Romane Junker
@rjunker.bsky.social
Bioinformatics
Microbial ecology and evolution 🧬
Postdoc @pasteur.fr GEM
PhD @inrae-maiage.bsky.social
Microbial ecology and evolution 🧬
Postdoc @pasteur.fr GEM
PhD @inrae-maiage.bsky.social
Reposted by Romane Junker
Now published in Peer Community Journal, #Microbiology section: The cutting type of vegetables influences the spontaneous fermentation rate
The cutting type of vegetables influences the spontaneous fermentation rate
Valence, Florence1 ; Junker, Romane2 ; Baty, Céline3 ; Rué, Olivier4, 2 ; Mariadassou, Mahendra2 ; Madec, Marie Noëlle1; Maillard, Marie-Bernadette1; Bage, Anne-Sophie1 ; Chuat, Victoria1 ;…
buff.ly
May 15, 2025 at 10:01 AM
Now published in Peer Community Journal, #Microbiology section: The cutting type of vegetables influences the spontaneous fermentation rate
Reposted by Romane Junker
New postdoc position in our lab (2 y+): evolutionary genomics of integrons and MGEs with focus on vibrio-phage interactions. Great environment @pasteur.fr for science, career building. Super collaborators @celineloot.bsky.social @amazeld.bsky.social @fredoleroux.bsky.social 3 weeks to apply!
April 16, 2025 at 7:14 AM
New postdoc position in our lab (2 y+): evolutionary genomics of integrons and MGEs with focus on vibrio-phage interactions. Great environment @pasteur.fr for science, career building. Super collaborators @celineloot.bsky.social @amazeld.bsky.social @fredoleroux.bsky.social 3 weeks to apply!
Reposted by Romane Junker
📢 A new #preprint recommendation: Florence Valence, @annemathilde-th.bsky.social et al. teach us to think twice before cutting our veggies for fermentation! - check it out here:
microbiol.peercommunityin.org/articles/rec...
🦠🥕🥬🍄🦠
microbiol.peercommunityin.org/articles/rec...
🦠🥕🥬🍄🦠
Cutting Type as a Key Factor in shaping Microbial Dynamics durin...
microbiol.peercommunityin.org
April 7, 2025 at 7:34 AM
📢 A new #preprint recommendation: Florence Valence, @annemathilde-th.bsky.social et al. teach us to think twice before cutting our veggies for fermentation! - check it out here:
microbiol.peercommunityin.org/articles/rec...
🦠🥕🥬🍄🦠
microbiol.peercommunityin.org/articles/rec...
🦠🥕🥬🍄🦠
Reposted by Romane Junker
📣 Un poste permanent d’IE en bioinformatique est ouvert sur la plateforme Migale.
👉 Description du profil sur jobs.inrae.fr/concours/con...
📝 Candidature jusqu’au 20 mars
Contactez-nous !
👉 Description du profil sur jobs.inrae.fr/concours/con...
📝 Candidature jusqu’au 20 mars
Contactez-nous !
February 18, 2025 at 11:29 AM
📣 Un poste permanent d’IE en bioinformatique est ouvert sur la plateforme Migale.
👉 Description du profil sur jobs.inrae.fr/concours/con...
📝 Candidature jusqu’au 20 mars
Contactez-nous !
👉 Description du profil sur jobs.inrae.fr/concours/con...
📝 Candidature jusqu’au 20 mars
Contactez-nous !
Reposted by Romane Junker
The contribution of natural transformation for the acquisition of novel genes has been notoriously difficult to quantify because it relies on recombination (which is affected by other processes). Here's a first estimate : doi.org/10.1101/2025... (for the very busy: 1-6% of gene gains) #MicroSky
January 27, 2025 at 1:11 PM
The contribution of natural transformation for the acquisition of novel genes has been notoriously difficult to quantify because it relies on recombination (which is affected by other processes). Here's a first estimate : doi.org/10.1101/2025... (for the very busy: 1-6% of gene gains) #MicroSky
Reposted by Romane Junker
1/9 🚨 New preprint alert!
Frustrated by strange results with your metagenomic data?
Meet CroCoDeEL, an accurate, easy-to-use tool to detect and quantify cross-sample contamination—no need for negative controls or sample positions!
🔗 doi.org/10.1101/2025...
Frustrated by strange results with your metagenomic data?
Meet CroCoDeEL, an accurate, easy-to-use tool to detect and quantify cross-sample contamination—no need for negative controls or sample positions!
🔗 doi.org/10.1101/2025...
CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data
Metagenomic sequencing provides profound insights into microbial communities, but it is often compromised by technical biases, including cross-sample contamination. This underexplored phenomenon arise...
doi.org
January 20, 2025 at 12:42 PM
1/9 🚨 New preprint alert!
Frustrated by strange results with your metagenomic data?
Meet CroCoDeEL, an accurate, easy-to-use tool to detect and quantify cross-sample contamination—no need for negative controls or sample positions!
🔗 doi.org/10.1101/2025...
Frustrated by strange results with your metagenomic data?
Meet CroCoDeEL, an accurate, easy-to-use tool to detect and quantify cross-sample contamination—no need for negative controls or sample positions!
🔗 doi.org/10.1101/2025...
Reposted by Romane Junker
SCARAP: scalable cross-species comparative genomics of prokaryotes https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae735/7921419 🧬🖥️🧪 https://github.com/swittouck/scarap
December 17, 2024 at 9:00 PM
SCARAP: scalable cross-species comparative genomics of prokaryotes https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae735/7921419 🧬🖥️🧪 https://github.com/swittouck/scarap
Reposted by Romane Junker
Our paper on identifying novel origins of transfer by conjugation is out! One can now expand the known oriTs from 1% to 80% in species like Acinetobacter baumannii. This contributes to unravel hitcher plasmid mobility beyond model elements. #microsky www.nature.com/articles/s41...
Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids - Nature Microbiology
Characterization of known plasmid oriT features facilitates identification of 21 oriT-containing sequence families which, alongside candidate sequence validation, expands our understanding of plasmid ...
www.nature.com
November 11, 2024 at 8:18 AM
Our paper on identifying novel origins of transfer by conjugation is out! One can now expand the known oriTs from 1% to 80% in species like Acinetobacter baumannii. This contributes to unravel hitcher plasmid mobility beyond model elements. #microsky www.nature.com/articles/s41...
Reposted by Romane Junker
Done ✅
Just published in JOSS: 'Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data.' https://doi.org/10.21105/joss.06704
November 15, 2024 at 9:43 AM
Done ✅
Reposted by Romane Junker
Integration of metataxonomic datasets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables https://www.biorxiv.org/content/10.1101/2023.11.10.566590v1
Integration of metataxonomic datasets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables https://www.biorxiv.org/content/10.1101/2023.11.10.566590v1
The management of food fermentation is still largely based on empirical knowledge, as the dynamics o
www.biorxiv.org
November 14, 2023 at 6:49 PM
Integration of metataxonomic datasets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables https://www.biorxiv.org/content/10.1101/2023.11.10.566590v1