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!

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...

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.)

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...

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

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!

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/

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!

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 www.nature.com/articles/s41...

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

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

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 !

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/

another banger @cbo.bsky.social

🌍 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!

Continuous multiplexed phage genome editing using recombitrons www.nature.com/articles/s41...

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.

🧪 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

One of the reasons I've been quiet on Bluesky for a few months is because I've been working on something big - something I'm really happy to share now! Pathoplexus.org A new, open-source database for pathogen sequence sharing. 👐🧬🌎 1/12

huge, love to see pathogen genomic data infrastructure that explicitly centers these ideals

Exactly one year after the preprint came out (!), our revised manuscript on predicting epistatic interactions in SARS-CoV-2 is out in Genome Biology! We added experimental validations and a visual explanation of our samples weighting scheme. Here: genomebiology.biomedcentral.com/articles/10....

Why it's a shame that social media is (still) so fragmented – particularly when faced with new problems that benefit from collaboration, peer-review of emerging evidence and fresh eyes on the data: kucharski.substack.com/p/why-twitte...

incredible #EvoSky

Crossposting this review piece on the evolution of antibiotic resistance by @celiasouque.bsky.social , Indra GO, and @baym.lol : 1/2 www.annualreviews.org/content/jour... 🧪 #MicroSky #EvoSky #AMR

Great stuff from @christianlandry.bsky.social #EvoSky www.science.org/doi/10.1126/...

This is fantastic #episky #VirEvol

Subscribe to the bookmark feed and comment your favourite posts with 📌. The bookmark feed contains only your personal favourites.

YO TURN UP next wednesday thesis defense 🦠 _Synthetic and computational biology tools to study #malaria parasites_ 🦠 Synthetic transcriptional control in #Plasmodium Evo- #epidemiology simulations info below there will be fried chicken (not delivered via zoom) #synbio #microsky #Episky

love this

Are you in Ithaca NY?? Are you awake on a Monday morning at 9 AM?? both are unlikely but come hang!! www.cheme.cornell.edu/events/cbe-s...

"babe, how often do you think about the roman empire" malaria edition: www.biorxiv.org/content/10.1...

This blog is putting out all bangers. This entry on Priority Review Vouchers for tropical disease drug dev: blog.jacobtrefethen.com/how-to-make-...

The future we need (or part of it): arxiv.org/abs/0906.5418

A new paper from our lab is out after peer review. In collaboration with Brandon Ogbunu at Yale, Juan Diaz-Colunga examined how global epistasis patterns change as the concentration of antimalarial drugs increases in the environment: www.nature.com/articles/s41...

How stable are bacterial genomes as they adapt to an environment? My collaboration with Anurag Limdi, Alex Couce, @relenski.bsky.social, and Olivier Tenaillon exploring this over 50,000 generations of evolution is out today! 1/ (cross-post from the other place) www.science.org/doi/10.1126/...

Announcing the Social Lives of Viruses 2024! Do you study social evolution in viruses? Do you want to? Join us in Puerto Rico this June for a 50-person meeting dedicated to viral sociality. All costs covered. Apply here: forms.gle/sHTEcHJjryDh... #ViroSky #MicroSky #EvoSky #SocialViruses

I'm biased (1st author is now a formal mentee), but this working paper is incredibly dope. Combines maritime history, w/ mathematical epidemiology. "Transoceanic pathogen circulation in the age of sail and steam." www.biorxiv.org/content/10.1...

Forecasting antimicrobial resistance evolution #TrendsMicrobiol Opinion from Jens Wolff and colleagues www.cell.com/trends/micro...

This is w i l d