Phil Ross
@philippzross.com
Vaccine scientist at ArkeaBio | Biologically inspired design for a better planet | Runner and anime enthusiast
Carl’s thread here is a much more detailed version of what I said today on the blog - bringing the receipts!
Carl T. Bergstrom@carlbergstrom.com · 2w ago1. The new Trump / Kratsios plan for US science appears explicitly designed to destroy US universities. Diverting money to tech donors is probably just a bonus. Gift link.
@trisre.bsky.social · last mo.1/ Happy to share our preprint! The Mtr complex catalyses the second-to-last step of the methanogenesis and is an essential bioenergetic machine in most methanogenic archaea. Anaerobic cryo-EM of Mtr reveals a nitrogenase-like metallocluster bound at its active site! www.biorxiv.org/content/10.6...
Our lab's paper on the de novo design of small-molecule binding proteins is out! In it, we show how neural nets can be trained and used to design binders to drugs with very high success rates. www.nature.com/articles/s41...
Zero-shot design of drug-binding proteins via neural iterative selection−expansion - Nature
By pairing two neural networks in an iterative optimization algorithm, small-molecule binding proteins can be designed from scratch with high accuracy, affinity and success rates, showing p...
nature.com
This is how I’m ending my seminars from now on.
Sahil Kapur@sahilkapur.bsky.social · 2mo agoHow Victor Wembanyama ended his post-game press conference: “Appreciate y’all. See y’all … never.”
Vaccines are humanity’s greatest scientific achievement.
Pregnancy vaccine reduces baby hospital admissions for RSV by 80%
A study confirms the vaccine gives excellent protection for babies against life-threatening chest infections.
bbc.co.uk
Tips are helpful, but I think the headline misses the point (again). Time flexibility is the best part of a PhD. Some people work more, some people less. All that should matter is the output and whether students are sufficiently trained. Upper time caps needed cuz $ www.nature.com/articles/d41...
The nine-to-five PhD: mere myth or an achievable goal?
Can you squeeze your graduate programme into a 40-hour working week? These 13 current and former PhD candidates reveal their top time-management tips.
nature.com
Meet the Microbes That Munch Mountains of Mining Waste Biomining uses engineered microbes to harvest critical minerals
Engineered Microbes Pull Critical Minerals from Mining Waste
Biomining uses engineered microbes to harvest critical minerals
scientificamerican.com
Didn't realize SCoV2 spike protein interacts with so many cell-surface receptors. Interesting that it appears to requires ACE2 for cell entry, but binds better to CNTN1. www.biorxiv.org/content/10.6...
biorxiv.org
"survival of the fittest" != "objectively best organisms survive" the same way that "if your discoveries were worth something, they’d be funded by the market" doesn't make any fucking sense...
A question for biologists: we often talk about evolutionary novelty. What does “novelty” mean for you? What’s your favorite definition if any? Or just a rule of thumb for what is and isn’t novel.
“Take AI seriously, but not everything that’s written about it” open.spotify.com/episode/6PN2...
AI Reality Check: Is the Economy About to Collapse?
open.spotify.com
Scientists have seen Asgard archaea crawling for the first time. When it comes to the origin of eukaryotes, this is like seeing a feathered dinosaur in the wild. (Video courtesy of Philipp Ralder)
What a breakthrough! Such a puzzle for 30 years, this is real progress! I wonder how general this mechanism of repression is for other systems where highly-selective expression is needed. www.biorxiv.org/content/10.6...
The transcription of a single olfactory receptor per neuron is enforced by epigenetic silencing of their enhancers
The ability to discriminate thousands of odors in our environment requires each olfactory neuron to express a single olfactory receptor from hundreds of available genes. The biochemical mechanism enfo...
biorxiv.org
Great new postdoc fellowship for foundational plant research. If you’re into genetics and genomics of plant reproductive evolution or adaptive convergence (incl in the cool and charismatic nightshades!) I’d be happy to talk about possible projects! www.simonsfoundation.org/grant/simons...
Simons Postdoctoral Fellowships in Plant Biology
Simons Postdoctoral Fellowships in Plant Biology on Simons Foundation
simonsfoundation.org
Thrilled to announce our new preprint, “Protein Hunter: Exploiting Structure Hallucination within Diffusion for Protein Design,” in collaboration with @Griffin, @GBhardwaj8 and @sokrypton.org 🧬Code and notebooks will be released by the end of this week. 🎧Golden- Kpop Demon Hunters
Out First Release in @science.org this week: The development of a directed evolution strategy with proof of concept in plant immune protein engineering. www.science.org/doi/10.1126/...
Engineered geminivirus replicons enable rapid in planta directed evolution
Directed evolution can rapidly generate genetic variants with new and enhanced properties, yet efficient platforms for performing such evolution directly in plant cells have been lacking. We developed...
science.org
Yesterday the president demanded that evidence about Covid vaccines be shown to the public. Today @apoorvanyt.bsky.social & I run through some of the studies made public over the past 4+ years that show that the vaccines work. Gift link: nyti.ms/46k17Tq
nyti.ms
Interested in doing a postdoc at DFCI/Harvard on computationally designing and experimentally characterizing mini-protein binders for biomedical applications? Eric Fischer and I are looking for someone to work in our groups starting asap! Email me or my admin with a CV to apply!
Introducing the 1,000 Flower Collection 🧬🌹 I’m creating 1,000 genetically designed flowers each crafted with new colors, patterns, and shapes. Here’s how I’m making it happen… and how you can join me on this journey 🧵(1/7)
Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.biorxiv.org/content/10.1...
The planktonic microbiome of the Great Barrier Reef
Large genome databases have markedly improved our understanding of marine microorganisms. Although these resources have focused on prokaryotes, genomes from many dominant marine lineages, such as Pela...
biorxiv.org
We are looking to hire (yes, even in this economy!) a jr. specialist to train in protein prep/structural biology related to our AVOID-ome work as part of openadmet.org. A great position for someone who is looking to be a tech for a few years before grad or med school. aprecruit.ucsf.edu/JPF05424
Junior/Assistant/Associate/Full Specialist Positions Available
University of California, San Francisco is hiring. Apply now!
aprecruit.ucsf.edu
Definitely one of my favorite things to learn recently: sweet proteins! And that companies like Oobli and Amai already exist
I remember having a drunken argument with @boughter.bsky.social over whether you focus efforts on exploring the earth's oceans or space first and I feel somewhat validated by this 😅 www.science.org/doi/10.1126/...
How little we’ve seen: A visual coverage estimate of the deep seafloor
In decades of deep-sea exploration, humans have observed only 0.001% of the deep seafloor, leaving 66% of planet Earth unseen.
science.org
Always a good day when I find out a new sensory receptor structure has been published! www.cell.com/cell/fulltex...
The structure of human sweetness
A single taste receptor initiates our reactions to both sugars and artificial sweeteners, triggering a signaling process that drives our intense attraction to sweet foods. Single-particle cryo-EM reve...
cell.com
Super excited to share a new preprint from our lab on design of small-molecule binding proteins using neural networks! The paper has a bit of everything. A new graph neural network, new design algorithms, and experimental validation. www.biorxiv.org/content/10.1... 🧵🧪
Zero-shot design of drug-binding proteins via neural selection-expansion
Computational design of molecular recognition remains challenging despite advances in deep learning. The design of proteins that bind to small molecules has been particularly difficult because it requ...
biorxiv.org
