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Pablo Cárdenas R.

@pcr-guy.bsky.social
1.3K followers 472 following 166 posts

🦠 🧬 🇨🇴 • pathogens + evo + synbio + modeling • prof and lab leader at @mseelab.org • banner pic by Melanconnie

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Pablo Cárdenas R. @pcr-guy.bsky.social · 19/09/2026
Finally sat down to write about AI in science and scientific training!
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Pablo Cárdenas R. @pcr-guy.bsky.social · 17/07/2026
It's go time!
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C. Brandon Ogbunu @cbo.bsky.social · 10/06/2026
A study I regularly circle back 2 from Dr. Pablo Cardenas-Ramirez, PI of @mseelab.org. Just now making use of the amazing computational tool (Opqua) that it introduces. With it, 1 can model fitness landscape scale ?s (e.g. valley crossing) @ the host-parasite scale www.science.org/doi/10.1126/...
science.org
Genomic epidemiological models describe pathogen evolution across fitness valleys
A software tool creates flexible epidemiological simulations of evolving pathogens and shows how competition limits evolution.
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Pablo Cárdenas R. @pcr-guy.bsky.social · 19/06/2026
Wow, took a break from social media (while v - sa was processing...) and what a way to be welcomed back!!! We should talk more, big updates coming soon! Here's a snapshot taken from a talk a couple weeks ago @uwgenome.bsky.social (huge thanks for the invitation!):
jOpqua has four key improvements:
1. Speed
2. Host groups
3. Host immunity
4. Host genetics
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Pablo Cárdenas R. @pcr-guy.bsky.social · 24/10/2025
Tetsu is an incredible scientist, mentor, and all-around person—can't recommend this lab enough. So stoked to be neighbors and get projects rolling!
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Tetsuhiro Harimoto @tetsuharimoto.bsky.social · 14/10/2025
My postdoc work is now on bioRxiv! We combined engineered bacteria and hydrogels to create implantable living materials that safely confine bacteria while letting them sense disease and release drugs from within. 🔗 www.biorxiv.org/content/10.1...
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Pablo Cárdenas R. @pcr-guy.bsky.social · 01/02/2025
Very nice
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Melissa Kline Struhl @mekline.bsky.social · 31/01/2025
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.)
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Richard Neher @neher.io · 11/01/2025
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...
biorxiv.org
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 ...
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Pablo Cárdenas R. @pcr-guy.bsky.social · 10/01/2025
📌
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Pablo Cárdenas R. @pcr-guy.bsky.social · 09/01/2025
📌
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Sebastian S. Cocioba @atinygreencell.bsky.social · 08/01/2025
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
youtu.be
Tears In Rain Ep5: Danielle Beckman
YouTube video by Sebastian Cocioba
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Pablo Cárdenas R. @pcr-guy.bsky.social · 07/01/2025
one of the best
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Tom Peacock @peacockflu.bsky.social · 07/01/2025
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!
biorxiv.org
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...
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Solid Evidence @solidevidence.bsky.social · 28/12/2024
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/... 1/
medrxiv.org
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...
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Dmitri Petrov @petrovadmitri.bsky.social · 26/12/2024
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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Pablo Cárdenas R. @pcr-guy.bsky.social · 21/12/2024
📌
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Pablo Cárdenas R. @pcr-guy.bsky.social · 19/12/2024
In case other folks have missed it: bsky.app/profile/rich... Great to see work on rabies!
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Pablo Cárdenas R. @pcr-guy.bsky.social · 17/12/2024
vote linear
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Pablo Cárdenas R. @pcr-guy.bsky.social · 22/11/2024
📌
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Bloom lab @jbloomlab.bsky.social · 21/11/2024
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
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NetScience @netscience.bsky.social · 21/11/2024
Web-browsing patterns reflect and shape mood and mental health www.nature.com/articles/s41...
nature.com
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...
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Pablo Cárdenas R. @pcr-guy.bsky.social · 21/11/2024
parfait, merci bien!
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Simon Cauchemez @scauchemez.bsky.social · 19/11/2024
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
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Pablo Cárdenas R. @pcr-guy.bsky.social · 20/11/2024
Love this! Would be happy to be added as well, I do evolutionary-epidemiological models!
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Jeremy Berg @jeremymberg.bsky.social · 20/11/2024
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. 1/n
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Pablo Cárdenas R. @pcr-guy.bsky.social · 20/11/2024
📌
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Pablo Cárdenas R. @pcr-guy.bsky.social · 19/11/2024
Katherine is a brilliant mentor and scientist and I am thrilled to see this happen!
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Kai Kupferschmidt @kakape.bsky.social · 20/10/2024
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.
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Pablo Cárdenas R. @pcr-guy.bsky.social · 18/10/2024
This was a cool read #openscience
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Pablo Cárdenas R. @pcr-guy.bsky.social · 18/10/2024
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...
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Pablo Cárdenas R. @pcr-guy.bsky.social · 17/10/2024
Saw this presented a while ago, really nice work @sangwoopark.bsky.social !
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Pablo Cárdenas R. @pcr-guy.bsky.social · 12/10/2024
📌
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Pablo Cárdenas R. @pcr-guy.bsky.social · 09/10/2024
wild, also very entertaining thread
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Pablo Cárdenas R. @pcr-guy.bsky.social · 09/10/2024
Tanja Kortemme @ ucsf!
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Pablo Cárdenas R. @pcr-guy.bsky.social · 09/10/2024
True! Perhaps the lesson is the systems complement each other. "Academic"-type research (heavy quotes) is good at sowing seeds of long-term innovation, but is prone to getting lost in the weeds. "Industry"-type research is better at getting solutions to a problem once one has been well defined.
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Pablo Cárdenas R. @pcr-guy.bsky.social · 09/10/2024
It's interesting to me that what seemed like an inexorable arrow of history to me as a first-year grad student seems uncertain now, after years of ups and downs in the biotech world. Anyway, let's all cultivate science everywhere we're at, it's an inherently a public matter! let's keep at it. 6/6
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Pablo Cárdenas R. @pcr-guy.bsky.social · 09/10/2024
The growth of private sector biology in the past decades will lead to more foundational advances. But ultimately, seminal discoveries hinge on other structures. A lot of folks are doing interesting experiments into what those structures can look like. 5/
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Pablo Cárdenas R. @pcr-guy.bsky.social · 09/10/2024
The time horizons over which discoveries are achieved usually exceed the limits of investor returns. Even many private donors eager to have institutes make a quick impact in their fields can be short-sighted. 4/
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Pablo Cárdenas R. @pcr-guy.bsky.social · 09/10/2024
However, the term "bleeding edge" is much more fitting for most science than neat, clean "cutting". Research is messy, diffuse. Its edges are only clearly seen (and retrospectively defined) in hindsight. 3/
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Pablo Cárdenas R. @pcr-guy.bsky.social · 09/10/2024
Google dumped resources into protein structure prediction because it was a problem with decades of intense attention and anticipated potential. It was the perfect proof of concept at a clearly-defined cutting edge of science. 2/
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Pablo Cárdenas R. @pcr-guy.bsky.social · 09/10/2024
When Google's AlphaFold stormed CASP in 2018, I thought it sigmalled the start of the era of private, for-profit cutting-edge discoveries in biology. Six years later, I think we might look back on it as an anomaly. 1/
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Pablo Cárdenas R. @pcr-guy.bsky.social · 05/10/2024
another banger @cbo.bsky.social
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Pablo Cárdenas R. @pcr-guy.bsky.social · 17/09/2024
📌
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Pablo Cárdenas R. @pcr-guy.bsky.social · 08/09/2024
@jccarden.bsky.social
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Mike Young @mkeyoung.bsky.social · 07/08/2024
🌍 We have just extracted a NEW global network of researchers and a global 100 scientist top ‘influencers’ on Bluesky. @lassehjorthmadsen.bsky.social and I show that scientists are in a series of distinct communities: mikeyoungacademy.dk/communities-... 😀 All 'likes' and reshares appreciated!
mikeyoungacademy.dk
Communities of scientists are emerging on Bluesky - Mike Young Academy
Global network data: The ‘nicer’ alternative to X is fortifying its presence in fields that range from philosophy to chemistry, finance, and beyond.
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Alex Crits-Christoph @acritschristoph.bsky.social · 08/09/2024
Continuous multiplexed phage genome editing using recombitrons www.nature.com/articles/s41...
nature.com
Continuous multiplexed phage genome editing using recombitrons - Nature Biotechnology
Phage genomes are readily engineered using retron recombineering.
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Tami Lieberman @contaminatedsci.bsky.social · 06/09/2024
Our work proposing an adaptive interpretation of dN/dS decay in bacterial genome is now published in eLife. I am excited about this work, which adds to the growing literature indicating that neutral evolution - and models in which purifying selection dominates dynamics - may be overestimated.
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Jeremy Kamil @macroliter.bsky.social · 27/08/2024
🧪 Long overdue and welcome alternative to GISAID. Hope the community embraces this type of solution in a major way. Rapid pathogen genome 🧬 data sharing matters so so much in pandemics and epidemics
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