Patrick Hoscheit
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patrickhoscheit.bsky.social
Patrick Hoscheit
@patrickhoscheit.bsky.social
Researcher in applied mathematics @INRAE_MaIAGE. Epidemics with trees and graphs.
Reposted by Patrick Hoscheit
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....

genzplyr is dplyr, but bussin fr fr no cap.
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
github.com
November 6, 2025 at 11:25 PM
Reposted by Patrick Hoscheit
Monarez: "Kennedy demanded 2 things of me that were were inconsistent w/ my oath of office. He directed me to commit in advance to approving every ACIP recommendation regardless of the scientific evidence. He also directed me to dismiss career officials responsible for vaccine policy without cause"
September 17, 2025 at 2:39 PM
Reposted by Patrick Hoscheit
This just might be the coolest thing you see today. And without @npr.org, I may have never known it existed. Give it a spin, then check link in the comments for the backstory.

#Queen #Zulu

www.youtube.com/watch?v=gblj...
Ndlovu Youth Choir - Bohemian Rhapsody (Official Music Video) isiZulu version
YouTube video by Ndlovu Youth Choir
www.youtube.com
August 31, 2025 at 5:40 PM
Reposted by Patrick Hoscheit
Special Report
Inside the CDC director’s ouster: Kennedy demanded acceptance of new vaccine policies; Susan Monarez refused
www.statnews.com/2025/08/28/c...
Inside the CDC director's ouster: Kennedy demanded acceptance of new vaccine policies; Susan Monarez refused
Susan Monarez’s resistance to Robert F. Kennedy Jr.’s moves to assert control over vaccine guidance is at the center of her dismissal as CDC director
www.statnews.com
August 28, 2025 at 4:19 PM
Reposted by Patrick Hoscheit
one thing that's making me feel particularly insane lately is how there is no longer any limit to the amount of wrong you can be
August 8, 2025 at 4:39 PM
Reposted by Patrick Hoscheit
“…by the time we recognize there are a bunch of H5N1 patients in a hospital, it will already be too late to contain.”

My thoughts exactly. And the level of arse covering that will follow will be unprecedented.

open.substack.com/pub/rasmusse...
Where Has All the Bird Flu Gone?
All quiet on the American front for H5N1, but not necessarily the good kind of quiet
open.substack.com
July 6, 2025 at 8:44 PM
Reposted by Patrick Hoscheit
AFD Blog `Preprint: Dairy Cows Infected with Influenza A(H5N1) Reveals Low Infectious Dose and Transmission Barriers' #H5N1 afludiary.blogspot.com/2025/06/prep...
Preprint: Dairy Cows Infected with Influenza A(H5N1) Reveals Low Infectious Dose and Transmission Barriers
Credit EID Journal #18,763 Today we have a preprint that suggests that a long-held belief about how HPAI H5 has been transmitting between ...
afludiary.blogspot.com
June 20, 2025 at 11:43 AM
Reposted by Patrick Hoscheit
Excited to share my new preprint developed with @matsen.bsky.social, in collaboration with Marius Brusselmans, Luiz Carvalho, @msuchard.bsky.social, and @guybaele.bsky.social, on the biological causes and impacts of tree space ruggedness in phylodynamic inference. 1/
www.biorxiv.org/content/10.1...
www.biorxiv.org
June 17, 2025 at 1:25 AM
Reposted by Patrick Hoscheit
New postdoc positions with a number of exciting epidemic modelling projects opening in our Unit at @pasteur.fr in beautiful Paris. Deadline for applications: 26th June.
research.pasteur.fr/en/job/postd...
Postdoctoral positions in epidemic mathematical/statistical modelling - Research
Job description We are recruiting postdocs to contribute to research projects in the Mathematical Modelling of Infectious Diseases Unit, at Institut Pasteur in Paris. The candidates will be expected t...
research.pasteur.fr
June 5, 2025 at 5:22 AM
Good Lord. This is amazing. Not just the rescaling stuff, all the other features are extremely useful.
Inkscape plugin to rescale figures without distorting the text, and other useful features!
github.com/burghoff/Sci...
June 2, 2025 at 2:37 PM
It's 23.53 here in Paris, so there's still time to wish you all a happy Glorious 25th. For truth, justice, freedom. And a hard-boiled egg.
May 25, 2025 at 9:57 PM
Reposted by Patrick Hoscheit
Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...
Ambitious project to develop low-cost genome sequencing for pathogens known and unknown - University of Birmingham
Project will build on research that helped diagnostic labs to adopt sequencing capacity for COVID-19 and permit characterisation of future infectious threats
www.birmingham.ac.uk
May 22, 2025 at 10:57 AM
Reposted by Patrick Hoscheit
open.substack.com/pub/rorycell... This post about the importance of knowing the difference between truth tellers and myth makers in healthcare has already attracted a comment from a member of the “plandemic” community which nicely makes my point about the dangers of disinformation
The Truth About the Covid App
Myths about its cost and effectiveness stop us learning lessons
open.substack.com
May 15, 2025 at 10:56 AM
Reposted by Patrick Hoscheit
An important read for this morning. A Harvard scientist wanting to perform research but detained in an ICE detention center in Louisiana for at least 3 months. 🧪 #science

Gift 🎁 link:
www.nytimes.com/2025/05/13/o...
Opinion | The Science I Would Be Doing if I Weren’t in ICE Detention
www.nytimes.com
May 13, 2025 at 9:41 AM
This week, I was attending the International Dynamics & Evolution of Human Viruses conference. 32nd meeting of the conference, first time for me. Today, the locations of the next meetings in the series was announced: Canada next year, Europe in 2027 and Mexico the year after that.
May 9, 2025 at 7:40 AM
I love the idea of creating a maze for AI crawlers to get lost. Next time I'm teaching Markov chains, I will add a section on tarpitting for sure.
Basically traps AI crawlers and sends them down an "infinite maze" of static files with no exit links, where they get stuck and thrash around for months. Once trapped, the crawlers can be fed gibberish data, aka Markov babble, which is designed to poison AI models arstechnica.com/tech-policy/...
AI haters build tarpits to trap and trick AI scrapers that ignore robots.txt
Attackers explain how an anti-spam defense became an AI weapon.
arstechnica.com
May 9, 2025 at 7:19 AM
Reposted by Patrick Hoscheit
Comparative phylogeography and recombination patterns of SARS CoV-1 and SARS CoV-2 related viruses. Both are derived from recent recombinations in their host bats, and then emerged in human hundreds of miles from their wild reservoirs.

www.cell.com/cell/fulltex...
The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2
Recombination-aware evolutionary analyses of the entire genomes of SARS-CoV-1-like and SARS-CoV-2-like viruses indicate that SARS-CoV-1 and SARS-CoV-2 descend from bat coronaviruses that circulated as...
www.cell.com
May 7, 2025 at 7:29 PM
I am starting to think about posting again. I'll probably split my account into a personal and a professional one. In the meantime, here's something at the intersection of both. This is the image I will most strongly remember of Pope Francis, who will be buried today in Santa Maria Maggiore.
April 26, 2025 at 7:18 AM