Pablo Cárdenas R.

It feels insane to write at this particular moment in history, but I'm starting a lab next year.

To be able to stay sane (and inspired by @cbo.bsky.social and others), I'm writing about it. I'm beginning with a roadmap for #science in these troubled times:

mseelab.substack.com/p/state-of-t...

"We must stand in support of science in the face of attacks and simultaneously admit that we've been doing it wrong. One thing is certain: The changes we make ourselves will be healthier than the ones our adversaries demand."

Full of brilliant, nuanced insights (as usual from @cbo.bsky.social )

This isn't my first or even second time at the rodeo. I dealt with Ronald Reagan & George Bush trying to kill my community by ignoring the AIDS epidemic. It happened again when I lived in South Africa with Thabo Mbeki. And we won twice. So: courage. We will beat them too. Stay focused. Get to work.

Very nice

Hey if anyone is considering backing up any datasets for some reason today, the Open Science Framework has free storage up to 5G/private repository, and up to 50G/public repository.

(The OSF is run by a 501c3 (Center for Open Science), so if you do this you might also consider making a donation.)

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 ...

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:

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www.biorxiv.org/content/10.1...

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YouTube video by Sebastian Cocioba Tears In Rain Ep5: Danielle Beckman

Tears In Rain Episode 5 is live!!!

I hung out with @daniellebeckman.bsky.social where she told us about her experiences as a student in Brazil that shaped her current interests in viruses inside the human brain. I hope you enjoy! Please like and subscribe for more!

youtu.be/27AtqcYNHa8

one of the best

Polymerase mutations underlie adaptation of H5N1 influenza virus to dairy cattle and other mammals. In early 2024, an unprecedented outbreak of H5N1 high pathogenicity avian influenza was detected in dairy cattle in the USA. The epidemic remains uncontrolled, with spillbacks into poultry, wild birds...

Really proud to share our preprint describing early adaptation of H5N1 to US dairy cattle, and showing how these mutations enhance the ability of the virus to infect other mammals, such as pigs and humans.

With @influenzal.bsky.social @vidhid.bsky.social @drclairesmith.bsky.social and many more!

Detecting SARS-CoV-2 Cryptic Lineages using Publicly Available Whole Genome Wastewater Sequencing Data Beginning in early 2021, unique and highly divergent lineages of SARS-CoV-2 were sporadically found in wastewater sewersheds using a sequencing strategy focused on the most mutagenic region of SARS-Co...

I’m pleased to share that we FINALLY submitted our latest manuscript on SARS-CoV-2 cryptic lineages and what they tell us about the origins of COVID-19.
This was a ton of work.
medrxiv.org/cgi/content/...
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It is that time of the year again when @odedrechavi.bsky.social and I do our annual “your favorite paper of the year” thread. Now only on Bluesky! Please link to your favorite paper in the comments and say a few words why you loved it so much. Happy holidays and happy reading!

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In case other folks have missed it: bsky.app/profile/rich...

Great to see work on rabies!

vote linear

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I’ve updated SARSCoV2 RBD antibody-escape calculator w new deep mutational scanning data of Yunlong Cao & Fanchong Jian.

My interpretation: antigenic evolution currently constrained by pleiotropic effects of mutations on RBD-ACE2 affinity, RBD up-down position & antibody neutralization

Web-browsing patterns reflect and shape mood and mental health - Nature Human Behaviour In four studies, Kelly and Sharot reveal that web-browsing both reflects and affects mental health. Poorer mental health leads to more negative content consumption, which in turn worsens mood. Highlig...

Web-browsing patterns reflect and shape mood and mental health www.nature.com/articles/s41...

parfait, merci bien!

Infectious Disease Modelling starter pack update! Many more colleagues have joined since last post so have a look at update to welcome them. Suggestions welcome! (bio should contain experience relevant for this pack)

go.bsky.app/86Ao1a5

Love this! Would be happy to be added as well, I do evolutionary-epidemiological models!

A thread on NIH Reorganization and the Scientific Management Review Board (SMRB)

Disclosure: I was involved with the SMRB since its inception and have very strong feelings about how it was used, misused, and abandoned. My passion on these issues will undoubtably show through.

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Katherine is a brilliant mentor and scientist and I am thrilled to see this happen!

Main take-away so far from very interesting presser on #Marburg outbreak in Rwanda: Health minister Sabin Nsanzimana says all cases are linked to known infection chains. The outbreak is one major cluster with three branches.

This was a cool read #openscience

I did exactly this 7 years ago and it was one of the best decisions of my life.

Four different intern positions available: #microbiology, synthetic biology ( #synbio), #biochemistry, #bioinformatics. Here's the info (but apps via LinkedIn will be disregarded!)

www.linkedin.com/jobs/view/40...

Saw this presented a while ago, really nice work @sangwoopark.bsky.social !

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