Julien Limenitakis
@jlimenitakis.bsky.social
📤 95
📥 139
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Senior computational immunologist at IMPRINT
@imprintlabs.bsky
.social
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.
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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...
https://www.cell.com/immunity/fulltext/S1074-7613%2825%2900245-6
5 months ago
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Julien Limenitakis
IMPRINT
10 months ago
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...
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Julien Limenitakis
IMPRINT
7 months ago
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:
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Imprint FRO
IMPRINT is developing tools to read and analyze immune memory signatures, providing a new approach to identify hidden causes of chronic disease.
https://www.imprint.org
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Julien Limenitakis
IMPRINT
7 months ago
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
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Jobs — Imprint FRO
Join our team—current openings at Imprint
https://www.imprint.org/jobs
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Julien Limenitakis
AIRR-Community
over 1 year ago
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
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Julien Limenitakis
Greg Priest
over 1 year ago
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
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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.
https://www.nature.com/articles/d41586-024-01477-8
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Julien Limenitakis
AIRR-Community
over 1 year ago
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
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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...
https://www.antibodysociety.org/the-airr-community/meetings/airr-community-meeting-vii-learnings-and-perspectives/
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Julien Limenitakis
Michael Brockhurst
over 1 year ago
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/...
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Julien Limenitakis
Bloom lab
over 1 year ago
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
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Corey Watson
over 1 year ago
Addressing technical pitfalls in pursuit of molecular factors that mediate immunoglobulin gene regulation
biorxiv.org/cgi/content/...
#biorxiv_genomic
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Julien Limenitakis
Stephen Turner
over 1 year ago
Review: Single-cell genomics meets human genetics
www.nature.com/articles/s41...
🧬🖥️
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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...
https://www.nature.com/articles/s41576-023-00599-5
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Julien Limenitakis
Stephen Turner
over 1 year ago
Bioframe: operations on genomic intervals in Pandas dataframes
academic.oup.com/bioinformati...
🧬🖥️
github.com/open2c/biofr...
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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
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae088/7613967
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Julien Limenitakis
Cameron Thrash
over 1 year ago
An optimized culturomics strategy for isolation of human milk microbiota
www.frontiersin.org/journals/mic...
#jcampubs
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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...
https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1272062/full
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Julien Limenitakis
Michael Hoffman
over 1 year ago
The Hallmarks of Cancer Research 🧪
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Julien Limenitakis
Hiutung Chu
almost 2 years ago
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...
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Julien Limenitakis
Ian M. Mackay, PhD (he/him) 🦠🤧🧬📑🦟🧀
almost 2 years ago
A nice summary by Jon Cohen 'COVID'S COLD COUSINS'
www.science.org/content/arti...
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Julien Limenitakis
Living Physics Lab
almost 2 years ago
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
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Julien Limenitakis
Bloom lab
almost 2 years ago
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...
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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
https://www.biorxiv.org/content/10.1101/2023.12.12.571235v1
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Julien Limenitakis
Erin Stephenson
almost 2 years ago
Closing out the year with a fresh preprint! 🤓🧪
add a skeleton here at some point
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Julien Limenitakis
Alex Crits-Christoph
almost 2 years ago
A very nice method for detection of sweeps in gut microbial populations:
add a skeleton here at some point
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Julien Limenitakis
SeppeKuehnLab
almost 2 years ago
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...
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Julien Limenitakis
Alvaro Rodriguez del Rio 🍉
almost 2 years ago
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...
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Functional and evolutionary significance of unknown genes from uncultivated taxa - Nature
Nature - Functional and evolutionary significance of unknown genes from uncultivated taxa
https://www.nature.com/articles/s41586-023-06955-z
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Julien Limenitakis
Cameron Thrash
almost 2 years ago
Multistability driven by cooperative growth in microbial communities
www.biorxiv.org/content/10.1...
#jcampubs
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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
https://www.biorxiv.org/content/10.1101/2023.12.12.571368v1
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Julien Limenitakis
Cameron Thrash
almost 2 years ago
Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies
www.biorxiv.org/content/10.1...
#jcampubs
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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
https://www.biorxiv.org/content/10.1101/2023.12.12.571215v1
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Julien Limenitakis
Eric Topol
almost 2 years ago
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
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Julien Limenitakis
Eric Topol
almost 2 years ago
Gaining life expectancy up to a decade longer with a healthy diet
nature.com/articles/s43...
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Julien Limenitakis
Matthew Sinton 🏳️🌈
almost 2 years ago
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
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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...
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002389
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Julien Limenitakis
Richard Sever
about 2 years ago
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...
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Julien Limenitakis
Wolfgang Huber
about 2 years ago
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...
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Julien Limenitakis
Ervin Fodor
about 2 years ago
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/...
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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, ...
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002370
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Julien Limenitakis
Ákos T Kovács
about 2 years ago
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...
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Julien Limenitakis
Diego del Alamo
about 2 years ago
“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...
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Julien Limenitakis
Mohamed ElTanbouly
about 2 years ago
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
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Julien Limenitakis
Melanie Mitchell
about 2 years ago
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...
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https://lensic.org/events/the-future-of-artificial-intelligence/
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Julien Limenitakis
Alex Rubinsteyn
about 2 years ago
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
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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...
https://www.nature.com/articles/s41586-021-03368-8
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Julien Limenitakis
Eric Topol
about 2 years ago
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...
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Julien Limenitakis
Noah Fierer
about 2 years ago
This is really cool - using the distribution of cells in a pipette tip for CFU quantification:
www.nature.com/articles/s41...
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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.
https://www.nature.com/articles/s41564-023-01513-9#Sec10
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Julien Limenitakis
bioRxiv Microbiology
about 2 years ago
A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity https://www.biorxiv.org/content/10.1101/2023.11.02.565382v1
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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
https://www.biorxiv.org/content/10.1101/2023.11.02.565382v1
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Julien Limenitakis
Greifflab
about 2 years ago
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.
add a skeleton here at some point
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Julien Limenitakis
Eva Smorodina
about 2 years ago
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
add a skeleton here at some point
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Julien Limenitakis
Kevin Ng
about 2 years ago
Targeting intracellular oncoproteins with dimeric IgA promotes expulsion from the cytoplasm and immune-mediated control of epithelial cancers
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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...
https://www.cell.com/immunity/fulltext/S1074-7613(23)00418-1
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Julien Limenitakis
Jeremy Barr
about 2 years ago
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
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HTTP Status 400 – Bad Request
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002341…
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Julien Limenitakis
bioRxiv Immunology
about 2 years ago
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
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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
https://www.biorxiv.org/content/10.1101/2023.10.23.563321v1
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Julien Limenitakis
Diego del Alamo
about 2 years ago
“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
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Julien Limenitakis
Eric Topol
about 2 years ago
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
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Maria Chernigovskaya
about 2 years ago
🎉 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
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Julien Limenitakis
Greifflab
about 2 years ago
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.
add a skeleton here at some point
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Julien Limenitakis
Cameron Thrash
about 2 years ago
Identification and cultivation of anaerobic bacterial scavengers of dead cells
www.nature.com/articles/s41...
#jcampubs
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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
https://www.nature.com/articles/s41396-023-01538-2
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Julien Limenitakis
C. Brandon Ogbunu
about 2 years ago
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
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Mutations that enhance evolvability may open doors to faster adaptation - Nature Communications
A recent study demonstrated the existence of mutations that facilitate access to efficient evolutionary solutions. Here I discuss the implications of this finding and the potential to open a new chapter in the study of evolvability.
https://www.nature.com/articles/s41467-023-41914-2
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Julien Limenitakis
Kat Coyte
about 2 years ago
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...
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What makes a temperate phage an effective bacterial weapon?
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
https://www.biorxiv.org/content/10.1101/2023.10.04.560906v1
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