Louise H. Moncla
@lhmoncla.bsky.social
Assistant Professor of Pathobiology at the University of Pennsylvania. We use trees to study RNA virus evolution and transmission, with a focus on avian influenza. viruses, sequencing, phylogenetics, pop gen. She/her
https://lmoncla.github.io/monclalab/
https://lmoncla.github.io/monclalab/
We hope these are useful, and plan to add more features and subtypes in the future! Get in touch if there are alternative features you'd love to see, or other subtypes you'd be excited about. Congrats Jordan, and thanks to CEIRR for the support!
October 15, 2025 at 3:44 PM
We hope these are useful, and plan to add more features and subtypes in the future! Get in touch if there are alternative features you'd love to see, or other subtypes you'd be excited about. Congrats Jordan, and thanks to CEIRR for the support!
like annotations for cleavage site sequences, and updated quality metrics to reflect the high circulating diversity. Our paper has all these details, and you can use these at clades.nextstrain.org by selecting he H5Nx, 2.3.2.1, or 2.3.4.4 datasets.
Nextclade
Genetic sequence alignment, clade assignment, mutation calling, phylogenetic placement, and quality checks for SARS-CoV-2, Influenza (Flu), Monkeypox, Respiratory Syncytial Virus (RSV) and other patho...
clades.nextstrain.org
October 15, 2025 at 3:44 PM
like annotations for cleavage site sequences, and updated quality metrics to reflect the high circulating diversity. Our paper has all these details, and you can use these at clades.nextstrain.org by selecting he H5Nx, 2.3.2.1, or 2.3.4.4 datasets.
Supported by the CEIRR Comp Modeling Core, we developed and validated datasets for H5Nx (all clades), and the 2.3.2.1 and 2.3.4.4 clades (which currently circulate). We benchmarked against LABEL, and show that NextClade based assignments are both fast and accurate. We added some H5 specific features
Nextclade
Genetic sequence alignment, clade assignment, mutation calling, phylogenetic placement, and quality checks for SARS-CoV-2, Influenza (Flu), Monkeypox, Respiratory Syncytial Virus (RSV) and other patho...
clades.nextstrain.org
October 15, 2025 at 3:44 PM
Supported by the CEIRR Comp Modeling Core, we developed and validated datasets for H5Nx (all clades), and the 2.3.2.1 and 2.3.4.4 clades (which currently circulate). We benchmarked against LABEL, and show that NextClade based assignments are both fast and accurate. We added some H5 specific features
Thanks Michelle! This preprint is now published in Virus Evolution academic.oup.com/ve/article/1...
Validate User
academic.oup.com
September 22, 2025 at 2:02 PM
Thanks Michelle! This preprint is now published in Virus Evolution academic.oup.com/ve/article/1...
Congrats @alisonfeder.bsky.social !!! This is so great to see!!
June 18, 2025 at 8:17 PM
Congrats @alisonfeder.bsky.social !!! This is so great to see!!
congrats @joeyzacks.bsky.social!!!! awesome to see
May 24, 2025 at 10:08 PM
congrats @joeyzacks.bsky.social!!!! awesome to see
I'm so sorry Michael. This is awful
May 15, 2025 at 12:56 AM
I'm so sorry Michael. This is awful
What the actual F. I'm so sorry. You're great, and these people are idiots.
March 21, 2025 at 8:38 PM
What the actual F. I'm so sorry. You're great, and these people are idiots.
Thank you!! This is helpful
February 28, 2025 at 8:24 PM
Thank you!! This is helpful
degrees of surveillance and varying lag times between detections and depopulation. Does anyone know of good studies of actual, estimated mortality rates in chickens in non-laboratory settings? The people asking this question earnestly wanted good, real information and I'd like to help them get it.
February 28, 2025 at 6:01 PM
degrees of surveillance and varying lag times between detections and depopulation. Does anyone know of good studies of actual, estimated mortality rates in chickens in non-laboratory settings? The people asking this question earnestly wanted good, real information and I'd like to help them get it.
and this is supported by experimental infection studies like this one. However, I'm having a hard time finding actual data/publications on estimated CFRs/mortality rates from the field. Theoretically, this should be knowable from past outbreaks and from comparisons between US states with varying ...
February 28, 2025 at 6:01 PM
and this is supported by experimental infection studies like this one. However, I'm having a hard time finding actual data/publications on estimated CFRs/mortality rates from the field. Theoretically, this should be knowable from past outbreaks and from comparisons between US states with varying ...
One common question from producers is why entire flocks need to be culled when one positive is detected on the farm. For farmers, this can look like these birds are healthy, and it's unclear why all birds are depopulated. My understanding is that H5N1 has essentially a 100% CFR in chickens...
February 28, 2025 at 6:01 PM
One common question from producers is why entire flocks need to be culled when one positive is detected on the farm. For farmers, this can look like these birds are healthy, and it's unclear why all birds are depopulated. My understanding is that H5N1 has essentially a 100% CFR in chickens...
edit: Jonathan Pekar
February 24, 2025 at 3:58 PM
edit: Jonathan Pekar