Finally sat down to write about AI in science and scientific training!

MsEE Lab@mseelab.org · last mo.

As the world grapples with the question of how to incorporate (or entirely avoid) GenAI into the education of future generations, we at MsEE Lab are faced with the same challenge. open.substack.com/pub/mseelab/...

It's go time!

MsEE Lab@mseelab.org · 4mo ago

A year on from our inaugural State of the Lab post, the lab is revving up and getting ready to go. Now it’s time to do some research! mseelab.substack.com/p/brewing-re...

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/...

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.

science.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!

Tetsuhiro Harimoto@tetsuharimoto.bsky.social · last yr.

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

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...

Very nice

Noémie Lefrancq@noemielefrancq.bsky.social · 2y ago

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

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...

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 ...

biorxiv.org

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

Tears In Rain Ep5: Danielle Beckman

YouTube video by Sebastian Cocioba

youtu.be

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!

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...

biorxiv.org

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/

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

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...

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...

nature.com

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!

Katherine Xue@ksxue.bsky.social · 2y ago

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

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

The Scholarly Kitchen@scholarlykitchen.bsky.social · 2y ago

PLOS’s Next Big Thing scholarlykitchen.sspnet.org/2024/10/08/p...

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

Jason Rasgon@vectorgen.bsky.social · 2y ago

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...

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

James Holland Jones@juemos.bsky.social · 2y ago

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...

🌍 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!

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.

mikeyoungacademy.dk

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

Continuous multiplexed phage genome editing using recombitrons - Nature Biotechnology

Phage genomes are readily engineered using retron recombineering.

nature.com

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.

Cameron Thrash@jcamthrash.bsky.social · 2y ago

Reversions mask the contribution of adaptive evolution in microbiomes elifesciences.org/articles/93146 #jcampubs

🧪 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

Pathoplexus@pathoplexus.org · 2y ago

📢 We're excited to introduce Pathoplexus, a specialized sequence database for human viral pathogens! 🌍 🧬 Launching with 4 viruses, Pathoplexus.org combines modern open-source software with transparent governance to improve global pathogen sequence sharing. 1/14

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

Pathoplexus| Home

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

pathoplexus.org