I am a fan of reading papers where a few people had such deep thought to create a written piece of art but this paper below might become the demise of the concept of a paper altogether and questions why papers are needed at all - such a crazy time we live in. www.nature.com/articles/s41...

Reimagining research papers as interactive and reliable AI agents - Nature

Paper2Agent converts research papers into interactive artificial intelligence agents by turning manuscripts, code and data into model context protocol-based tool-invoking systems that reproduce origin...

nature.com

www.businesswire.com/news/home/20.... Here is a new Mass spec to structure challenge for #metabolomics $50K in prizes.

Good day biking in the mountains.

Can the probabilistic reasoning that leads to LLM hallucinations be harnessed for scientific discovery? This work demonstrates that agentic AI can become another tool in the structural elucidation toolbox, generating testable hypotheses for new metabolites. #metabolomics Preprint: lnkd.in/gJpDdXkP

A new web tool called #StructureMASST lets anyone search the world’s public #metabolomics data by chemical structure. #Pharmacy #BigData #SearchEnginge @ucsdpharmacy.bsky.social @pieterdorrestein.bsky.social buff.ly/NXH5r3f

From Molecules to Meaning: A Search Engine for the Chemistry of Life

A new web tool called StructureMASST lets anyone search the world’s public metabolomics data by chemical structure.

today.ucsd.edu

🚨 I'm delighted to share that I'll be a funded through the Eric & Wendy Schmidt AI in Science Postdoctoral Fellowship! Excited to push the boundaries of ML in metabolomics for human health. Thank you to my mentor @pieterdorrestein.bsky.social and Dorrestein lab team!🚀

Harvest from the yard.

Such a joy picking avocados.

Extracting information pan-repositories using structures or substructures have just become possible - see terrific thread by Yasin below.

Yasin El Abiead@yelabiead.bsky.social · 5mo ago

Where has this molecule been detected before across samples, organisms, body parts, and environments? With StructureMASST, you can explore this directly by entering a molecule name and running a search in your browser. 🔗 structure-masst.gnps2.org 📄 www.nature.com/articles/s41...

Where has this molecule been detected before across samples, organisms, body parts, and environments? With StructureMASST, you can explore this directly by entering a molecule name and running a search in your browser. 🔗 structure-masst.gnps2.org 📄 www.nature.com/articles/s41...

Love it when early fruiting season starts.

Wonderful day biking in the mountains

Good way to start the day - local bike ride.

Our new paper on the presence of xenobiotics in marine dissolved organic matter just come out. Thanks to Jarmo Kalinski and our awesome collaborators, we were able to reanalyze more than 20 public LC-MS/MS datasets from seawater and ask how many anthropogenic compounds we can detect. rdcu.be/e8q6C

For anyone that has moderate to severe atopic dermatitis and current treatments work poorly - this is a phase II clinical trial to consider. Disclosure - I am a scientific co-founder of the company enveda.com/atopic-derma...

New preprint from the Theriot lab and collaborators, which looks at how strain-dependent bile acid transformations by commensal Clostridia attenuate C. difficile virulence and disease without decreasing colonization! www.biorxiv.org/content/10.6...

Yet another new function of bile acids -and relevance of the microbiome in regulating the efficacy of medications. #microbiome #IBD. Discovered using #metabolomics repository scale analysis. #opendata Thanks to all the collaborators and Vincent for leading it. www.biorxiv.org/content/10.6...

It only took 182242.7 CPU hours :). Only had to be done once and it will be a resource to mine for a long time. Can’t wait to see the results.

A wonderful day biking in Cyamaca and Anza Borrego just 45 min drive from San Diego.

Always so nice to come to @scrippsocean.bsky.social to be part of a thesis defense. Can’t wait to see the great science.

Today was the last day of the microbial metabolite keystone meeting. The posters and talks were beyond my wildest expectations. Safe travels to everyone that attended - thanks for making it a meeting to remember.

Keystone Symposia@keystonesymposia.bsky.social · 8mo ago

🎉 From beautiful Banff 🇨🇦❄️ Congrats to the Microbiome Metabolism & Metabolites / Human Microbiome awardees, thanks to @krfoundation.org! @pieterdorrestein.bsky.social @mfgrp.bsky.social @gargneha.bsky.social @inesthiele.bsky.social @contaminatedsci.bsky.social #KSMicrobiome26 #KSMicroMetab26

🎉 From beautiful Banff 🇨🇦❄️ Congrats to the Microbiome Metabolism & Metabolites / Human Microbiome awardees, thanks to @krfoundation.org! @pieterdorrestein.bsky.social @mfgrp.bsky.social @gargneha.bsky.social @inesthiele.bsky.social @contaminatedsci.bsky.social #KSMicrobiome26 #KSMicroMetab26

The best keychain ever - ty. This was a molecule discovered in this work www.cell.com/cell/fulltex... . To Prof. Ipsita - I can’t wait to see what you will discover in your own lab at Penn State. Such a pleasure to have had you as a co-worker in the lab. @ipsitamohanty.bsky.social

The underappreciated diversity of bile acid modifications

Using mass spectrometry-based tools to mine public untargeted MS/MS data revealed the vastly underappreciated diversity of bile acids hidden in plain sight and led to the discovery of previously unkno...

cell.com

This is an important paper to read for people that are trying to understand metabolomics data. Ions detected (features) are not molecules and molecules will generate many ion forms. Be aware of MS ion forms - understand and leverage them. Dark metabolome has a lot of discovery potential.

Yasin El Abiead@yelabiead.bsky.social · 10mo ago

The existence of unintentional fragmentation (often referred to as in-source fragments) in untargeted #metabolomics data can cause uncertainty among newcomers to the field and skepticism among data consumers such as medical experts or biologists. pubs.acs.org/doi/10.1021/...

Loving our local kitties.

Such amazing early clinical results from Enveda during my visit to Colorado. Seeing the elimination of lifelong health conditions in 6 weeks is humbling. Within three years to medications in ppl. Nature has done the drug discovery for us- we are just leveraging metabolomics data science to read it.

California in beautiful. Waking up to this view over thanksgiving break is amazing.

From the mountains to the beach. Such an amazing day today.

We are delighted to sponsor the Natural Products in the 'Omics Era' symposium at @pacifichem.bsky.social! Keynote speakers include @pieterdorrestein.bsky.social whose research focuses on new MS-based methods to understand the chemistry of microbes #ORG018 📅19-20 December 2025 🔗pacifichem.org