Julien Guglielmini
@julmini.bsky.social
Reposted by Julien Guglielmini
L’Union européenne capitule pour éviter une guerre commerciale avec Trump
Par @romaricgodin.bsky.social
Par @romaricgodin.bsky.social
L’Union européenne capitule pour éviter une guerre commerciale avec Trump
La présidente de la Commission européenne, Ursula von der Leyen, a conclu dimanche soir un accord avec Donald Trump qui fait la part belle aux exigences de Washington. Un droit de douane global de 15 % sera appliqué, mais Bruxelles promet aussi de financer massivement l’économie états-unienne.
l.mediapart.fr
July 28, 2025 at 6:33 AM
L’Union européenne capitule pour éviter une guerre commerciale avec Trump
Par @romaricgodin.bsky.social
Par @romaricgodin.bsky.social
Reposted by Julien Guglielmini
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
July 23, 2025 at 7:35 AM
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
Reposted by Julien Guglielmini
1/8 - New in @natcomms.nature.com !
☣️ Meet Yersinia enterocolitica (Ye) — a lesser-known but still dangerous cousin of Yersinia pestis.
We uncover how this invasive pathogen can survive and adapt for 14 years inside a human host under constant antibiotic pressure 👇
www.nature.com/articles/s41...
☣️ Meet Yersinia enterocolitica (Ye) — a lesser-known but still dangerous cousin of Yersinia pestis.
We uncover how this invasive pathogen can survive and adapt for 14 years inside a human host under constant antibiotic pressure 👇
www.nature.com/articles/s41...
In-host evolution of Yersinia enterocolitica during a chronic human infection - Nature Communications
This study documents the evolution of antibiotic resistance and major growth defects in Yersinia enterocolitica in a patient over 14 years, revealing genetic changes that shed light on bacterial adapt...
www.nature.com
July 1, 2025 at 6:05 PM
1/8 - New in @natcomms.nature.com !
☣️ Meet Yersinia enterocolitica (Ye) — a lesser-known but still dangerous cousin of Yersinia pestis.
We uncover how this invasive pathogen can survive and adapt for 14 years inside a human host under constant antibiotic pressure 👇
www.nature.com/articles/s41...
☣️ Meet Yersinia enterocolitica (Ye) — a lesser-known but still dangerous cousin of Yersinia pestis.
We uncover how this invasive pathogen can survive and adapt for 14 years inside a human host under constant antibiotic pressure 👇
www.nature.com/articles/s41...
Reposted by Julien Guglielmini
Excited to share this preprint focused on the genomic taxonomy of C. diphtheriae #diphtheria
➡️ www.biorxiv.org/content/10.1...
Hope it helps advance research and surveillance of this relevant bacterial pathogen. Thanks to @sylvainbrisse.bsky.social and BEBP and BIGSdb teams for making it possible!
➡️ www.biorxiv.org/content/10.1...
Hope it helps advance research and surveillance of this relevant bacterial pathogen. Thanks to @sylvainbrisse.bsky.social and BEBP and BIGSdb teams for making it possible!
June 23, 2025 at 4:50 PM
Excited to share this preprint focused on the genomic taxonomy of C. diphtheriae #diphtheria
➡️ www.biorxiv.org/content/10.1...
Hope it helps advance research and surveillance of this relevant bacterial pathogen. Thanks to @sylvainbrisse.bsky.social and BEBP and BIGSdb teams for making it possible!
➡️ www.biorxiv.org/content/10.1...
Hope it helps advance research and surveillance of this relevant bacterial pathogen. Thanks to @sylvainbrisse.bsky.social and BEBP and BIGSdb teams for making it possible!
Reposted by Julien Guglielmini
Avis aux amateurs : France Travail propose environ 12 millions d'euros pour lui développer un "agent conversationnel" pour échanger avec les demandeurs d'emplois par SMS. www.boamp.fr/pages/avis/?...
June 12, 2025 at 5:20 AM
Avis aux amateurs : France Travail propose environ 12 millions d'euros pour lui développer un "agent conversationnel" pour échanger avec les demandeurs d'emplois par SMS. www.boamp.fr/pages/avis/?...
Reposted by Julien Guglielmini
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
May 22, 2025 at 12:42 PM
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
Reposted by Julien Guglielmini
RAxML-NG v2.0 beta is here
github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...
github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...
Release RAxML-NG v2.0-beta2 · amkozlov/raxml-ng
Main new features
Adaptive tree search heuristic (Togkousidis 2023) , (Togkousidis 2024)
Multiple fast branch support measures
Integrated model testing
Full Changelog: 1.2.2...2.0-beta2
github.com
May 15, 2025 at 5:35 AM
RAxML-NG v2.0 beta is here
github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...
github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...
Reposted by Julien Guglielmini
Au même moment, les agences fédérales de la Défense ont reçu ordre d'annuler toutes activités autour de 11 évènements annuels sur la diversité américaine, dont le Black History Month, le Women History Month, la LGBT Pride Month, le Holocaust Remembrance Day... www.nbcnews.com/politics/don...
Federal agencies bar Black History Month and other 'special observances'
A number of federal agencies have banned celebrations related to MLK Jr. Day, Women's History Month and other such observances to comply with Trump's executive orders.
www.nbcnews.com
February 2, 2025 at 2:11 PM
Au même moment, les agences fédérales de la Défense ont reçu ordre d'annuler toutes activités autour de 11 évènements annuels sur la diversité américaine, dont le Black History Month, le Women History Month, la LGBT Pride Month, le Holocaust Remembrance Day... www.nbcnews.com/politics/don...
Reposted by Julien Guglielmini
Donald Trump lance sa guerre commerciale mondiale
Par Martine Orange
Par Martine Orange
Donald Trump lance sa guerre commerciale mondiale
Après avoir confirmé les sanctions douanières contre le Mexique et le Canada, Donald Trump vise désormais l’Union européenne. Des droits douaniers pourraient être imposés très rapidement. Tous...
www.mediapart.fr
February 1, 2025 at 7:34 PM
Donald Trump lance sa guerre commerciale mondiale
Par Martine Orange
Par Martine Orange
Reposted by Julien Guglielmini
Le groupe TotalEnergies fait des dons à l’université de Strasbourg, notamment pour l’école de chimie. Une convention de mécénat dévoile l’emprise que la multinationale souhaite établir dans l’enseignement supérieur et la recherche. https://www.mediapart.fr/journal/france/310125/strasbourg-contre-so…
À Strasbourg, contre son mécénat, Total demande à « s’impliquer fortement » à l’université de Strasbourg
Le groupe TotalEnergies fait des dons à l’université de Strasbourg, notamment pour l’école de chimie. Une convention de mécénat dévoile l’emprise que la multinationale souhaite établir dans...
www.mediapart.fr
January 31, 2025 at 6:45 PM
Le groupe TotalEnergies fait des dons à l’université de Strasbourg, notamment pour l’école de chimie. Une convention de mécénat dévoile l’emprise que la multinationale souhaite établir dans l’enseignement supérieur et la recherche. https://www.mediapart.fr/journal/france/310125/strasbourg-contre-so…
Reposted by Julien Guglielmini
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 Julien Guglielmini
La conversion de tout le secteur de la technologie au trumpisme est le fruit de son modèle économique. Pour poursuivre sa logique prédatrice, il a trouvé dans l’extrême droite un débouché politique utile. https://www.mediapart.fr/journal/economie-et-social/190125/les-big-tech-basculent-l-extreme-dr…
Les Big Tech basculent à l’extrême droite : c’est l’économie, idiot !
La conversion de tout le secteur de la technologie au trumpisme est le fruit de son modèle économique. Pour poursuivre sa logique prédatrice, il a trouvé dans l’extrême droite un débouché politique...
www.mediapart.fr
January 19, 2025 at 8:28 PM
La conversion de tout le secteur de la technologie au trumpisme est le fruit de son modèle économique. Pour poursuivre sa logique prédatrice, il a trouvé dans l’extrême droite un débouché politique utile. https://www.mediapart.fr/journal/economie-et-social/190125/les-big-tech-basculent-l-extreme-dr…
Reposted by Julien Guglielmini
This preprint makes a point that is valid for a lot of machine learning approaches. Organisms or genes are linked by evolutionary history; they are not independent. This results in correlation between learning and test sets, and often in over-optimistic evaluations of the methods' outcome.
Interested in predicting AMR in bacteria? We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. With @nwheeler443.bsky.social and former PhD student Yanying Yu. 🦠🧫🧬🖥️🧪
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Biased sampling confounds machine learning prediction of antimicrobial resistance
Antimicrobial resistance (AMR) poses a growing threat to human health. Increasingly, genome sequencing is being applied for the surveillance of bacterial pathogens, producing a wealth of data to train...
www.biorxiv.org
January 18, 2025 at 6:25 PM
This preprint makes a point that is valid for a lot of machine learning approaches. Organisms or genes are linked by evolutionary history; they are not independent. This results in correlation between learning and test sets, and often in over-optimistic evaluations of the methods' outcome.
Reposted by Julien Guglielmini
L'équipe de Mediapart arrive progressivement sur Bluesky
Les comptes à suivre sont dans notre starter pack 👇
go.bsky.app/5ueP6wM
Les comptes à suivre sont dans notre starter pack 👇
go.bsky.app/5ueP6wM
November 19, 2024 at 11:09 AM
L'équipe de Mediapart arrive progressivement sur Bluesky
Les comptes à suivre sont dans notre starter pack 👇
go.bsky.app/5ueP6wM
Les comptes à suivre sont dans notre starter pack 👇
go.bsky.app/5ueP6wM
Reposted by Julien Guglielmini
University websites are like distant stars, when you look at them you see the scientists as they used to be many years ago
November 12, 2024 at 7:22 AM
University websites are like distant stars, when you look at them you see the scientists as they used to be many years ago
Reposted by Julien Guglielmini
First paper from my student Daria Frolova's PhD now on biorxiv:
www.biorxiv.org/content/10.1...
The key question: plasmids change structurally ~as fast as they mutate, so how can we decide whether 2 plasmids are "the same plasmid" for epi purposes?
1/n
www.biorxiv.org/content/10.1...
The key question: plasmids change structurally ~as fast as they mutate, so how can we decide whether 2 plasmids are "the same plasmid" for epi purposes?
1/n
www.biorxiv.org
June 13, 2024 at 2:13 PM
First paper from my student Daria Frolova's PhD now on biorxiv:
www.biorxiv.org/content/10.1...
The key question: plasmids change structurally ~as fast as they mutate, so how can we decide whether 2 plasmids are "the same plasmid" for epi purposes?
1/n
www.biorxiv.org/content/10.1...
The key question: plasmids change structurally ~as fast as they mutate, so how can we decide whether 2 plasmids are "the same plasmid" for epi purposes?
1/n
Reposted by Julien Guglielmini
New paper from the lab, the mysteries involving the genetic elements that move by being mobilized by other MGEs. Hitcher Genetic Elements are distinctive, ancient and diverse.
ecoevorxiv.org/repository/v...
ecoevorxiv.org/repository/v...
Hijackers, hitchhikers, or co-drivers? The mysteries of microbial mobilizable genetic elements
ecoevorxiv.org
April 29, 2024 at 9:44 AM
New paper from the lab, the mysteries involving the genetic elements that move by being mobilized by other MGEs. Hitcher Genetic Elements are distinctive, ancient and diverse.
ecoevorxiv.org/repository/v...
ecoevorxiv.org/repository/v...
Reposted by Julien Guglielmini
New job offer: we search a postdoc (bioinformatics) to work on mobile genetic elements and gene flow in bacteria, with a focus on antibiotic resistance within a consortium including bioinformatics, synthetic biology, epidemiology & biochemistry. See research.pasteur.fr/en/job/postd... #MicroSky
April 4, 2024 at 4:33 PM
New job offer: we search a postdoc (bioinformatics) to work on mobile genetic elements and gene flow in bacteria, with a focus on antibiotic resistance within a consortium including bioinformatics, synthetic biology, epidemiology & biochemistry. See research.pasteur.fr/en/job/postd... #MicroSky
Reposted by Julien Guglielmini
New preprint out now - stable bacterial strain nomenclature with Life Identification Numbers using a gene-by-gene approach. From our wonderful collaborators at the Institut Pasteur.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Bacterial strain nomenclature in the genomic era: Life Identification Numbers using a gene-by-gene approach
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
March 13, 2024 at 10:07 AM
New preprint out now - stable bacterial strain nomenclature with Life Identification Numbers using a gene-by-gene approach. From our wonderful collaborators at the Institut Pasteur.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Julien Guglielmini
First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset)
www.biorxiv.org/content/10.1...
#microsky
www.biorxiv.org/content/10.1...
#microsky
March 11, 2024 at 1:45 PM
First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset)
www.biorxiv.org/content/10.1...
#microsky
www.biorxiv.org/content/10.1...
#microsky
Reposted by Julien Guglielmini
Our latest work is finally out!
How #capsule serotypes of #Klebsiella pneumoniae influences #phage adsorption and infection, and #plasmid conjugation efficiency.
Plasmids care about size-phages dont!
Great work led by Matthieu Haudiquet in the lab @epcrocha.bsky.social
doi.org/10.1038/s414...
How #capsule serotypes of #Klebsiella pneumoniae influences #phage adsorption and infection, and #plasmid conjugation efficiency.
Plasmids care about size-phages dont!
Great work led by Matthieu Haudiquet in the lab @epcrocha.bsky.social
doi.org/10.1038/s414...
Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency - Nature Communications
Bacterial capsules provide protection against the environment, including host immune systems. Authors swap capsule loci in Klebsiella pneumoniae to reveal the role of these sugar coats against plasmid...
doi.org
March 7, 2024 at 2:11 PM
Our latest work is finally out!
How #capsule serotypes of #Klebsiella pneumoniae influences #phage adsorption and infection, and #plasmid conjugation efficiency.
Plasmids care about size-phages dont!
Great work led by Matthieu Haudiquet in the lab @epcrocha.bsky.social
doi.org/10.1038/s414...
How #capsule serotypes of #Klebsiella pneumoniae influences #phage adsorption and infection, and #plasmid conjugation efficiency.
Plasmids care about size-phages dont!
Great work led by Matthieu Haudiquet in the lab @epcrocha.bsky.social
doi.org/10.1038/s414...
Reposted by Julien Guglielmini
I recently made a comic complaining that NASA refuses to listen to my good ideas for improving the Solar System (xkcd.com/2750).
To my delight, NASA’s Science Mission Directorate has sent me an actual expert panel evaluation of my “flatten the planets” proposal! Sadly, they decided not to fund it.
To my delight, NASA’s Science Mission Directorate has sent me an actual expert panel evaluation of my “flatten the planets” proposal! Sadly, they decided not to fund it.
February 22, 2024 at 2:45 PM
I recently made a comic complaining that NASA refuses to listen to my good ideas for improving the Solar System (xkcd.com/2750).
To my delight, NASA’s Science Mission Directorate has sent me an actual expert panel evaluation of my “flatten the planets” proposal! Sadly, they decided not to fund it.
To my delight, NASA’s Science Mission Directorate has sent me an actual expert panel evaluation of my “flatten the planets” proposal! Sadly, they decided not to fund it.
Reposted by Julien Guglielmini
New from the lab. We were stuck studying plasmid mobility because we ignored most origins of transfer by conjugation. Using the occurrences of known oriT, we developed a method to find novel unrelated families. Works well. We now cover most conjugative plasmids of E coli, K pneumo & A baumannii.
Identification of novel origins of transfer across bacterial plasmids https://www.biorxiv.org/content/10.1101/2024.01.30.577996v1
Identification of novel origins of transfer across bacterial plasmids https://www.biorxiv.org/content/10.1101/2024.01.30.577996v1
Conjugative plasmids are important drivers of bacterial evolution, but most plasmids lack genes for
www.biorxiv.org
January 31, 2024 at 1:58 PM
New from the lab. We were stuck studying plasmid mobility because we ignored most origins of transfer by conjugation. Using the occurrences of known oriT, we developed a method to find novel unrelated families. Works well. We now cover most conjugative plasmids of E coli, K pneumo & A baumannii.
Reposted by Julien Guglielmini
Oh non ! James Herbert Brennan, l'auteur de l'incroyable cycle Quête du Graal des Livres Dont Vous Êtes Le Héros, s'en est allé rejoindre le funestre paragraphe 14 à l'âge de 83 ans. Il laisse derrière lui une génération de jeunes Pip endeuillés.
RIP :'(
rip.ie/death-notice...
RIP :'(
rip.ie/death-notice...
January 9, 2024 at 1:34 PM
Oh non ! James Herbert Brennan, l'auteur de l'incroyable cycle Quête du Graal des Livres Dont Vous Êtes Le Héros, s'en est allé rejoindre le funestre paragraphe 14 à l'âge de 83 ans. Il laisse derrière lui une génération de jeunes Pip endeuillés.
RIP :'(
rip.ie/death-notice...
RIP :'(
rip.ie/death-notice...