topol @erictopol.bsky.social · 06/12/2023
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
04016
Reposted by Julien Limenitakis
Eric Topol @erictopol.bsky.social · 20/11/2023
Gaining life expectancy up to a decade longer with a healthy diet nature.com/articles/s43...
34821
Reposted by Julien Limenitakis
Matthew Sinton 🏳️‍🌈 @mcsinton.bsky.social · 20/11/2023
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
journals.plos.org
The murine meninges acquire lymphoid tissue properties and harbour autoreactive B cells during chron...
This study shows that chronic brain infection with African trypanosomes induces broad meningeal responses resulting in the development of ectopic lymphoid aggregates containing autoreactive B cells; m...
1147
Reposted by Julien Limenitakis
Richard Sever @richardsever.bsky.social · 13/11/2023
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...
02212
Reposted by Julien Limenitakis
Wolfgang Huber @wkhuber.bsky.social · 13/11/2023
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...
Conference Poster
0106
Reposted by Julien Limenitakis
Ervin Fodor @efodor.bsky.social · 10/11/2023
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/...
journals.plos.org
Defining the minimal components of the influenza A virus replication machinery via an in vitro recon...
The influenza A virus genome is composed of eight single-stranded RNA segments. This study reconstitutes the replication of RNA genome segments in a test tube, using purified viral and host proteins, ...
02817
Reposted by Julien Limenitakis
Ákos T Kovács @evolvedbiofilm.bsky.social · 12/11/2023
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...
0158
Reposted by Julien Limenitakis
Diego del Alamo @delalamo.xyz · 11/11/2023
“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...
0134
Reposted by Julien Limenitakis
Mohamed ElTanbouly @plasmacellguy.bsky.social · 11/11/2023
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
From "The generative grammar of the immune system" by Niels K Jerne (EMBO, 1985) PMID: 2410261

Also see his Nobel lecture of the same title.
1168
Reposted by Julien Limenitakis
Melanie Mitchell @melaniemitchell.bsky.social · 02/11/2023
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...
lensic.org
32711
Reposted by Julien Limenitakis
Alex Rubinsteyn @alexr.bsky.social · 03/11/2023
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
nature.com
Identification of bacteria-derived HLA-bound peptides in melanoma - Nature
HLA peptidomic analysis identifies recurrent intracellular bacteria-derived peptides presented on HLA-I and HLA-II molecules in melanoma tumours, revealing how bacteria can modulate immune functions a...
131
Reposted by Julien Limenitakis
Eric Topol @erictopol.bsky.social · 03/11/2023
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...
012542
Reposted by Julien Limenitakis
Noah Fierer @noahfierer.bsky.social · 03/11/2023
This is really cool - using the distribution of cells in a pipette tip for CFU quantification: www.nature.com/articles/s41...
nature.com
A high-throughput and low-waste viability assay for microbes - Nature Microbiology
Using agar media suspended in pipette tips and a standard camera, the geometric viability assay provides a user-friendly and scalable update to standard colony-forming-unit-count approaches.
66529
Reposted by Julien Limenitakis
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 04/11/2023
A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity www.biorxiv.org/content/10.1101/202…
biorxiv.org
A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity https://www.biorxiv.org/content/10.1101/2023.11.02.565382v1
Diet can protect from autoimmune disease; however, whether diet acts via the host and/or microbiome
198
Reposted by Julien Limenitakis
Greifflab @victorgreiff.bsky.social · 31/10/2023
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.
152
Reposted by Julien Limenitakis
Eva Smorodina @evasmorodina.bsky.social · 31/10/2023
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
285
Reposted by Julien Limenitakis
kevin @kevinng.bsky.social · 30/10/2023
Targeting intracellular oncoproteins with dimeric IgA promotes expulsion from the cytoplasm and immune-mediated control of epithelial cancers
cell.com
Targeting intracellular oncoproteins with dimeric IgA promotes expulsion from the cytoplasm and immu...
Despite their long half-life, therapeutic antibodies are considered ineffective against intracellular antigens. Biswas et al. demonstrate that dimeric IgA undergoes transcytosis through PIGR+ epithel...
031
Reposted by Julien Limenitakis
Jeremy Barr @jeremyjbarr.bsky.social · 27/10/2023
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
journals.plos.org
HTTP Status 400 – Bad Request
63119
Reposted by Julien Limenitakis
bioRxiv Immunology @biorxiv-immuno.bsky.social · 25/10/2023
Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry www.biorxiv.org/content/10.1101/202…
biorxiv.org
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
Immunoglobulins (IGs), critical components of the human immune system, are composed of heavy and lig
012
Reposted by Julien Limenitakis
Diego del Alamo @delalamo.xyz · 24/10/2023
“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
023
Reposted by Julien Limenitakis
Eric Topol @erictopol.bsky.social · 23/10/2023
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
214959
Reposted by Julien Limenitakis
Maria Chernigovskaya @mchernigovskaya.bsky.social · 24/10/2023
🎉 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
093
Reposted by Julien Limenitakis
Greifflab @victorgreiff.bsky.social · 24/10/2023
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.
135
Reposted by Julien Limenitakis
Cameron Thrash @jcamthrash.bsky.social · 24/10/2023
Identification and cultivation of anaerobic bacterial scavengers of dead cells www.nature.com/articles/s41... #jcampubs
nature.com
Identification and cultivation of anaerobic bacterial scavengers of dead cells - The ISME Journal
The ISME Journal - Identification and cultivation of anaerobic bacterial scavengers of dead cells
063