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Pieter Dorrestein

@pieterdorrestein.bsky.social
1.6K followers 260 following 340 posts

I love molecules microbes make and mass spectrometry. I can spend hours looking at MS/MS with the dream we can annotate every molecule.

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Pieter Dorrestein @pieterdorrestein.bsky.social · 17/09/2026
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...
nature.com
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...
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Pieter Dorrestein @pieterdorrestein.bsky.social · 16/09/2026
www.businesswire.com/news/home/20.... Here is a new Mass spec to structure challenge for #metabolomics $50K in prizes.
businesswire.com
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Pieter Dorrestein @pieterdorrestein.bsky.social · 06/09/2026
Good day biking in the mountains.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 27/06/2026
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
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UC San Diego Health Sciences @ucsdhealthsci.bsky.social · 13/05/2026
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
today.ucsd.edu
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.
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Harsha Gouda @harshagouda.bsky.social · 23/04/2026
🚨 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!🚀
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Pieter Dorrestein @pieterdorrestein.bsky.social · 20/04/2026
Harvest from the yard.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 18/04/2026
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Pieter Dorrestein @pieterdorrestein.bsky.social · 18/04/2026
Such a joy picking avocados.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 16/04/2026
Extracting information pan-repositories using structures or substructures have just become possible - see terrific thread by Yasin below.
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Yasin El Abiead @yelabiead.bsky.social · 16/04/2026
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...
structure-masst.gnps2.org
Streamlit
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Pieter Dorrestein @pieterdorrestein.bsky.social · 12/04/2026
Love it when early fruiting season starts.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 05/04/2026
Wonderful day biking in the mountains
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Pieter Dorrestein @pieterdorrestein.bsky.social · 22/03/2026
Good way to start the day - local bike ride.
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Daniel Petras @daniel-petras.bsky.social · 17/03/2026
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
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Pieter Dorrestein @pieterdorrestein.bsky.social · 16/03/2026
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...
enveda.com
Atopic Dermatitis Clinical Trial
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Casey Theriot @theriotmicrobe.bsky.social · 13/03/2026
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...
biorxiv.org
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Pieter Dorrestein @pieterdorrestein.bsky.social · 05/03/2026
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...
biorxiv.org
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Pieter Dorrestein @pieterdorrestein.bsky.social · 04/02/2026
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.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 01/02/2026
A wonderful day biking in Cyamaca and Anza Borrego just 45 min drive from San Diego.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 30/01/2026
Always so nice to come to @scrippsocean.bsky.social to be part of a thesis defense. Can’t wait to see the great science.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 23/01/2026
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.
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Keystone Symposia @keystonesymposia.bsky.social · 22/01/2026
🎉 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
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Pieter Dorrestein @pieterdorrestein.bsky.social · 12/12/2025
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
cell.com
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...
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Pieter Dorrestein @pieterdorrestein.bsky.social · 07/12/2025
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.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 07/12/2025
Loving our local kitties.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 07/12/2025
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.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 07/12/2025
California in beautiful. Waking up to this view over thanksgiving break is amazing.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 24/11/2025
From the mountains to the beach. Such an amazing day today.
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Natural Product Reports @natprodreports.rsc.org · 19/11/2025
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
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Pieter Dorrestein @pieterdorrestein.bsky.social · 13/11/2025
Thanks to @NIDDK for supporting the collaborative microbial metabolite center and the training and yearly meeting it provides. A fun filled day on microbial metabolites.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 10/11/2025
It’s not even my birthday.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 09/11/2025
Riding local trails in the mist. So nice out.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 09/11/2025
Nice biking day in the San Diego mountains.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 30/10/2025
Nice mango harvest
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Nature Metabolism @natmetabolism.nature.com · 23/10/2025
🚨Job Alert🚨 If you are interested in being an editor at Nature Metabolism and Nature Communications, apply below by Oct 26🧪
bit.ly
Associate or Senior Editor (Nature Metabolism and Nature Communications)
Job Title: Associate or Senior Editor (Nature Metabolism and Nature Communications) Location(s): New York, Jersey City, Philadelphia, Beijing or Shanghai Application Deadline: October 26th, 2025 About Springer Nature Springer Nature is one of the leading publishers of research in the world. We publish the largest number of journals and books and are a pioneer in open research. Through our leading brands, trusted for more than 180 years, we provide technology-enabled products, platforms and services that help researchers to uncover new ideas and share their discoveries, health professionals to stay at the forefront of medical science, and educators to advance learning. We are proud to be part of progress, working together with the communities we serve to share knowledge and bring greater understanding to the world. For more information, please visit about.springernature.com and @SpringerNature. About the Brand Nature Portfolio is a flagship portfolio of journals, products and services including Nature and the Nature-branded journals, dedicated to serving the scientific community. Visit nature.com and follow @Nature / @NaturePortfolio Nature Portfolio is a world leader in publishing high-quality research. The Nature Portfolio journals include Nature, the Nature Research journals, the Nature Reviews journals, Nature Communications as well as the Communications journals and NPJ series. Nature Communications is the leading Nature Portfolio fully open Open Access journal publishing high-quality scientific research across natural, clinical, social and applied sciences. About the Role Do you love science but feel that a career at the bench isn’t enough to satisfy your desire to learn more about scientific research? Do you enjoy reading papers outside your chosen area of research? If the answer is ‘yes’ to any or all these questions, you could be the person we’re looking for to join the Nature Portfolio editorial team! To help us build on the success of the portfolio, we’re seeking an editor with experience in metabolic disease research who has a critical eye, a deep understanding of their subject and interests beyond, and who can think on their feet. Knowledge of liver disease (MAFLD/MASH), lipid biology or immunometabolism is desirable, although we are open to applications from scientists working in any discipline covered by the journal. This is a permanent position within the Nature Portfolio. The successful candidate will primarily support Nature Metabolism but collaborate closely with the translational and clinical research team, and other teams, at Nature Communications. Please note that responsibilities and journal assignments may evolve over time in response to portfolio needs Nature Metabolism publishes high-quality papers in all areas of metabolic research and metabolic health - from fundamental cell biology to basic biomedical and translational research - providing a highly visible forum for communicating important advances to a broad readership. Role Responsibilities: Handling original research papers and working closely with editor teams on all aspects of the editorial process, including manuscript selection and overseeing peer review. Making well-reasoned editorial decisions on submitted manuscripts in the light of expert advice. Contributing to content and strategy in this area at Nature Metabolism and Nature Communications. Commissioning, editing content such as Reviews, or writing editorials. Liaising extensively with editors at other journals in the Nature Portfolio and with experts in the international scientific community. Attending conferences and visiting research institutions. Experience, Skills & Qualifications: A PhD (or equivalent) in a relevant research field covered by the journal Additional research experience is preferred but not required. A thorough understanding of recent trends and developments in the field is essential. A passion for science and a thirst to learn more. You must be able to demonstrate the breadth of your interest in scientific research, both within and beyond your speciality. The ability to read and assess the novelty, context and implications of research submitted to the journal from different areas of this discipline. Excellent communication and interpersonal skills, including fluent English (written and spoken). Be eager to travel and meet scientists worldwide, learn more about them and their research, and help them learn more about us and what we are looking for in the papers we seek to publish. Editorial experience is not required, although applicants with editorial experience are encouraged to apply and may be considered for Senior Editor positions. The successful candidates will report to the Chief Editor of Nature Metabolism. This demanding and intellectually stimulating role is in either of our offices in New York, New Jersey, Philadelphia, Shanghai or Beijing. We are open to applications from internal candidates from any of our offices. The position is offered on a permanent basis, and its starting date is envisaged as soon as possible. To Apply: Applicants should include a CV, a cover letter explaining their interest in the position, preferred office of employment, and a concise (300-400 words) discussion of recent developments or trends in the wider metabolism field, which you have found particularly exciting (and explaining why). Application Deadline: October 26th, 2025. Candidates will be considered as they apply. Springer Nature US provides a comprehensive and competitive benefits package which includes the benefit offerings listed below: Medical, Dental and Vision 401(k) with company match and contribution Hybrid office working policy, Summer Hours, and paid time off Flexible Spending and Commuter programs Multiple Life insurance options Disability coverage Tuition Assistance Voluntary benefits: Identity Theft Protection, Pet Insurance, and Legal Assistance Insurance Employee Assistance Program Family friendly benefits and a variety of employee discounts An array of Employee Social Networks US Annualized Base Salary Range: Associate Editor: $80,000 / Senior Editor: $95,000. The salary offer may vary based on work experience, education, skill level and equity. The US salary range does not align with the salary ranges in other countries when converted to the currency of that country. Springer Nature is an Equal Opportunity Employer that complies with the laws and regulations set forth in the following https://www.eeoc.gov/sites/default/files/2023-06/22-088_EEOC_KnowYourRights6.12ScreenRdr.pdf poster. At Springer Nature, we value the diversity of our teams and work to build an inclusive culture, where people are treated fairly and can bring their differences to work and thrive. We empower our colleagues and value their diverse perspectives as we strive to attract, nurture and develop the very best talent. Springer Nature was awarded Diversity Team of the Year at the 2022 British Diversity Awards. Find out more about our DEI work here: https://group.springernature.com/gp/group/taking-responsibility/diversity-equity-inclusion. If you have any access needs related to disability, neurodivergence or a chronic condition, please contact us so we can make all necessary accommodation. For more information about career opportunities in Springer Nature please visit https://springernature.wd3.myworkdayjobs.com/SpringerNatureCareers/ #LI-MD1 Job Posting End Date: 27-10-2025 Wir sind ein ehrgeiziges und dynamisches Unternehmen, das einige der bekanntesten Namen in den Bereichen Forschung, Bildung und professionelles Verlagswesen beheimatet. Wir sind im Mittelpunkt einer sich wandelnden Branche und sind immer auf der Suche nach großartigen Mitarbeitern, denen es wichtig ist, unseren Kunden und den Gemeinschaften, mit denen wir zusammenarbeiten, Qualität zu liefern. Im Gegenzug werden Sie feststellen, dass wir allen unseren Mitarbeitern die Türen zur Entdeckung öffnen - wir bieten die Möglichkeit, von einigen der Besten der Branche zu lernen, mit einer Kultur, die Neugierde fördert und Menschen dazu befähigt, bestmögliche Lösungen zu finden. Ganz gleich, ob Sie am Anfang Ihrer Karriere stehen oder ein erfahrener Profi sind, wir laden Sie ein, mehr über die von uns angebotenen Aufgaben zu erfahren und unsere aktuellen Stellenangebote zu erkunden. We are a global and progressive business, founded on a heritage of trusted and respected brands – including Springer, founded in 1842, Macmillan, founded in 1843 and Nature, first published in 1869. Nearly two centuries of progress and advancement in science and education have helped shape the business we are today. Research and learning continues to be the cornerstone of progress, and we will continue to open doors to discovery through trusted brands and innovative products and services. Springer Nature Group was created in May 2015 through the combination of Nature Publishing Group, Macmillan Education and Springer Science+Business Media.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 06/10/2025
Such an amazing school of metabolomics in Brazil. Such a beautiful county. Thanks for the invite to describe why metabolomics is like reading a book with 93% of words missing.
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Proceedings of the National Academy of Sciences @pnas.org · 29/09/2025
Switching the clocks twice a year hurts Americans' health. A modeling study of county-level solar light patterns, time policy, health data, and circadian models suggests a permanent shift to Standard Time would reduce obesity and strokes. In PNAS: www.pnas.org/doi/10.1073/...
Switching from the United States’ current policy to Standard Time reduces overall obesity prevalence more than switching to Daylight Saving Time.
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Pieter Dorrestein @pieterdorrestein.bsky.social · 27/09/2025
Such awesome day today at UC-Riverside. Got to spend time with two of my science children and their team (science grandchildren). Just so fun thanks to Ming for the pic. And got to go biking with @func-metabo-lab.bsky.social
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Keystone Symposia @keystonesymposia.bsky.social · 22/09/2025
Excited to see science from @pieterdorrestein.bsky.social, @mfgrp.bsky.social, @inesthiele.bsky.social, @contaminatedsci.bsky.social and many others pushing the frontiers of microbiome research! #Microbiome #KeystoneSymposia
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Eric Topol @erictopol.bsky.social · 15/09/2025
A simple way to help reduce obesity and stroke? Stop the shifts in our clocks twice a year www.pnas.org/doi/abs/10.1...
pnas.org
Circadian-informed modeling predicts regional variation in obesity and stroke outcomes under different permanent US time policies | PNAS
Seasonal changes in time policy, such as switching between Standard Time (SDT) and Daylight Saving Time (DST), have been adopted by many countries,...
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Pieter Dorrestein @pieterdorrestein.bsky.social · 13/09/2025
Such a good - but chilly start - bike ride in #SanDiego
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West Coast Metabolomics Center UCDavis @metabolomics-wcmc.bsky.social · 12/09/2025
WCMC Guest lecture: September 17, 2025 | 10:00–11:30 AM (online) Prof. Heather M. Stapleton will present: “The Personal Chemical Exposome: Using Silicone Wristbands to Advance Exposure & Health Science” Zoom registration: lnkd.in/gaM3rV_X #metabolomics @pieterdorrestein.bsky.social
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UC San Diego School of Medicine @ucsdmedschool.bsky.social · 09/09/2025
Lindsey Yourman, M.D., associate clinical professor in the Department of Geriatrics has been appointed by Office of @cagovernornewsom.bsky.social to the California Commission On Aging. 🩺 Read more ➡️ go.ucsd.edu/46ByOPF
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Marnix Medema @marnixmedema.bsky.social · 08/09/2025
We are looking for a 3-year postdoc to work with Daniel Probst, Justin van der Hooft and myself on an exciting project involving federated learning and integrative omics for discovery of new antibiotics from natural products. Apply here: www.wur.nl/en/vacancy/p... Please share!
wur.nl
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Pieter Dorrestein @pieterdorrestein.bsky.social · 07/09/2025
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Pieter Dorrestein @pieterdorrestein.bsky.social · 07/09/2025
Good morning for a swim.
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BioMassSpec @realbiomassspec.bsky.social · 07/09/2025
HT SpaceM: A high-throughput and reproducible method for small-molecule single-cell metabolomics #Cell #MassSpec www.cell.com/cell/fulltex...
cell.com
HT SpaceM: A high-throughput and reproducible method for small-molecule single-cell metabolomics
Single-cell metabolomics (SCM) can probe metabolic heterogeneity but is hindered by low sensitivity for small molecules, limited scalability, and the lack of standardized frameworks for data analysis....
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Pieter Dorrestein @pieterdorrestein.bsky.social · 05/09/2025
It started with a concept of using data science and mass spectrometry for drug discovery with the goal to help people improve quality of their lives enveda.com. Now it’s a 🦄 that is getting a real shot at doing so with great clinical leads and in clinical trials www.youtube.com/watch?v=VafS....
enveda.com
Home
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Pieter Dorrestein @pieterdorrestein.bsky.social · 31/08/2025
Nice day on the bike. Great way to spend Labor Day week-end.
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