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Eduardo Rocha

@epcrocha.bsky.social
3K followers 578 following 123 posts

Scientist, genomics, evolution, microbiology, computational biology, Institut Pasteur/CNRS, Paris

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Reposted by Eduardo Rocha
Vivek Mutalik @vivekmutalik.bsky.social · 18h
Happy to share that @averynoonan.bsky.social paper “Phylogeny-agnostic strain-level prediction of phage–host interactions from genomes using machine learning” is now published in @natmicrobiol.nature.com 🎉🎊 👉🏽 rdcu.be/nR2NizD7H5va
Machine learning workflow for GenoPHI platform
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Brian D. Wade @astrobrian.bsky.social · 28/09/2026
Bacterial chromosomal gene positioning is likely shaped by selection on both mean and growth-dependent expression #genomes #genetics #genes #evolution #evoSky #scienceSky journals.plos.org/plosgenetics...
journals.plos.org
Bacterial chromosomal gene positioning is likely shaped by selection on both mean and growth-dependent expression
Author summary Bacterial gene positioning affects gene expression because genes near the origin of chromosomal replication are replicated earlier than those near the terminus and thus have higher gene...
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ASM @aussocmic.bsky.social · 28/09/2026
The latest issue of Microbiology Australia is now online! connectsci.au/ma/issue/47/3
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Alexander Harms @aharms485.bsky.social · 25/09/2026
The final version of our manuscript on TnSeq in bacteriophages (“HIDEN-SEQ”) is out today – if you have an interesting phage phenotype and want to know the underlying genetic basis, this one is for you! 1/4
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Kate Baker @ksbakes.bsky.social · 25/09/2026
We have an open Assistant/Associate Professor position in Pathogen Biology at the Department of Genetics - come and join us! 🦠 🧫 🧬https://www.cam.ac.uk/jobs/assistantassociate-professor-in-pathogen-genetics-pc51175
cam.ac.uk
Assistant/Associate Professor in Pathogen Genetics
Applications are invited for an Assistant or Associate Professorship in Pathogen Genetics to be held in the Department of Genetics. We are searching for a talented individual with a track record of fu...
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Tom Gauld @tomgauld.bsky.social · 24/09/2026
My latest @newscientist.com cartoon. many more here: www.newscientist.com/author/tom-gauld/
Image: A graph with lots of red dots clustered together in a curve. The are all looking upwards at a single red dot wearing sunglasses. 

Caption: Mike was an outlier and would probably be excluded from the study, but all the other data points secretly thought he was really cool.
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Noah Houpt @noahhoupt.bsky.social · 22/09/2026
*PLEASE RE-POST* Applications for the trainee-focussed GRS immediately preceding this meeting are also now open! We will begin accepting applicants on *January 15th, 2027*. We will expedite our review for applicants requiring Visas, so please submit ASAP. www.grc.org/microbial-po...
grc.org
2027 Microbial Population Biology (GRS) Seminar GRC
The 2027 Gordon Research Seminar on Microbial Population Biology (GRS) will be held in Andover, New Hampshire. Apply today to reserve your spot.
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Eduardo Rocha @epcrocha.bsky.social · 22/09/2026
Fun collaboration with the Van Melderen lab, led by Ludovic Belot on the acquisition and erosion of toxin-antitoxin systems in bacterial chromosomes. academic.oup.com/mbe/article/...
academic.oup.com
Acquisition and erosion of toxin-antitoxin systems in bacterial chromosomes
Abstract. Toxin-antitoxin systems (TAs) are widespread in bacterial genomes. Yet, their integration, persistence, and impact in chromosome dynamics remain
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Eduardo Rocha @epcrocha.bsky.social · 22/09/2026
Great work led by @tomipou.bsky.social and @jrpenades.bsky.social with contributions of Yiqing Wang from our lab. While plasmid conduction has a very long history, there is a flood of papers coming on the combinatorics of plasmid co-integrations and excisions. Makes research fun, but not easier...
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Eduardo Rocha @epcrocha.bsky.social · 22/09/2026
Great work led by @jmouradesousa.bsky.social, where we find that phage and satellite defense hotspots change by recombination exceedingly fast, producing novel defenses. Oddly, phage & their satellites exchange defenses with lots of elements from theirs and other types, but not among the two.
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Vivek Mutalik @vivekmutalik.bsky.social · 19/09/2026
Some of the smallest 😎 viruses on Earth are all around us. Three or four genes 😍 each, in nearly every environment. We keep finding thousands by sequencing, yet don't know who they infect, can't easily isolate them, or even how the few we have infect a cell. Our new preprint takes this on 🧵👇
Schematics of how single strand RNA and DNA phages infect bacteria with F-pilus
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David Bikard @dbikard.bsky.social · 21/09/2026
New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. doi.org/10.1038/s41564-026-02471-8
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Didier Mazel @amazeld.bsky.social · 18/09/2026
Dear all, I have the pleasure to inform you that the online course "Resistance to Antibacterial Agents", produced by the Institut Pasteur, will start on November 3, 2026. How does ABR emerge and spread? ... 🔗 www.fun-mooc.fr/en/courses/r...
fun-mooc.fr
Resistance to antibacterial agents
The origin, risks, diagnosis, epidemiology of resistance to antibacterial agents in man and livestock worldwide, as well as preventive and countermeasures, in a « one health » perspective.
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Benoit Pons @benoitjpons.bsky.social · 17/09/2026
🧬Phages in Toulouse — November 18–20, 2026! 🦠 We are delighted to announce the next edition of Phages.fr congress, Phages in Toulouse, bringing together the phage research community for 3 days of talks, presentations & scientific discussions! 📍 Toulouse, France 📅 Nov. 18–20
phages.fr
Réseau Bactériophage France
Bienvenue sur le site du réseau “Phages.fr” Le réseau “Phages.fr” regroupe des scientifiques qui travaillent sur les thématiques incluant les bactériophages dont l’étude des structures, interactions moléculaires & cellulaires, écologie & évolution, thérapie phagique et biocontrôle en santé humaine, végétale & animale et industrie ainsi que des Sciences humaines et sociales. Ces scientifiques appartiennent à différents instituts publics français de recherche tels que CNRS (principal financeur), INRAE, INSERM, ANSES, Institut Pasteur mais aussi de nombreuses universités (Bordeaux, Lyon, Marseille, Montpellier, Nancy, Paris, etc) et hôpitaux, avec aussi la participation de membres d’entreprises.
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Dmitri Petrov @petrovadmitri.bsky.social · 17/09/2026
We are searching for an Assistant Professor in Evolutionary Biology! Looking for colleagues asking fundamental questions relating to evolutionary processes and drivers of evolutionary patterns. If you think it is you, please do apply! And please repost. facultypositions.stanford.edu/jobs/assista...
facultypositions.stanford.edu
Assistant Professor in Evolutionary Biology - Stanford University, California, United States
The Department of Biology at Stanford University seeks applicants for a tenure-track Assistant Professor in Evolutionary Biology. A successful candidate will conduct research that asks fundamental que...
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Eduardo Rocha @epcrocha.bsky.social · 16/09/2026
Bravo! Much deserved! What a year.
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Will Ratcliff @wcratcliff.bsky.social · 15/09/2026
1/17 Submissions are now open for the 2027 Microbial Population Biology GRC! We expect this meeting to be extraordinarily oversubscribed. If you want to come, time is of the essence--apply ASAP! June 27–July 2 • Andover, NH www.grc.org/microbial-po...
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Will Matlock @wtmatlock.bsky.social · 09/09/2026
Does an AMR gene on a plasmid diversify differently to an AMR gene on a chromosome? We are looking for a PhD student to work on this question in Bath!
gw4biomed.ac.uk
Turning up the volume: plasmid copy number and gene duplications as drivers of antimicrobial resistance evolution - GW4 BioMed MRC DTP
Project Code IIAR27Ba Matlock Project Type Wet lab Research Theme Infection, Immunity, and Antimicrobial Resistance Project Summary Download Summary Plasmids are important drivers of antimicrobial res...
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Julian Parkhill @julianparkhill.bsky.social · 08/09/2026
Chair in Bacteriology in Cambridge Department of Medicine. A great opportunity. Please circulate. www.cam.ac.uk/jobs/researc...
cam.ac.uk
Research Professor in the field of Bacteriology
Strengthening Cambridge's leadership in bacteriology research Bacterial infection and antimicrobial resistance remain among the most pressing global health challenges of our time. At Cambridge, the De...
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Eduardo Rocha @epcrocha.bsky.social · 07/09/2026
Manuel , it was an immense pleasure to work with you here. I’m looking forward to learn about your incoming great scientific achievements!!
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Flora Gaudillière-Jami @fgaudilliere.bsky.social · 07/09/2026
Our paper is now out in the @isme-microbes.bsky.social Journal (and selected as editor's choice)! We use an ecological framework to analyze the distribution of small transposable elements in over 30,000 prokaryotic genomes, characterizing their genomic niche doi.org/10.1093/isme...
doi.org
Characterizing the ecological niche of insertion sequences within prokaryotic genomes
Abstract. Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious
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Rachel M. Wheatley @rachelmwheatley.bsky.social · 02/09/2026
Our special issue on the social lives of bacteria is out today 🎉 it was a pleasure to edit this collection over the last year with @friendlymicrobe.bsky.social. Read our editorial here: portlandpress.com/essaysbioche...
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Joshua Weitz @joshuasweitz.bsky.social · 01/09/2026
Delighted to share news that our preprint “Slower-than-exponential viral decay is prevalent and can reshape virus-microbe dynamics” is now online, led by Akash Arani (UMD-BEES PhD), Paul Fremont (UMD-Biology postdoc) and Emma Wachter (former UMD Honors Bio student) www.biorxiv.org/content/10.6...
Examples of viral decay curves spanning biphasic (red), exponential (blue-dashed) fit to data (black points). ~50% are better represented by biphasic rather than exponential.

https://www.biorxiv.org/content/10.64898/2026.08.27.747580v2.full.pdf
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Curtis Suttle @virosphere.bsky.social · 13/08/2026
Professor in Bacteriophage Biology & Evolution at the University of British Columbia (UBC). Closing date 1 October, with an expected start date no earlier than January 1, 2027, and a salary within the range of $200,000 to $270,000 per year. For details: ubc.wd10.myworkdayjobs.com/en-US/ubcfac...
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Institut Pasteur | 130 years of biomedical research @pasteur.fr · 23/07/2026
Institut Pasteur researchers describe LIN codes in PLOS Biology: a standardized numerical system for identifying bacterial strains from genome data, now used in BIGSdb-Pasteur and Pathogenwatch for outbreak surveillance. @sylvainbrisse.bsky.social ↘️ doi.org/10.1371/journal.pbio.3003781
doi.org
Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens
Unified bacterial strain taxonomies are needed for coherent communication of findings in microbiological research. This Essay provides an overview of a novel bacterial strain taxonomy and describes ho...
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Craig Kaplan @triggerloop.bsky.social · 22/07/2026
Some bacteria use the CRISPR/Cas systems as transcriptional repressors of other anti-phage systems, such that when CRISPR interfered with, gene expression of repressed anti-phage systems goes up www.nature.com/articles/s41...
nature.com
CRISPR–Cas regulates expression of embedded anti-phage defence systems - Nature
CRISPR–Cas systems transcriptionally tune diverse innate defences using CRISPR RNA-like guides to balance antiviral protection with fitness, and hyperactivate these defences when compromised, establis...
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Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 21/07/2026
1/4 Every good defence needs a backup! 🛡️⚔ Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉 🔗 www.nature.com/articles/s41...
nature.com
Immune safeguarding as a conserved principle of antiviral defence - Nature Reviews Microbiology
All organisms defend against viral infections through active immunity mechanisms that clear the virus or population-level mechanisms that cause regulated cell death. Recent research increasingly shows...
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Rob Edwards @linsalrob.bsky.social · 22/07/2026
Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time
A computer generated 3D reconstruction of a phage, based solely on its genome sequence. For this image, we started with the genome, and used PholdAPhage to create the structures. Colours are based on pLDDT scores.
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Aude Bernheim @audeber.bsky.social · 21/07/2026
Out @cp-cellhostmicrobe.bsky.social, natural products meet bacterial immunity! We used genomics to identify lanthivirins: a family of >2,000 lanthipeptide BGCs that protect Actinobacteria against phages. Led by @hshomar.bsky.social & @mariegllm.bsky.social www.sciencedirect.com/science/arti...
sciencedirect.com
A family of lanthipeptides with anti-phage function
Bacteria produce natural products to adapt to their environments, with phage interactions as major ecological and evolutionary drivers. While some nat…
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Zamin Iqbal @zaminiqbal.bsky.social · 20/07/2026
Significant update to the AllTheBacteria paper, including discovering new antimicrobial peptides and testing in vitro and vivo. This has grown into a fantastic collaboration!
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Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 16/07/2026
1/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 biorxiv.org/content/10.6...
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Joshua Weitz @joshuasweitz.bsky.social · 15/07/2026
Bacteriophage continue to have so much to teach us. It's in our interest to understand how they work and impact human & environmental health. New joint work led by @mariandm.bsky.social & @rantahan.bsky.social inferring single-cell latent period & burst size heterogeneity from population dynamics.
science.org
Inferring single-cell heterogeneity of bacteriophage lysis-associated life-history traits from population-scale dynamics
Theory-guided experiments reveal single-cell heterogeneity of lysis-associated bacteriophage traits from population scale data.
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Structural Biology and Chemistry Dpt - Institut Pasteur @ipdbsc.bsky.social · 15/07/2026
Job Opportunity: #CNRS Chemistry - #InstitutPasteur Mid-Career Group Leader (Chemistry for Health) is open in Paris, France. This is a fantastic opportunity for a standout chemist to establish themselves in a world-class environment. research.pasteur.fr/en/call/mid-...
research.pasteur.fr
Mid-career Group Leader position in Chemistry for Health at Institut Pasteur, Paris - Research
Institut Pasteur and the CNRS are launching a joint call for a mid-career group leader position in Medicinal Chemistry and Chemistry for Health. We are looking for an experienced researcher (typically...
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Cameron Thrash @jcamthrash.bsky.social · 13/07/2026
Characterizing the ecological niche of insertion sequences within prokaryotic genomes academic.oup.com/ismej/advanc... #jcampubs
academic.oup.com
Characterizing the ecological niche of insertion sequences within prokaryotic genomes
Abstract. Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious
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Tominaga K. (tomiken) @pacyc184.bsky.social · 14/07/2026
Fate of Horizontally Acquired Genes: Rapid Initial Turnover Followed by Long-Term Persistence | Molecular Biology and Evolution | Oxford Academic
dx.doi.org
The Fate of Horizontally Acquired Genes: Rapid Initial Turnover Followed by Long-Term Persistence
Abstract. A major driver of bacterial evolution is horizontal gene transfer (HGT), the acquisition of genes from other strains or species. Transfers betwee
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Eugen Pfeifer @eugenpfeifer.bsky.social · 10/07/2026
We are looking for a motivated PhD student in phage genomics! Please find the details attached. Application deadline 24/07. Don't hesitate to spread the word!
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Rémi Fronzes @fronzeslab.bsky.social · 09/07/2026
Les nouvelles règles d'éligibilité de l'AAPG 2027 de @agencerecherche.bsky.social sont une catastrophe. Comment se fait-il qu'il n'y ait pas plus de réactions dans la communauté ? Sommes-nous à ce point résignés, ou individualistes ? #ESR
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Xavier Charpentier @labxc.bsky.social · 07/07/2026
#microsky New preprint from the lab! Widespread immune systems protect bacteria against conjugative plasmids www.biorxiv.org/content/10.6... Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab. 🧵⬇️
biorxiv.org
Widespread immune systems protect bacteria against conjugative plasmids
Conjugative plasmids are a class of mobile genetic elements capable of efficient transfer between bacterial cells. Although they can introduce beneficial traits such as antibiotic resistance to recipi...
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Sorek Lab @soreklab.bsky.social · 07/07/2026
Discovery of bacterial immunity against plasmid conjugation. Massive effort, impressive work
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Sophie Abby @soabby.bsky.social · 03/07/2026
Glad to see it finally out in #mSystems @asm.org! 🥳 See the thread below to read what it is about! journals.asm.org/doi/10.1128/...
journals.asm.org
Global distribution of isoprenoid quinones across Bacteria | mSystems
Isoprenoid quinones are small electron-carrying molecules found in the membranes of organisms that produce energy through photosynthesis or respiration and participate in other important cellular processes. Recent advances in the characterization of their biosynthesis pathways enable their automated annotation from genome analyses. In this article, we performed the genomic analysis of over 26,000 cultured and uncultured bacteria, which was complemented by literature data compiled on over 6,000 cultured bacteria. This enabled us to provide an unprecedented overview of quinone distribution across the bacterial diversity. Creating such a comprehensive data set revealed new information about quinone distribution and evolutionary paths and will facilitate future exploration of various aspects of quinone biology, including their role in the evolution and diversification of bacterial metabolism.
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Tracy Palmer @proftracypalmer.bsky.social · 24/06/2026
Check out our latest T7SS toxin story. These reverse toxins aren’t as rare as we thought!
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 21/06/2026
Le @cnrsbiologie.bsky.social #CNRS #ESR recherche son futur Directeur/sa future Directrice Poste à pourvoir janvier 2027 Candidature avant 1er septembre 2026 carrieres.cnrs.fr/recrutement-...
carrieres.cnrs.fr
Recrutement des cadres supérieurs - CNRS Carrières
Pour assurer la ligne managériale de l’établissement et représenter la diversité de ses métiers et de ses fonctions, le CNRS recrute tout au long de l’année des profils avec une expertise scientifique et/ou de management.
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Andrew Roger @andrewjroger.bsky.social · 19/06/2026
1/ Deep-time phylogenetics is hard: overly simplistic substitution models can mislead tree estimation at the billion year timescale. Our new preprint introduces GTRspmix, a protein modeling framework designed to more realistically model site-to-site heterogeneity in amino acid replacement. 🧵
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Noah Fierer @noahfierer.bsky.social · 19/06/2026
New preprint up: the power of protein language models - using a single gene (adenylate kinase) to predict the temperature optima of bacteria and bacterial communities from genomes or metagenomes www.biorxiv.org/content/10.6...
biorxiv.org
Predicting optimal growth temperatures of bacteria using learned structural information from a single protein
Temperature is a fundamental determinant of bacterial physiology and ecology. Optimal growth temperature (OGT) is highly variable across species, contributing to differences in where and when species ...
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Jesse Shapiro @bjesseshapiro.bsky.social · 15/06/2026
How useful are phages in explaining cholera disease severity? Accordingly to our latest little paper, possibly quite useful — up there with patient age and hospital location, and possibly more important than antibiotic exposures!
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Vivek Mutalik @vivekmutalik.bsky.social · 11/06/2026
Phage therapy via receptor-constrained evolutionary traps: Trends in Microbiology www.cell.com/trends/micro... #phage #phagesky
cell.com
Phage therapy via receptor-constrained evolutionary traps
Phage therapy often fails when bacteria evolve resistance. We argue that phage selection should begin with receptors whose modification imposes predictable costs, turning resistance into reduced virul...
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Michael Okun @michael-okun.bsky.social · 10/06/2026
I’ve officially resigned as Associate Editor for Frontiers in Systems Neuroscience. It used to be a reputable journal, but became a case study in how forced automation destroys academic integrity. 👇
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Rafal Mostowy @rafalmostowy.bsky.social · 10/06/2026
Phage receptor-binding proteins are known for their LEGO-like modularity, but we still do not fully understand their evolutionary potential and how it shapes phage host range. Our new preprint examines this systematically in Klebsiella phages. 🔗 www.biorxiv.org/content/10.6... Thread 🧵
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Camille Berthelot @camilleberthelot.bsky.social · 10/06/2026
sPYce is now published in Nature Ecology and Evolution! sPYce is a method to integrate single-cell regulatory data across species, without requiring whole-genome alignments between species. More below ⬇️ www.nature.com/articles/s41...
nature.com
Alignment-free integration of single-nucleus ATAC-seq across species with sPYce - Nature Ecology & Evolution
This paper presents sPYce, a method that integrates single-nucleus ATAC-seq data across species, allowing for comparison of gene regulatory evolution across species.
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Paul Rainey @paulbrainey.bsky.social · 09/06/2026
Our piece about academic renewal is now out in the Times Higher Education. It deals with a familiar topic on which there have been multiple high-level declarations. We need to move beyond the symbolic. Early career researchers, pls read + ask questions! www.timeshighereducation.com/depth/academ...
timeshighereducation.com
Academic renewal needs pressure from below and responsibility from above
High-level declarations pledging not to misuse metrics in research assessment are important, but they are far from enough. Senior academics, in particular, must use their influence to ensure instituti...
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