Franklin Nobrega

Pediatric Infectious Diseases/Microbiology - Professor Series (tenure track/tenure), Open Rank University of California, Irvine is hiring. Apply now!

🚨New faculty job opportunity 🚨

Please share this ad for a faculty position in our department at UC Irvine, in the fields of microbiology and infectious disease. MD/PhDs and PhDs are desired and should apply!

recruit.ap.uci.edu/JPF09954

Summer school:<br> Evolutionary Biology in Guarda Information about the annual summer school Evolutionary Biology in Guarda

The 2026 Guarda Summer Course in Evolutionary Biology is now accepting applications. Amazing place, amazing course, amazing opportunity for early grad students.

tb.ethz.ch/education/gu...

Happy to share that I’m opening my lab at the Weizmann Institute of Science!
We’ll study systems-level regulation of bacterial defense, driven by RNA-protein interactions shaping cell fate.
Now recruiting PhD students & postdocs
tinyurl.com/4yfa55vd
Please reach out and share!

Leveraging defense system modularity to discover anti-phage systems Bacterial exposure to constant phage attack drives rapid diversification of anti-phage defense systems, often through the exchange of modular defensive domains. Here, we leverage this modularity signa...

Exciting pre-print on new variants of anti-phage defense systems including CBASS, Pycsar, and Gabija!

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

✨New preprint!

🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬

🔗👇

Working at HIRI At the HIRI, we do not just value excellent research. Short distances, an open door policy, and a good working atmosphere—this is what distinguishes us from others. Have a look at our current job…

🚀 We're hiring!
We are offering several exciting #PhD & #postdoc positions spanning a range of topics, from jumbo phage biology & phage therapy to programmable RNA therapeutics & Fusobacterium nucleatum research. The application deadline is Jan 11. Learn more: www.helmholtz-hiri.de/en/jobs-tale...

Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...

Fredston Lab: Postdoctoral Scholar University of California, Santa Cruz is hiring. Apply now!

in a week, I'll start reviewing applications for this postdoc. come work with me in Santa Cruz, CA on fitting Bayesian hierarchical models to whale tag and photo datasets.

position starts in fall 2026. ask me questions and apply here: recruit.ucsc.edu/JPF02003

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

Phages are full of genes of unknown function that are likely adaptive in specific conditions.
New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out
tinyurl.com/bdcfrejh

#microsky

KlebPhaCol: a community-driven resource for Klebsiella research identified a novel phage family Abstract. The growing threat of multidrug-resistant Klebsiella pneumoniae, coupled with its role in gut colonisation, has intensified the search for new tr

KlebPhaCol: a community-driven resource for Klebsiella research identified a novel phage family

#phage #phagesky

Amazing effort by @fnobrega.bsky.social lab

academic.oup.com/nar/article/...

Group Leader (f/m/d) at the Rudolf Virchow Center for Integrative and Translational Bioimaging - Würzburg (Stadt), Bayern (DE) job with University of Würzburg - Rudolf Virchow Center for Integrative a... The Rudolf Virchow Center for Integrative and Translational Bioimaging (RVZ) ist now inviting applications for the position of Group Leader (f/m/d).

We have an open call for a group leader at the Rudolf Virchow Center for Integrative and Translational Bioimaging in Würzburg, Germany.

Generous starting package, vibrant and highly interdisciplinary biomedical research environment.
www.nature.com/naturecareer...

Please spread the word.

Mid-career Group Leader position in AI in genomics at Institut Pasteur, Paris - Research Institut Pasteur and the CNRS are launching a call for a mid-career group leader position in AI in genomics. We are looking for an experienced researcher (typically with > 8 years of research experien...

Opening of a Group Leader position in AI in genomics at Institut Pasteur @pasteur.fr , Paris research.pasteur.fr/en/call/mid-...

Polymyxins slow down lateral diffusion of proteins and lipopolysaccharide in the E. coli outer membrane - Communications Biology Multi-scale molecular dynamics simulations reveal that polymyxins form polymyxin-protein aggregates upon associating with the E. coli outer membrane thereby reducing lateral mobility of outer membrane...

Our paper on polymyxin interacting with the E. coli outer membrane is out! Simulations by the very talented @dheerajprakaash.bsky.social www.nature.com/articles/s42...

To scale outer membrane protein island simulated at coarse-grained resolution with portions refined at all atom resolution.

A commensal bacterium secretes effector proteins to establish population heterogeneity in the gut Zagieboylo and colleagues demonstrate that the human commensal Bacteroides thetaiotaomicron secretes two self-targeting proteins that induce heterogeneity within its own population. Differential expre...

#microsky 😳

www.cell.com/cell-host-mi...

Systematic discovery of TIR-based immune signaling systems in bacteria Toll/interleukin-1 receptor (TIR) domains are important for immune signaling across humans, plants and bacteria. These domains were recently found to produce immune signaling molecules in plant immuni...

#microsky #phagesky #phge defence

Preprint from the @soreklab.bsky.social reporting a plethora of novel TIR-based immune signalling systems

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

Amazing dataset describing the metabolic profiles of 66 E. coli transporter knockouts by @sulheim.bsky.social with Peter Doubleday and @nzamboni.bsky.social. The tool, set up by @lambdapp.bsky.social and Eric Ulrich allows you to explore for yourself. Enjoy! Pre-print here: doi.org/10.1101/2025...

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

CryoET of microbes inside an animal organ? Yes it’s possible! Check out our new preprint showing how we did it! What an amazing collaboration with amazing scientists who made this possible!

Diagram illustrating "feed the enemy's enemy": ampicillin inhibits Pseudomonas aeruginosa. Citrobacter freundii acidifies the environment, further inhibiting P. aeruginosa.

New preprint from our lab www.biorxiv.org/content/10.1...! Andrea Dos Santos and Clément Vulin combine experiments and models showing how adding glucose can strengthen negative interactions between microbial species. This can be used in tandem with antibiotic treatment to inhibit pathogens!

🚨 We are hiring a group leader in Virology at CIRI !

Join us in the beautiful city of Lyon 🇫🇷

Deadline on March 31st 2026

Life Identification Numbers: A bacterial strain nomenclature approach Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.

Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses Abstract. Taxonomic classification underlies all biological science and is the basis for comparative analysis of biological organisms and therefore our und

#microsky #phagesky #phage #virus

academic.oup.com/nar/advance-...

A cloning strategy as depicted in the OpenCloning website

#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software

✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨‍🔬 Built by a researcher — for researchers!

👉 Check it out at opencloning.org

Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years

#phagesky

www.nature.com/articles/s41...

Advancing urinary tract infection treatment through on-chip technological innovation at University of Southampton on FindAPhD.com PhD Project - Advancing urinary tract infection treatment through on-chip technological innovation at University of Southampton, listed on FindAPhD.com

PhD Opportunity: Advance UTI treatment with on-chip tech! 🔬🧫
Work at the microbiology-bioengineering interface with Hywel Morgan, @fnobrega.bsky.social and me.
Program EPSRC/MOD CISDnS CDT cisdns-cdt.ac.uk
Co-funded by IfLS Southampton
tinyurl.com/infoUTI
tinyurl.com/applyUTI
Deadline: 8 Dec 2025

BarTn7: Optimizing Bacterial Lineage Tracking at Sub-Species Resolution for Population Dynamics in Ecological and Evolutionary Studies Communities of bacteria undergo population bottlenecks which are crucial to their population, ecological, and evolutionary dynamics. However, conventional amplicon sequencing cannot distinguish such d...

Very excited to share a big part of my dissertation work with the Deutschbauer lab at LBNL and @ucberkeleyofficial.bsky.social! BarTn7: A method for bacterial lineage tracking at sub-species resolution in population, ecological, and evolutionary experiments.
www.biorxiv.org/content/10.1...

Now online at @cp-cellhostmicrobe.bsky.social from co-first authors @erinedoherty.bsky.social & @jnoms.bsky.social