Noémie Lefrancq
@noemielefrancq.bsky.social
Phylogenetics 🧬 , infectious disease dynamics 🦠 & modelling 💻 #IDSky #IDModelling
Postdoctoral fellow @ETH Zürich (in Basel)
Previously @Cambridge_Uni and @institutpasteur
Postdoctoral fellow @ETH Zürich (in Basel)
Previously @Cambridge_Uni and @institutpasteur
Pinned
Learning the fitness dynamics of pathogens from phylogenies - Nature
Phylowave, an innovative phylogenetic approach, can identify the main circulating pathogen lineages with increased fitness and the associated genetic changes, enabling the timely identification of…
buff.ly
Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
Reposted by Noémie Lefrancq
By Julia Marshall as first author and led by Professors Kate Baker and Henrik Salje as co-leading authors (@hsalje.bsky.social @ksbakes.bsky.social), please see our new article about the genomic epidemiology of the spread of sexually transmitted #Shigella:
www.thelancet.com/journals/lan...
🛟🧪🧬🖥️🦠💉🧫😷
www.thelancet.com/journals/lan...
🛟🧪🧬🖥️🦠💉🧫😷
The spread of sexually transmissible drug-resistant shigellosis in England: a genomic epidemiology study
Our study shows the distinct and intensifying sexual transmission of shigellosis,
highlighting the urgent need to address sexually transmissible shigellosis as a distinct
health threat. Traditional in...
www.thelancet.com
July 12, 2026 at 11:23 AM
By Julia Marshall as first author and led by Professors Kate Baker and Henrik Salje as co-leading authors (@hsalje.bsky.social @ksbakes.bsky.social), please see our new article about the genomic epidemiology of the spread of sexually transmitted #Shigella:
www.thelancet.com/journals/lan...
🛟🧪🧬🖥️🦠💉🧫😷
www.thelancet.com/journals/lan...
🛟🧪🧬🖥️🦠💉🧫😷
Reposted by Noémie Lefrancq
The final piece of my PhD work is now published in Science Translational Medicine! We present a new framework to jointly infer epidemiological and antigenic parameters from multi-pathogen population serological studies🦠
www.science.org/stoken/autho...
www.science.org/stoken/autho...
December 18, 2025 at 10:04 AM
The final piece of my PhD work is now published in Science Translational Medicine! We present a new framework to jointly infer epidemiological and antigenic parameters from multi-pathogen population serological studies🦠
www.science.org/stoken/autho...
www.science.org/stoken/autho...
For the first time, we found phylogenetic evidence of importations and local transmission of Macrolide-resistant #pertussis strains in France. Needs further monitoring!
Great work led by Valérie Bouchez, Carla Rodrigues and @sylvainbrisse.bsky.social!
Paper: shorturl.at/2Npmm
🦠 🧪 🛟
Great work led by Valérie Bouchez, Carla Rodrigues and @sylvainbrisse.bsky.social!
Paper: shorturl.at/2Npmm
🦠 🧪 🛟
July 3, 2025 at 8:30 AM
For the first time, we found phylogenetic evidence of importations and local transmission of Macrolide-resistant #pertussis strains in France. Needs further monitoring!
Great work led by Valérie Bouchez, Carla Rodrigues and @sylvainbrisse.bsky.social!
Paper: shorturl.at/2Npmm
🦠 🧪 🛟
Great work led by Valérie Bouchez, Carla Rodrigues and @sylvainbrisse.bsky.social!
Paper: shorturl.at/2Npmm
🦠 🧪 🛟
Reposted by Noémie Lefrancq
Pathogen genomes can provide insights into underlying disease transmission patterns but new methods are needed to analyze large genome datasets. Our work using identical pathogen sequences to characterize fine scale SARS-CoV-2 transmission was just published in @nature.com tinyurl.com/bdzk9xjj 🥳
Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences - Nature
The analysis of pairs of identical SARS-CoV-2 genome sequences enables characterization of transmission patterns between geographies and age groups.
tinyurl.com
March 5, 2025 at 4:48 PM
Pathogen genomes can provide insights into underlying disease transmission patterns but new methods are needed to analyze large genome datasets. Our work using identical pathogen sequences to characterize fine scale SARS-CoV-2 transmission was just published in @nature.com tinyurl.com/bdzk9xjj 🥳
Reposted by Noémie Lefrancq
AI is poised to accelerate understanding in infectious diseases, but its value needs to be demonstrated through close collaboration between research, industry, society, and policy.
Paper free to read: rdcu.be/eaxEw
Summary here: www.ox.ac.uk/news/2025-02...
Paper free to read: rdcu.be/eaxEw
Summary here: www.ox.ac.uk/news/2025-02...
Artificial intelligence for modelling infectious disease epidemics
Nature - This Perspective considers the application to infectious disease modelling of AI systems that combine machine learning, computational statistics, information retrieval and data science.
rdcu.be
February 20, 2025 at 10:13 AM
AI is poised to accelerate understanding in infectious diseases, but its value needs to be demonstrated through close collaboration between research, industry, society, and policy.
Paper free to read: rdcu.be/eaxEw
Summary here: www.ox.ac.uk/news/2025-02...
Paper free to read: rdcu.be/eaxEw
Summary here: www.ox.ac.uk/news/2025-02...
Reposted by Noémie Lefrancq
Building on the UShER tree of millions of SARS-CoV-2 genomes maintained by Angie Hinrichs, Hugh Haddox and Georg Angehrn (and others in @matsen.bsky.social lab and @jbloomlab.bsky.social) have looked into how the neutral mutation rate varies along the genome:
[1/N]
www.biorxiv.org/content/10.1...
[1/N]
www.biorxiv.org/content/10.1...
The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure
RNA viruses like SARS-CoV-2 have a high mutation rate, which contributes to their rapid evolution. The rate of mutations depends on the mutation type (e.g., A→C, A→G, etc.) and can vary between sites ...
www.biorxiv.org
January 11, 2025 at 5:37 PM
Building on the UShER tree of millions of SARS-CoV-2 genomes maintained by Angie Hinrichs, Hugh Haddox and Georg Angehrn (and others in @matsen.bsky.social lab and @jbloomlab.bsky.social) have looked into how the neutral mutation rate varies along the genome:
[1/N]
www.biorxiv.org/content/10.1...
[1/N]
www.biorxiv.org/content/10.1...
Reposted by Noémie Lefrancq
Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
Learning the fitness dynamics of pathogens from phylogenies - Nature
Phylowave, an innovative phylogenetic approach, can identify the main circulating pathogen lineages with increased fitness and the associated genetic changes, enabling the timely identification of…
buff.ly
January 2, 2025 at 8:03 AM
Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
Reposted by Noémie Lefrancq
🦠🔍 Tracking Pathogen Evolution in Real Time
A new tool, 'phylowave', has been developed to help scientists track how viruses and bacteria evolve. It identifies new variants with increased fitness, offering insights into diseases like #COVID19 and flu.
🔗 www.nature.com/articles/s41...
#SciComm 🧪
A new tool, 'phylowave', has been developed to help scientists track how viruses and bacteria evolve. It identifies new variants with increased fitness, offering insights into diseases like #COVID19 and flu.
🔗 www.nature.com/articles/s41...
#SciComm 🧪
Learning the fitness dynamics of pathogens from phylogenies - Nature
Phylowave, an innovative phylogenetic approach, can identify the main circulating pathogen lineages with increased fitness and the associated genetic changes, enabling the timely identification of eme...
www.nature.com
January 3, 2025 at 5:59 AM
🦠🔍 Tracking Pathogen Evolution in Real Time
A new tool, 'phylowave', has been developed to help scientists track how viruses and bacteria evolve. It identifies new variants with increased fitness, offering insights into diseases like #COVID19 and flu.
🔗 www.nature.com/articles/s41...
#SciComm 🧪
A new tool, 'phylowave', has been developed to help scientists track how viruses and bacteria evolve. It identifies new variants with increased fitness, offering insights into diseases like #COVID19 and flu.
🔗 www.nature.com/articles/s41...
#SciComm 🧪
Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
Learning the fitness dynamics of pathogens from phylogenies - Nature
Phylowave, an innovative phylogenetic approach, can identify the main circulating pathogen lineages with increased fitness and the associated genetic changes, enabling the timely identification of…
buff.ly
January 2, 2025 at 8:03 AM
Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
https://buff.ly/4gyYCzx
We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies.
🧵 A thread... 1/n
#IDSky #IDModelling
Reposted by Noémie Lefrancq
* rolls up newspaper *
No Guardian! Bad Guardian! An infection is not a microbiome! www.theguardian.com/lifeandstyle...
No Guardian! Bad Guardian! An infection is not a microbiome! www.theguardian.com/lifeandstyle...
The brain microbiome: could understanding it help prevent dementia?
Long thought to be sterile, our brains are now believed to harbour all sorts of micro-organisms, from bacteria to fungi. How big a part do they play in Alzheimer’s and similar diseases?
www.theguardian.com
December 2, 2024 at 10:10 AM
* rolls up newspaper *
No Guardian! Bad Guardian! An infection is not a microbiome! www.theguardian.com/lifeandstyle...
No Guardian! Bad Guardian! An infection is not a microbiome! www.theguardian.com/lifeandstyle...
Reposted by Noémie Lefrancq
Disease prevalence in US states before & after vaccine introduction
Graphic from Edward Tufte
More graphics.wsj.com/infectious-d... 🧪
Graphic from Edward Tufte
More graphics.wsj.com/infectious-d... 🧪
November 15, 2024 at 5:00 AM
Disease prevalence in US states before & after vaccine introduction
Graphic from Edward Tufte
More graphics.wsj.com/infectious-d... 🧪
Graphic from Edward Tufte
More graphics.wsj.com/infectious-d... 🧪
Super resource to explore publicly available genome sequencing data! Currently supports H5N1, West Nile, RSV-A, RSV-B and SARS-CoV-2
GenSpectrum.org
#IDSky
GenSpectrum.org
#IDSky
November 25, 2024 at 1:13 PM
Super resource to explore publicly available genome sequencing data! Currently supports H5N1, West Nile, RSV-A, RSV-B and SARS-CoV-2
GenSpectrum.org
#IDSky
GenSpectrum.org
#IDSky
Thrilled to have received this award, thank you @gensocuk.bsky.social! Many thanks to @hsalje.bsky.social @julianparkhill.bsky.social, Sylvain Brisse and the amazing research groups without whom the work wouldn't have been possible!
A big congratulations to Noémie Lefrancq on being awarded the Sir Kenneth Mather Memorial Prize🏅 for their exceptional PhD thesis on global dynamics of the bacterium behind whooping cough, using genomes from throughout Europe and the world!
genetics.org.uk/medals-and-p...
genetics.org.uk/medals-and-p...
November 22, 2024 at 1:23 PM
Thrilled to have received this award, thank you @gensocuk.bsky.social! Many thanks to @hsalje.bsky.social @julianparkhill.bsky.social, Sylvain Brisse and the amazing research groups without whom the work wouldn't have been possible!
Reposted by Noémie Lefrancq
Infectious Disease Modelling starter pack update! First pack is full so I created a second one. Pls keep on sending suggestions! (bio should contain experience relevant for this pack)
IDModelling pack 1: go.bsky.app/86Ao1a5
IDModelling pack 2 : go.bsky.app/2oBB7KX
IDModelling pack 1: go.bsky.app/86Ao1a5
IDModelling pack 2 : go.bsky.app/2oBB7KX
Infectious Disease Modelling #IDModelling
Join the conversation
go.bsky.app
November 22, 2024 at 8:08 AM
Infectious Disease Modelling starter pack update! First pack is full so I created a second one. Pls keep on sending suggestions! (bio should contain experience relevant for this pack)
IDModelling pack 1: go.bsky.app/86Ao1a5
IDModelling pack 2 : go.bsky.app/2oBB7KX
IDModelling pack 1: go.bsky.app/86Ao1a5
IDModelling pack 2 : go.bsky.app/2oBB7KX
Reposted by Noémie Lefrancq
Hey bluesky! It's great to see so many new folks jumping on the #IDSky wagon. If you're at #TropMed24 drop by my poster tomorrow at 11am. We can talk all things chikungunya burden, sex and age-dependent disease risk, and potential vaccine impact!
November 15, 2024 at 3:00 PM
Hey bluesky! It's great to see so many new folks jumping on the #IDSky wagon. If you're at #TropMed24 drop by my poster tomorrow at 11am. We can talk all things chikungunya burden, sex and age-dependent disease risk, and potential vaccine impact!
Reposted by Noémie Lefrancq
November 10, 2024 at 6:06 PM
Reposted by Noémie Lefrancq
New work led by Wei Wang characterises the dynamics of measles immunity in infant&child cohorts in China. @hsalje.bsky.social www.nature.com/articles/s41...
Dynamics of measles immunity from birth and following vaccination - Nature Microbiology
Serological data modelling informs on immune interference from maternal antibodies on measles vaccine responses in infants and children.
www.nature.com
May 14, 2024 at 7:46 AM
New work led by Wei Wang characterises the dynamics of measles immunity in infant&child cohorts in China. @hsalje.bsky.social www.nature.com/articles/s41...
Reposted by Noémie Lefrancq
We’re hiring!! postdoc and research assistant (with potential for PhD) positions on mathematical modeling of infectious diseases at Cambridge (UK). Mainly of arboviruses including with longitudinal cohorts, disease mapping and models applied to multiplex serology in Africa. jobs.cam.ac.uk/job/44461/
December 19, 2023 at 6:44 PM
We’re hiring!! postdoc and research assistant (with potential for PhD) positions on mathematical modeling of infectious diseases at Cambridge (UK). Mainly of arboviruses including with longitudinal cohorts, disease mapping and models applied to multiplex serology in Africa. jobs.cam.ac.uk/job/44461/