Pablo Cárdenas R.
@pcr-guy.bsky.social
🦠 🧬 🇨🇴
• pathogens + evo + synbio + modeling
• postdoc @Ragon Institute
• banner pic by Melanconnie
• Incoming prof. 2026 at @mseelab.org
• pathogens + evo + synbio + modeling
• postdoc @Ragon Institute
• banner pic by Melanconnie
• Incoming prof. 2026 at @mseelab.org
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!
I’ll be starting a lab as an Assistant Professor at Cornell @cornellengineering.bsky.social in 2026!
We’ll combine synthetic biology and materials science to engineer microbes into living materials & therapies.
We're recruiting PhD students & postdocs - please get in touch!
🔗 harimotolab.com
We’ll combine synthetic biology and materials science to engineer microbes into living materials & therapies.
We're recruiting PhD students & postdocs - please get in touch!
🔗 harimotolab.com
October 24, 2025 at 11:08 AM
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!
Reposted by Pablo Cárdenas R.
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...
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...
October 14, 2025 at 6:42 PM
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...
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...
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...
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...
May 26, 2025 at 2:50 PM
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...
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 )
Full of brilliant, nuanced insights (as usual from @cbo.bsky.social )
"One thing is certain: The changes we make ourselves will be healthier than the ones our adversaries demand."
New work for @undark.org:
undark.org/2025/02/06/o...
New work for @undark.org:
undark.org/2025/02/06/o...
The End of Science’s Peacetime
Opinion | Defending the practice of science from its adversaries will require dealing with some uncomfortable truths.
undark.org
February 11, 2025 at 4:02 PM
"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 )
Full of brilliant, nuanced insights (as usual from @cbo.bsky.social )
Reposted by Pablo Cárdenas R.
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.
February 2, 2025 at 10:19 PM
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
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
February 1, 2025 at 12:13 PM
Very nice
Reposted by Pablo Cárdenas R.
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 OSF is run by a 501c3 (Center for Open Science), so if you do this you might also consider making a donation.)
January 31, 2025 at 6:04 PM
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 OSF is run by a 501c3 (Center for Open Science), so if you do this you might also consider making a donation.)
Reposted by Pablo Cárdenas R.
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 Pablo Cárdenas R.
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
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
Tears In Rain Ep5: Danielle Beckman
YouTube video by Sebastian Cocioba
youtu.be
January 8, 2025 at 11:41 PM
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
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
Reposted by Pablo Cárdenas R.
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!
With @influenzal.bsky.social @vidhid.bsky.social @drclairesmith.bsky.social and many more!
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...
www.biorxiv.org
January 7, 2025 at 7:59 AM
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!
With @influenzal.bsky.social @vidhid.bsky.social @drclairesmith.bsky.social and many more!
Reposted by Pablo Cárdenas R.
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/
This was a ton of work.
medrxiv.org/cgi/content/...
1/
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...
medrxiv.org
December 28, 2024 at 11:17 AM
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/
This was a ton of work.
medrxiv.org/cgi/content/...
1/
Reposted by Pablo Cárdenas R.
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!
December 26, 2024 at 4:35 PM
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!
Reposted by Pablo Cárdenas R.
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
My interpretation: antigenic evolution currently constrained by pleiotropic effects of mutations on RBD-ACE2 affinity, RBD up-down position & antibody neutralization
November 21, 2024 at 11:22 PM
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
My interpretation: antigenic evolution currently constrained by pleiotropic effects of mutations on RBD-ACE2 affinity, RBD up-down position & antibody neutralization
Reposted by Pablo Cárdenas R.
Web-browsing patterns reflect and shape mood and mental health www.nature.com/articles/s41...
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...
www.nature.com
November 21, 2024 at 1:32 PM
Web-browsing patterns reflect and shape mood and mental health www.nature.com/articles/s41...
Reposted by Pablo Cárdenas R.
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
go.bsky.app/86Ao1a5
November 19, 2024 at 9:56 AM
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
go.bsky.app/86Ao1a5
Reposted by Pablo Cárdenas R.
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
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
November 20, 2024 at 12:39 PM
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
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
Katherine is a brilliant mentor and scientist and I am thrilled to see this happen!
Hi friends new and old! I study how microbes interact and evolve in complex communities like the human gut microbiome.🦠🧬💩 I'm thrilled to share that I'm starting a lab at UC Irvine in April 2025 and am recruiting at all levels - please spread the word! kxuelab.com More about my work below...🧵1/n
Xue lab at UC Irvine
Ecology and evolution in the human gut microbiome
kxuelab.com
November 19, 2024 at 11:59 PM
Katherine is a brilliant mentor and scientist and I am thrilled to see this happen!
Reposted by Pablo Cárdenas R.
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.
October 20, 2024 at 12:46 PM
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
PLOS’s Next Big Thing scholarlykitchen.sspnet.org/2024/10/08/p...
PLOS’s Next Big Thing - The Scholarly Kitchen
In this post, Alice Meadows shares some thoughts about PLOS's recently announced R&D project to help overcome the lack of recognition for Open Science contributions, and the lack of affordability for ...
scholarlykitchen.sspnet.org
October 18, 2024 at 1:15 PM
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...
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...
October 18, 2024 at 2:52 AM
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...
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 !
October 17, 2024 at 1:07 PM
Saw this presented a while ago, really nice work @sangwoopark.bsky.social !
wild, also very entertaining thread
So. Here it is. The ABSOLUTELY nuttiest study we have ever done in my 25+ years as a scientist working on mosquitoes
"Revisiting the paradigm of anhematophagy in male mosquitoes"
Let's dive into the paper
www.biorxiv.org/content/10.1...
"Revisiting the paradigm of anhematophagy in male mosquitoes"
Let's dive into the paper
www.biorxiv.org/content/10.1...
Revisiting the paradigm of anhematophagy in male mosquitoes
Female mosquitoes are reproductively obligate bloodfeeders which feed on vertebrate blood to obtain nutrients required for egg production (driving transmission of vector-borne pathogens in the process...
www.biorxiv.org
October 9, 2024 at 8:32 PM
wild, also very entertaining thread
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/
Six years later, I think we might look back on it as an anomaly.
1/
October 9, 2024 at 2:14 PM
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/
Six years later, I think we might look back on it as an anomaly.
1/
another banger @cbo.bsky.social
Important opinion piece by @cbo.bsky.social
Biology is certainly in their sights.
We need to develop a strategy to counter the escalating war on higher education.
undark.org/2024/10/03/o...
Biology is certainly in their sights.
We need to develop a strategy to counter the escalating war on higher education.
undark.org/2024/10/03/o...
In the Authoritarians’ New War on Ideas, Biology Might Be Next
Opinion | The debate over the teaching of history in schools portends a future war on ideas that includes the natural sciences.
undark.org
October 5, 2024 at 1:57 PM
another banger @cbo.bsky.social