Eduardo Rocha
@epcrocha.bsky.social
Scientist, genomics, evolution, microbiology, computational biology, Institut Pasteur/CNRS, Paris
Pinned
Eduardo Rocha
@epcrocha.bsky.social
· Jan 14
Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
www.biorxiv.org
Here, we find that many Genomic islands have origins of transfer (oriT) mobilisable by conjugation, incl. known Pathogenicity & defense islands. iOriT use only an oriT for transfer by hitching on conjugative elements: they make abundant, diverse, ancient families of mobile genetic elements. See🧵
Reposted by Eduardo Rocha
On this fabulous day celebrating André Citroën's birthday 🥖🚗, I’m happy to share my main paper from my postdoc in @jrpenades.bsky.social Lab.
If you want to hear about how plasmid evolution is driven by mobile genetic elements, please come and read this preprint!
www.biorxiv.org/content/10.6...
If you want to hear about how plasmid evolution is driven by mobile genetic elements, please come and read this preprint!
www.biorxiv.org/content/10.6...
www.biorxiv.org
February 5, 2026 at 4:04 PM
On this fabulous day celebrating André Citroën's birthday 🥖🚗, I’m happy to share my main paper from my postdoc in @jrpenades.bsky.social Lab.
If you want to hear about how plasmid evolution is driven by mobile genetic elements, please come and read this preprint!
www.biorxiv.org/content/10.6...
If you want to hear about how plasmid evolution is driven by mobile genetic elements, please come and read this preprint!
www.biorxiv.org/content/10.6...
Reposted by Eduardo Rocha
Huge thanks to @asn-amnat.bsky.social for inviting our review on the evolutionary and ecological consequences of cooperation. @annadewar.bsky.social @asgriffin.bsky.social @lauriebelch.bsky.social www.journals.uchicago.edu/doi/10.1086/...
February 12, 2026 at 8:18 PM
Huge thanks to @asn-amnat.bsky.social for inviting our review on the evolutionary and ecological consequences of cooperation. @annadewar.bsky.social @asgriffin.bsky.social @lauriebelch.bsky.social www.journals.uchicago.edu/doi/10.1086/...
Reposted by Eduardo Rocha
I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.
February 12, 2026 at 7:18 PM
I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.
Reposted by Eduardo Rocha
Happy #DarwinDay 🧬🌿! To celebrate, why not share a story about #evolution with a #FutureScientist? My book, Little Changes, is a fun bedtime story for young readers to explore how small changes shape the living world.
littlestories.co.uk/little-chang...
#ScienceForKids #STEMBooks
littlestories.co.uk/little-chang...
#ScienceForKids #STEMBooks
Little Changes
an introduction to evolution Click on the image below, to read the story. Meet the Rinkidinks. They live together in one large happy family, carefree and untroubled by the rest of the world. Until …
littlestories.co.uk
February 12, 2026 at 11:51 AM
Happy #DarwinDay 🧬🌿! To celebrate, why not share a story about #evolution with a #FutureScientist? My book, Little Changes, is a fun bedtime story for young readers to explore how small changes shape the living world.
littlestories.co.uk/little-chang...
#ScienceForKids #STEMBooks
littlestories.co.uk/little-chang...
#ScienceForKids #STEMBooks
Reposted by Eduardo Rocha
Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠
We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵
We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵
February 12, 2026 at 12:42 AM
Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠
We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵
We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵
Reposted by Eduardo Rocha
@carolinamicro.bsky.social Huang & @lbobay.bsky.social investigated genomic rearrangements across 121 microbial species, showing that rearrangements occur at a variable pace across bacteria and archaea, pointing to different selective constraints.
🔗 doi.org/10.1093/gbe/evag002
#genome #evolution
🔗 doi.org/10.1093/gbe/evag002
#genome #evolution
Prevalence and Evolutionary Implications of Genome Rearrangements in Bacteria
Abstract. The genetic material of bacteria and archaea is organized into various structures and setups, attesting that genome architecture is dynamic in th
doi.org
February 11, 2026 at 3:57 PM
@carolinamicro.bsky.social Huang & @lbobay.bsky.social investigated genomic rearrangements across 121 microbial species, showing that rearrangements occur at a variable pace across bacteria and archaea, pointing to different selective constraints.
🔗 doi.org/10.1093/gbe/evag002
#genome #evolution
🔗 doi.org/10.1093/gbe/evag002
#genome #evolution
Reposted by Eduardo Rocha
Now out & nicely formatted in @isme-microbes.bsky.social
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.
A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.
A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny
Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring
doi.org
February 9, 2026 at 8:31 PM
Now out & nicely formatted in @isme-microbes.bsky.social
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.
A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.
A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
Reposted by Eduardo Rocha
Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
February 8, 2026 at 2:08 AM
Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Eduardo Rocha
How do bacterial pangenomes evolve, what controls their dynamics, why do they exist?
Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle
Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle
February 9, 2026 at 10:55 AM
How do bacterial pangenomes evolve, what controls their dynamics, why do they exist?
Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle
Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle
Reposted by Eduardo Rocha
There are over 18,000 types of lichen in existence. My personal favourite is ‘village bench lichen’, which devotes its entire existence selflessly to gradually making communal public seating more furry and comfortable.
February 6, 2026 at 9:41 PM
There are over 18,000 types of lichen in existence. My personal favourite is ‘village bench lichen’, which devotes its entire existence selflessly to gradually making communal public seating more furry and comfortable.
Reposted by Eduardo Rocha
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology
The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...
www.nature.com
February 6, 2026 at 3:15 PM
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Eduardo Rocha
Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein: iScience www.cell.com/iscience/ful...
🎊Congrats to my fantastic lab members @noemiematthey.bsky.social , Giorgia Wennubst and Nicolas Pellaton, and to our precious GTF collaborators! 🎉
🎊Congrats to my fantastic lab members @noemiematthey.bsky.social , Giorgia Wennubst and Nicolas Pellaton, and to our precious GTF collaborators! 🎉
Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein
Properties of biomolecules; Epigenetics; Microbial genomics; Transcriptomics
www.cell.com
February 6, 2026 at 12:31 PM
Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein: iScience www.cell.com/iscience/ful...
🎊Congrats to my fantastic lab members @noemiematthey.bsky.social , Giorgia Wennubst and Nicolas Pellaton, and to our precious GTF collaborators! 🎉
🎊Congrats to my fantastic lab members @noemiematthey.bsky.social , Giorgia Wennubst and Nicolas Pellaton, and to our precious GTF collaborators! 🎉
Reposted by Eduardo Rocha
New #BehindThePaper for our latest paper in @natcomms.nature.com (rdcu.be/e2qMK)
Secret Invasion: Strain Fate Across Microbiomes
Cover illustration by Helena Klein (@illuzation.bsky.social).
communities.springernature.com/posts/secret...
Secret Invasion: Strain Fate Across Microbiomes
Cover illustration by Helena Klein (@illuzation.bsky.social).
communities.springernature.com/posts/secret...
Secret Invasion: Strain Fate Across Microbiomes
communities.springernature.com
February 5, 2026 at 7:33 AM
New #BehindThePaper for our latest paper in @natcomms.nature.com (rdcu.be/e2qMK)
Secret Invasion: Strain Fate Across Microbiomes
Cover illustration by Helena Klein (@illuzation.bsky.social).
communities.springernature.com/posts/secret...
Secret Invasion: Strain Fate Across Microbiomes
Cover illustration by Helena Klein (@illuzation.bsky.social).
communities.springernature.com/posts/secret...
Reposted by Eduardo Rocha
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning - Nature Biotechnology
PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.
www.nature.com
February 4, 2026 at 8:20 PM
Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs
Reposted by Eduardo Rocha
How does population density affect evolutionary trajectory?
Microbes construct their own niche which in turn reshapes their evolution.
Preprint drop from grad student @noahhoupt.bsky.social whose evolution experiments featured blue/white colonies, 1000 generations, a lab move, and much more!
Microbes construct their own niche which in turn reshapes their evolution.
Preprint drop from grad student @noahhoupt.bsky.social whose evolution experiments featured blue/white colonies, 1000 generations, a lab move, and much more!
Interested in eco-evolutionary feedbacks? Microbial experimental evolution? Pleiotropy? Filamentous phages??
Check out our latest preprint, now up on BioRxiv!
biorxiv.org/content/10.6...
For a quick summary, peep the thread below...🧵 (1/10)
Check out our latest preprint, now up on BioRxiv!
biorxiv.org/content/10.6...
For a quick summary, peep the thread below...🧵 (1/10)
biorxiv.org
February 5, 2026 at 2:08 AM
How does population density affect evolutionary trajectory?
Microbes construct their own niche which in turn reshapes their evolution.
Preprint drop from grad student @noahhoupt.bsky.social whose evolution experiments featured blue/white colonies, 1000 generations, a lab move, and much more!
Microbes construct their own niche which in turn reshapes their evolution.
Preprint drop from grad student @noahhoupt.bsky.social whose evolution experiments featured blue/white colonies, 1000 generations, a lab move, and much more!
Reposted by Eduardo Rocha
🔬 Discover the latest advances from Labex IBEID
We have released a new white paper highlighting recent scientific and technological advances from the partners.
➡️ Key results
➡️ Latest innovations
➡️ Future challenges for Emerging Infectious Diseases research
www.labexibeid.fr/en/ibeid-whi...
We have released a new white paper highlighting recent scientific and technological advances from the partners.
➡️ Key results
➡️ Latest innovations
➡️ Future challenges for Emerging Infectious Diseases research
www.labexibeid.fr/en/ibeid-whi...
February 2, 2026 at 12:30 PM
🔬 Discover the latest advances from Labex IBEID
We have released a new white paper highlighting recent scientific and technological advances from the partners.
➡️ Key results
➡️ Latest innovations
➡️ Future challenges for Emerging Infectious Diseases research
www.labexibeid.fr/en/ibeid-whi...
We have released a new white paper highlighting recent scientific and technological advances from the partners.
➡️ Key results
➡️ Latest innovations
➡️ Future challenges for Emerging Infectious Diseases research
www.labexibeid.fr/en/ibeid-whi...
Reposted by Eduardo Rocha
A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41...
How bacteria evolved thousands of precision nanoinjectors?
Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
How bacteria evolved thousands of precision nanoinjectors?
Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
A comprehensive catalogue of receptor-binding domains in extracellular contractile injection systems - Nature Communications
Extracellular contractile injection systems (eCISs) are bacteriophage tail-derived toxin delivery complexes that are present in many prokaryotes. Here, the authors present an analysis of eCIS tail fib...
www.nature.com
January 26, 2026 at 1:26 PM
A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41...
How bacteria evolved thousands of precision nanoinjectors?
Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
How bacteria evolved thousands of precision nanoinjectors?
Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
Reposted by Eduardo Rocha
🌟 New preprint alert! 🌟 We’re excited to share the latest work from @francoisleulier.bsky.social lab, now on bioRxiv!
Symbiosis through lysis: prophage activation underlies Lactiplantibacillus plantarum probiotic function https://www.biorxiv.org/content/10.64898/2025.12.15.694388v1
December 16, 2025 at 7:03 AM
🌟 New preprint alert! 🌟 We’re excited to share the latest work from @francoisleulier.bsky.social lab, now on bioRxiv!
Reposted by Eduardo Rocha
Un poste de Maître de Conférence est ouvert pour rejoindre notre unité à Lyon !
Possibilité de rejoindre mon équipe pour travailler sur:
- caractérisation des mécanismes de défense anti-phage
- transfert horizontal et interactions entre éléments génétiques mobiles
N'hésitez pas à me contacter
Possibilité de rejoindre mon équipe pour travailler sur:
- caractérisation des mécanismes de défense anti-phage
- transfert horizontal et interactions entre éléments génétiques mobiles
N'hésitez pas à me contacter
📢 Recrutement d’un(e) Maître(sses) de conférence en Biochimie générale, spécialité bactériologie moléculaire à MMSB
🔬Recherche
*Immunité anti-phages
*Réponse au stress, modulation de la croissance bactérienne
✉️ christophe.grangeasse@cnrs.fr
📚Enseignement : Université Lyon I
✉️ patrice.gouet@ibcp.fr
🔬Recherche
*Immunité anti-phages
*Réponse au stress, modulation de la croissance bactérienne
✉️ christophe.grangeasse@cnrs.fr
📚Enseignement : Université Lyon I
✉️ patrice.gouet@ibcp.fr
January 29, 2026 at 8:39 PM
Un poste de Maître de Conférence est ouvert pour rejoindre notre unité à Lyon !
Possibilité de rejoindre mon équipe pour travailler sur:
- caractérisation des mécanismes de défense anti-phage
- transfert horizontal et interactions entre éléments génétiques mobiles
N'hésitez pas à me contacter
Possibilité de rejoindre mon équipe pour travailler sur:
- caractérisation des mécanismes de défense anti-phage
- transfert horizontal et interactions entre éléments génétiques mobiles
N'hésitez pas à me contacter
Reposted by Eduardo Rocha
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
www.science.org
January 30, 2026 at 6:11 AM
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Reposted by Eduardo Rocha
Wow. Journals like this should be immediately removed from the Clarivate database.
Wiley: "We’re supporting responsible research assessment practices" onlinelibrary.wiley.com/journal/1520...
Also Wiley: "Prove that your article is a good fit for this journal 😉😉😉😉😉 by citing at least two of our articles in your manuscript before we will even consider reviewing it" 🤡
Also Wiley: "Prove that your article is a good fit for this journal 😉😉😉😉😉 by citing at least two of our articles in your manuscript before we will even consider reviewing it" 🤡
January 30, 2026 at 4:09 PM
Wow. Journals like this should be immediately removed from the Clarivate database.
Reposted by Eduardo Rocha
We are hiring for group leaders again — EBI is a great place to start your research group!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
Research Group Leader
Do you want to lead groundbreaking research in computational biology? Join us at EMBL-EBI! EMBL's European Bioinformatics Institute (EMBL-EBI) is seeking talented and highly-motivated scientists to jo...
embl.wd103.myworkdayjobs.com
January 30, 2026 at 9:02 AM
We are hiring for group leaders again — EBI is a great place to start your research group!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
Reposted by Eduardo Rocha
I couldn’t agree more! Help support Wikipedia.
It has been a pillar of high-quality knowledge sharing since the early web, and it’s more relevant than ever in the fuzzy age of AI
www.nature.com/articles/d41...
It has been a pillar of high-quality knowledge sharing since the early web, and it’s more relevant than ever in the fuzzy age of AI
www.nature.com/articles/d41...
Wikipedia is needed now more than ever, 25 years on
The online encyclopedia is an antidote to an increasingly poisoned information ecosystem. Researchers should help to nourish it.
www.nature.com
January 30, 2026 at 1:44 PM
I couldn’t agree more! Help support Wikipedia.
It has been a pillar of high-quality knowledge sharing since the early web, and it’s more relevant than ever in the fuzzy age of AI
www.nature.com/articles/d41...
It has been a pillar of high-quality knowledge sharing since the early web, and it’s more relevant than ever in the fuzzy age of AI
www.nature.com/articles/d41...
Reposted by Eduardo Rocha
Calling all OrthoFinder users!
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
www.biorxiv.org
January 29, 2026 at 12:07 PM
Calling all OrthoFinder users!
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
Reposted by Eduardo Rocha
We have an open position for a bioinformatics/theoretical microbial ecology PhD student to study viral strategies in the global Microverse! Join us at the @microverse.bsky.social at @uni-jena.de, please apply through this link:
jobs.uni-jena.de/jobposting/9...
jobs.uni-jena.de/jobposting/9...
PhD student bioinformatics: Viral strategies in the global Microverse
jobs.uni-jena.de
January 29, 2026 at 12:08 PM
We have an open position for a bioinformatics/theoretical microbial ecology PhD student to study viral strategies in the global Microverse! Join us at the @microverse.bsky.social at @uni-jena.de, please apply through this link:
jobs.uni-jena.de/jobposting/9...
jobs.uni-jena.de/jobposting/9...