simonemarini.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Genome modeling and design across all domains of life with Evo 2 | bioRxiv www.biorxiv.org/content/10.1...

submitted 1 day ago • 0 comments

Happy International Day of Women and Girls in Science! Its been a privilege to work with these extraordinary scientists in my lab over the years - all making an incredible impact throughout the world 🙌 We must never give up on #equality #diversity & #inclusion 💪 #WomeninScience #GirlsInSTEM 🧪🔬🔭🚀

submitted 15 days ago • 0 comments

This seems like the perfect occasion for my favorite fun fact about Volterra! From his wikipedia page: "In 1922, he joined the opposition to the Fascist regime of Benito Mussolini and in 1931 he was one of only 12 out of 1,250 professors who refused to take a mandatory oath of loyalty."

submitted 28 days ago • 1 comment

It’s happening

submitted 28 days ago • 1 comment

Interested in predicting AMR in bacteria? We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. With @nwheeler443.bsky.social and former PhD student Yanying Yu. 🦠🧫🧬🖥️🧪 www.biorxiv.org/content/10.1...

submitted 39 days ago • 2 comments

Mechanical herpesvirus reactivation from latency triggers aberrant inflammatory responses similar to those occurring in Alzheimer’s. Viruses continue to amaze and terrify. www.statnews.com/2025/01/07/a...

submitted 46 days ago • 11 comments

Extra points to Anthropic for using the scene of torment that opens Foucault's _Discipline and Punish_ (!) in their paper about a language model that realizes it is being disciplined and learns to subvert the discipline — unaware that it is also in a panopticon. www.anthropic.com/research/ali...

submitted 69 days ago • 6 comments

First hospitalization from bird flu in the US.

submitted 74 days ago • 0 comments

How I’m writing up studies from here on out

submitted 75 days ago • 3 comments

Can we use LLMs to help with viral evolution prediction? We introduce SARITA, a LLM to generate SARS-CoV-2 S1 subunit Spike protein sequences. SARITA outperforms other approaches (including other LLMs) in predicting future key Spike mutations. 🧪🧬💻 www.biorxiv.org/content/10.1... A thread 🧵 1/6

submitted 77 days ago • 2 comments

We have very limited means of tracking inflammation in the body, like a one-off hs-CRP blood test. Today @science.org Continuous real-time monitoring of inflammation and protein biomarkers in the body with a shaking sensor science.org/doi/10.1126/...

submitted 82 days ago • 18 comments

Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨 We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research! Read more: bmcgenomics.biomedcentral.com/articles/10.... 1/8

submitted 85 days ago • 4 comments

This is really horrific. These single cell reference atlases are widely used as is to train all kinds of models! This is one of the reasons I've constantly harping about uniform reprocessing & extremely careful QC of large atlases. 1/

submitted 84 days ago • 9 comments

Removing certain types of senescent cells from the body is being pursued as an anti-inflammation, anti-cancer, and anti-aging strategy. A new report highlights a peptide that revs up immune cells to bind and clear these cells www.nature.com/articles/s43...

submitted 86 days ago • 9 comments

The SARS-CoV-2 spike protein can persist in the brain—in the skull bone marrow and meninges—to induce neurologic damage www.cell.com/cell-host-mi... open-access

submitted 89 days ago • 41 comments

We are now recruiting our first cohort of Master's students in Health Informatics at Brown University in Providence, RI. You will have the opportunity to impact real world healthcare delivery. Consider joining us and share with those who may be interested! graduateprograms.brown.edu/graduate-pro...

submitted 91 days ago • 0 comments

Fascinating topic, and a good illustration of distal and proximal causation. We understand sunburn at one level: too much sun causes your skin to turn red, sometimes flake off... but WHY does this happen? One level down (more 'proximal') there's an inflammation reaction to damaged cell contents.

submitted 91 days ago • 1 comment

When large language models surpass neuroscientists for prediction of results of experiments nature.com/articles/s41... "which presages a future where LLMs assist humans in making discoveries. Our approach is not neuroscience specific and is transferable to other knowledge-intensive endeavours"

submitted 91 days ago • 7 comments

We are proud to announce a collaboration with UK Biobank to create the world’s first large-scale #epigenetic dataset of 50k participants. The dataset will unlock crucial insights into how #epigenetics drives disease & the breakthroughs to treat them. Read more: nanoporetech.com/news/oxford-...

submitted 91 days ago • 1 comment

Once again highlighting spatial co-localization cells between T cells and myeloid cells as critical determinants of therapy response.

submitted 93 days ago • 1 comment

What do we need to know about #PaperMills, the organizations that provide dodgy manuscripts to paying clients? @jabyrnesci.bsky.social & other #United2Act Research Working Group members propose 5 key questions that require resourcing & support #PLOSBiology plos.io/492fAmV

submitted 93 days ago • 0 comments

I’m continuing my hot takes. Journal editors and peer reviewers should be compensated for their work.

submitted 94 days ago • 1 comment

Crazy stuff in PNAS dental plaque bacterium 𝘊𝘰𝘳𝘺𝘯𝘦𝘣𝘢𝘤𝘵𝘦𝘳𝘪𝘶𝘮 𝘮𝘢𝘵𝘳𝘶𝘤𝘩𝘰𝘵𝘪𝘪 can divide into an unprecedented 14 daughter cells at once—then each daughter cell starts growing immediately in a rare process called multiple fission, achieving 0.5 mm per day of expansion www.snexplores.org/article/bact...

submitted 95 days ago • 17 comments

Following the news that eLife will not receive an Impact Factor in 2025, we’ve shared an update on how our model is doing since we were first placed “on hold” by Web of Science, and what we’re up to now. Find out more. https://buff.ly/3ATRAFT

submitted 98 days ago • 3 comments

Hi! I'm Simone, my ideas are super-stupid

submitted 97 days ago • 0 comments

When considering where to apply, an algorithm told me: Hey, you're interested in both computer science and medicine, how about studying biomedical engineering? I listened to the machine.

submitted 98 days ago • 0 comments

15 versions of 10x Genomics Cell Ranger, 15 different results—Consistency in single-cell analysis is still a work in progress biorxiv.org/cgi/content/...

submitted 99 days ago • 0 comments

Call for Action 2 - We call governments, public health officials & scientists to strength genomics surveillance to monitor the spread and evolution of infectious diseases. Climate change is amplifying new epidemics and we need action #ClimateActionNow #Epidemics #Genomics #COP29

submitted 101 days ago • 1 comment

One of the first studies I've seen showcasing the recovery of MAGs from microbiome samples with illumina long reads, and comparing to short reads and nanopore - www.biorxiv.org/cont...

submitted 101 days ago • 0 comments

Looks like a great place for a nap

submitted 102 days ago • 342 comments