Eduardo Rocha
@epcrocha.bsky.social
Scientist, genomics, evolution, microbiology, computational biology, Institut Pasteur/CNRS, Paris
Pinned
Eduardo Rocha
@epcrocha.bsky.social
· Mar 17
From Trading Genes to Crafting New Tricks: How Horizontal Gene Transfer Potentiates the Emergence of Novel Functions
ecoevorxiv.org
Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky
Reposted by Eduardo Rocha
🧬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
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
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.
Phages.fr
September 17, 2026 at 1:02 PM
🧬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
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
Reposted by Eduardo Rocha
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...
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...
facultypositions.stanford.edu
September 17, 2026 at 8:46 PM
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...
Bravo! Much deserved! What a year.
As a wonderful way to wrap up these past few months, I’m deeply honored to receive the Plasmid Biology Prize from the International Society for Plasmid Biology at #ISPB2026 Berlin. 🍾🥳
Many thanks to the Society, and to all the friends, colleagues, and mentors I’m lucky to meet at these meetings.
Many thanks to the Society, and to all the friends, colleagues, and mentors I’m lucky to meet at these meetings.
September 16, 2026 at 7:59 AM
Bravo! Much deserved! What a year.
Reposted by Eduardo Rocha
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...
June 27–July 2 • Andover, NH
www.grc.org/microbial-po...
September 15, 2026 at 10:40 PM
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...
June 27–July 2 • Andover, NH
www.grc.org/microbial-po...
Reposted by Eduardo Rocha
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!
We are looking for a PhD student to work on this question in Bath!
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...
gw4biomed.ac.uk
September 9, 2026 at 8:08 AM
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!
We are looking for a PhD student to work on this question in Bath!
Reposted by Eduardo Rocha
Chair in Bacteriology in Cambridge Department of Medicine. A great opportunity. Please circulate.
www.cam.ac.uk/jobs/researc...
www.cam.ac.uk/jobs/researc...
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...
www.cam.ac.uk
September 8, 2026 at 8:53 AM
Chair in Bacteriology in Cambridge Department of Medicine. A great opportunity. Please circulate.
www.cam.ac.uk/jobs/researc...
www.cam.ac.uk/jobs/researc...
Manuel , it was an immense pleasure to work with you here. I’m looking forward to learn about your incoming great scientific achievements!!
Big news! Deeply honored to receive an #ERCStG from @erc.europa.eu! 🍾
Over the next five years, E-MOTION will study how interactions between Mobile Genetic Elements shape bacterial evolution in clinical settings.
Exciting science and opportunities ahead: stay tuned, positions will be opening soon!
Over the next five years, E-MOTION will study how interactions between Mobile Genetic Elements shape bacterial evolution in clinical settings.
Exciting science and opportunities ahead: stay tuned, positions will be opening soon!
📣 Good news! 📣
Results of the ERC 2026 Starting Grant call are out!
Funding worth a total of €705 million will go to 421 early-career researchers across Europe.
Discover who, what and where 👉 link.europa.eu/9M3MmN
🧪 #ERCStG #FrontierResearch #HorizonEurope
🇪🇺 @scienceinnovation.ec.europa.eu
Results of the ERC 2026 Starting Grant call are out!
Funding worth a total of €705 million will go to 421 early-career researchers across Europe.
Discover who, what and where 👉 link.europa.eu/9M3MmN
🧪 #ERCStG #FrontierResearch #HorizonEurope
🇪🇺 @scienceinnovation.ec.europa.eu
September 7, 2026 at 4:19 PM
Manuel , it was an immense pleasure to work with you here. I’m looking forward to learn about your incoming great scientific achievements!!
Reposted by Eduardo Rocha
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...
September 7, 2026 at 2:32 PM
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...
Reposted by Eduardo Rocha
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...
September 2, 2026 at 11:05 AM
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...
Reposted by Eduardo Rocha
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...
www.biorxiv.org/content/10.6...
September 1, 2026 at 1:50 AM
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...
www.biorxiv.org/content/10.6...
Reposted by Eduardo Rocha
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...
August 13, 2026 at 4:37 AM
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...
Reposted by Eduardo Rocha
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/10.1371/journal.pbio.3003781
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...
doi.org
July 23, 2026 at 8:53 AM
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/10.1371/journal.pbio.3003781
Reposted by Eduardo Rocha
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...
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...
www.nature.com
July 22, 2026 at 5:21 PM
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...
Reposted by Eduardo Rocha
1/4
Every good defence needs a backup! 🛡️⚔
Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉
🔗 www.nature.com/articles/s41...
Every good defence needs a backup! 🛡️⚔
Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉
🔗 www.nature.com/articles/s41...
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...
www.nature.com
July 21, 2026 at 8:26 AM
1/4
Every good defence needs a backup! 🛡️⚔
Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉
🔗 www.nature.com/articles/s41...
Every good defence needs a backup! 🛡️⚔
Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉
🔗 www.nature.com/articles/s41...
Reposted by Eduardo Rocha
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
Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time
July 22, 2026 at 1:36 AM
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
Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time
Reposted by Eduardo Rocha
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...
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...
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…
www.sciencedirect.com
July 21, 2026 at 10:24 AM
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...
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...
Reposted by Eduardo Rocha
Significant update to the AllTheBacteria paper, including discovering new antimicrobial peptides and testing in vitro and vivo. This has grown into a fantastic collaboration!
Biology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics
Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not...
www.biorxiv.org
July 20, 2026 at 1:05 PM
Significant update to the AllTheBacteria paper, including discovering new antimicrobial peptides and testing in vitro and vivo. This has grown into a fantastic collaboration!
Reposted by Eduardo Rocha
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...
🚨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...
July 16, 2026 at 6:59 PM
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...
🚨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...
Reposted by Eduardo Rocha
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.
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.
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.
www.science.org
July 15, 2026 at 6:50 PM
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.
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.
Reposted by Eduardo Rocha
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-...
This is a fantastic opportunity for a standout chemist to establish themselves in a world-class environment.
research.pasteur.fr/en/call/mid-...
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...
research.pasteur.fr
July 15, 2026 at 7:35 AM
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-...
This is a fantastic opportunity for a standout chemist to establish themselves in a world-class environment.
research.pasteur.fr/en/call/mid-...
Reposted by Eduardo Rocha
Characterizing the ecological niche of insertion sequences within prokaryotic genomes academic.oup.com/ismej/advanc... #jcampubs
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
academic.oup.com
July 13, 2026 at 5:42 PM
Characterizing the ecological niche of insertion sequences within prokaryotic genomes academic.oup.com/ismej/advanc... #jcampubs
Reposted by Eduardo Rocha
Fate of Horizontally Acquired Genes: Rapid Initial Turnover Followed by Long-Term Persistence | Molecular Biology and Evolution | Oxford Academic
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
dx.doi.org
July 14, 2026 at 8:25 AM
Fate of Horizontally Acquired Genes: Rapid Initial Turnover Followed by Long-Term Persistence | Molecular Biology and Evolution | Oxford Academic
Reposted by Eduardo Rocha
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!
July 10, 2026 at 8:53 AM
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!
Reposted by Eduardo Rocha
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
July 9, 2026 at 7:27 AM
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
Reposted by Eduardo Rocha
#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.
🧵⬇️
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.
🧵⬇️
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...
www.biorxiv.org
July 7, 2026 at 7:58 AM
#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.
🧵⬇️
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.
🧵⬇️