Biswa Misra
@biswamisra.bsky.social
BiOmician #Delhite #Omics #Drugs |Alumni: @IITKgp @ETH_en @USMOfficial1969 @UF @txbiomed @wakehealth| Founding Fellow at Enveda
Multi-omics-driven precision medicine (MODPM) is understood as a multiscale decision architecture that links molecular heterogeneity, tissue context, and patient-level trajectories. onlinelibrary.wiley.com/doi/10.1002/...
Multi‐omics–driven precision medicine
Multi-omics-driven precision medicine (MODPM) provides a multiscale, continuously learnable framework that integrates genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiome prof...
onlinelibrary.wiley.com
Read more in #STAT @statnews's coverage about ENV-308, our second clinical-stage molecule to clear Phase 1 and the first drug ever tested in humans designed to harness the effects of exercise: statnews.com/2026/08/18/env… #Enveda #ExercisePill #LearningFromLife #PRISM #weightloss #obesity
🧧 #Exercise in a #Pill 🧧 (as simple that 🧠 😇 ) - in our Enveda #CEO🎓 Viswa Colluru’s own words!!! 🎉 #Enveda Reports Positive Phase 1 Results for ENV-308 👉 www.businesswire.com/news/home/20... 🔖 Watch the 📹 chat Senior VP, 🎓 Nadeem Sarwar & 🎓 Jonathan Z. Long lnkd.in/gDwg6bya #obesity #GLP1
🧧 #Exercise in a #Pill 🧧 (as simple that 🧠 😇 ) - in our Enveda #CEO🎓 Viswa Colluru’s own words!!! 🎉 #Enveda Reports Positive Phase 1 Results for ENV-308 👉 www.businesswire.com/news/home/20... 🔖 Watch the 📹 chat Senior VP, 🎓 Nadeem Sarwar & 🎓 Jonathan Z. Long lnkd.in/gDwg6bya #obesity #GLP1
MetaboApps: modular web applications for simplifying and enhancing downstream analysis in GNPS2. www.nature.com/articles/s41...
Bridging complexity and accessibility in metabolomics with MetaboApps - Nature Methods
Nature Methods - Bridging complexity and accessibility in metabolomics with MetaboApps
nature.com
Paper | ExchangeXplorer: an R/Shiny application for processing and visualization of LC–HDX-MS data in metabolomics, lipidomics, and exposomics | #Metabolomics #Lipidomics #Exposomics #HDX #HDXMS #LCMS #MassSpectrometry #Bioinformatics | doi.org/10.1016/j.ac...
#Teamwork #ProudPI in #CompMetabolomics 😎 Doing untargeted mass spectrometry-based #metabolomics? Want to boost your chances in correctly matching your mass spectra to library spectra? Give our new #SpecReBoot resampling strategy a try! 🙂 www.linkedin.com/posts/jjjvan...
SpecReBoot Library Matching Preprint | Justin J.J. van der Hooft
🚨 New Preprint Alert 🚨 Congratulations 👏 🎉 to the CompMet team for presenting this preprint on boosting library matching for untargeted mass spectrometry-based metabolomics workflows 🙌 Metabolite a...
linkedin.com
Bridging complexity and accessibility in metabolomics with MetaboApps ->Nature | More on "Metabolomics data analysis open tools" at BigEarthData.ai
Bridging complexity and accessibility in metabolomics with MetaboApps
• PostMN MassQL: https://github.com/helenamrusso/massql_post_MN • Multi-step MassQL: https://github.com/wilhan-nunes/streamlit-Multi-Step-MassQL • Reference Data-Driven: https://github.com/bittremieux-lab/gnps-rdd • Drug Readout: https://github.com/wilhan-nunes/streamlit_drug_readouts • Food Readout: https://github.com/wilhan-nunes/streamlit-food-readouts • CMMC dashboard: https://github.com/wilhan-nunes/streamlit_CMMC_analysis-dashboard • FBMN-Stats: https://github.com/Functional-Metabolomics-Lab/FBMN-STATS • Chemical Proportionality: https://github.com/Functional-Metabolomics-Lab/ChemProp-Web-App • CorrOmics: https://github.com/Functional-Metabolomics-Lab/Corromics • Conjugated Metabolome Explorer: https://github.com/Philipbear/conjugated_metabolome • Reverse Metabolomics: https://github.com/wilhan-nunes/streamlit-Reverse-Metabolomics Documentation can be accessed at https://wang-bioinformatics-lab.github.io/GNPS2_Documentation/metaboapps_overview/. For developers from the metabolomics or broader community interested in contributing new MetaboApps, we provide resources and documentation. The core infrastructure is accessible through three key repositories. The Streamlit App GNPS2 template (https://github.com/Wang-Bioinformatics-Lab/Template_Streamlit_App) offers a preconfigured template with GNPS2 integration guidelines for a quick start. GNPSDataPackage (https://github.com/Wang-Bioinformatics-Lab/GNPSDataPackage) is a Python library that enables programmatic access to GNPS2 workflow results via task IDs for postprocessing, providing the tools to work directly with analysis outputs (which are mainly CSV tables, MGF spectra files or GraphML network files). For more experienced developers, we recommend the Dash template (https://github.com/Wang-Bioinformatics-Lab/Dash_Multipage_Template), which provides a framework for building multipage applications. Pull requests are evaluated by core GNPS2 developers for code quality, efficiency and infrastructure compatibility. Developers wishing to implement new MetaboApps in GNPS2 should contact the GNPS2 team to initiate the integration and deployment process. Applications are encouraged to include clear documentation and user-friendly interfaces. We thank the...
nature.com
Front Cover Art for our 📑 : "Trends in #Computational #Metabolomics: A Perspective on Five Years of #Software Development, Challenges, and Opportunities (2021–2025)* : pubs.acs.org/doi/10.1021/... in #AnalyticalChemistry journal with #ACSPublications is out! #Enveda #MyACSCover
Front Cover Art for our 📑 : "Trends in #Computational #Metabolomics: A Perspective on Five Years of #Software Development, Challenges, and Opportunities (2021–2025)* : pubs.acs.org/doi/10.1021/... in #AnalyticalChemistry journal with #ACSPublications is out! #Enveda #MyACSCover
Or, #AI solves #metabolite #annotation s that have been propagating via #manual errors over the decades ! Early indications from #DeepMet #MS2Mol #DreaMS indicate exciting times in #AI for metabolomics.
The Analytical Scientist @analyticalsci.bsky.social · 2mo ago"It is not yet a crisis, but it could be heading there." Ian Wilson discusses metabolite misidentification, data validation, and why AI could amplify errors if the metabolomics community doesn't act. Read more: https://ow.ly/al1A50Z7uZu #Metabolomics #MassSpec
Join us for our biannual iSLS14 in Singapore. We have expanded from #lipidomics to include #metabolomics and the #exposome. 20-23 Apr 2027, with the first day being workshops Travel #awards will be available 🎉 Registration and award applications will open end of July. www.sling.sg/news-events/...
(BioRxiv All) Agentic AI for Structural Elucidation and Discovery of Drug Metabolites from Mass Spectrometry Data: The majority of chemical signals detected in public metabolomics repositories remain structurally undefined. Large language models (LLMs) are probabilistic… #BioRxiv #MassSpecRSS
Agentic AI for Structural Elucidation and Discovery of Drug Metabolites from Mass Spectrometry Data
The majority of chemical signals detected in public metabolomics repositories remain structurally undefined. Large language models (LLMs) are probabilistic systems whose capacity to generate outputs beyond their training data, which can cause hallucinations, makes them also potentially suited to hypothesize structures for molecules that have never been described. We aimed to build a system that could harness this LLM generative capacity combined with domain specific tools/framework to constrain hallucination and produce validated discoveries. We developed a GNPS2 agentic AI system that interprets LC-MS/MS data by integrating spectral alignment, molecular formula inference, rule-based structural enumeration, machine learning-based spectrum prediction, and translates natural language hypotheses from domain experts into dynamically generated analytical workflows. We demonstrate the annotation of unknown drug metabolites from public data guided by chemical hypotheses. The agent predicted, and we experimentally confirmed, a phosphorylated hydroxyzine, an acetaminophen-p-coumaric acid ester, and identified two new oxidative ibuprofen-carnitine conjugates from public repositories. These results demonstrate that LLM-driven agentic reasoning, when combined with domain expertise, can indeed generate experimentally testable structural hypotheses for previously uncharacterized metabolites leveraging pan repository data.
dlvr.it
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
Or, #AI solves #metabolite #annotation s that have been propagating via #manual errors over the decades ! Early indications from #DeepMet #MS2Mol #DreaMS indicate exciting times in #AI for metabolomics.
The Analytical Scientist @analyticalsci.bsky.social · 2mo ago"It is not yet a crisis, but it could be heading there." Ian Wilson discusses metabolite misidentification, data validation, and why AI could amplify errors if the metabolomics community doesn't act. Read more: https://ow.ly/al1A50Z7uZu #Metabolomics #MassSpec
New preprint! Untargeted metabolomics via LC-MS/MS is a powerful tool to characterize molecular phenotypes. We show that the #stickleback liver metabolome varies between lake populations in coastal Alaska, and.... www.biorxiv.org/content/10.6... /t
Today at #MetSoc2026 I gave a keynote presentation on self-evolving, multi-agent AI for metabolomics — from @holobiomicslab.bsky.social. The headline outcome: we're releasing the first ASB Skill Collection — open, evidence-grounded metabolomics building blocks for any scientific AI agents. 🧵👇
The source corpus builds on the computational-metabolomics review series started by @biswamisra.bsky.social (2014) @jjjvanderhooft.bsky.social , now maintained by Enveda — thanks to Tobias Kind for great team work in Dagstuhl. 11/
Try it in Claude Code in two lines: /plugin marketplace add HolobiomicsLab/asb-skill-collections /plugin install metabolomics@asb-skill-collections Repo + other runtimes: github.com/HolobiomicsL... 9/
GitHub - HolobiomicsLab/asb-skill-collections: Curated, evidence-grounded skill and software-tool collections for scientific AI agents, generated by the AgenticScienceBuilder
Curated, evidence-grounded skill and software-tool collections for scientific AI agents, generated by the AgenticScienceBuilder - HolobiomicsLab/asb-skill-collections
github.com
👉 The release: the first ASB Skill Collection for metabolomics. 🔹 5,865 skills · 909 tools · 568 papers 🔹 LC-MS/MS + GC-MS, MS-imaging, ion mobility, lipidomics, NMR 🔹 evidence-grounded, EDAM-annotated, open (CC-BY-4.0) 8/
Trends in Computational Metabolomics: A Perspective on Five Years of Software Development, Challenges, and Opportunities (2021–2025) | Analytical Chemistry pubs.acs.org/doi/10.1021/...
Trends in Computational Metabolomics: A Perspective on Five Years of Software Development, Challenges, and Opportunities (2021–2025)
Metabolomics software development has accelerated rapidly, yet no recent systematic analysis has quantified how the landscape is evolving across computational methods, geographies, and the research co...
pubs.acs.org
I’m presenting a poster at #ASMS2026! Our RIPUP workflow uses alternative proteases + TMT to reveal the dark epigenome — histone succinylation & glutarylation usually missed by standard methods. 🧬 📍 Hall ABC, TP639 📅 Tues June 2, 10:30a–2:30pm Come say hi! #proteomics #massspec 🇦🇺 🇺🇸
Okay, here are the Thermo #ASMS2026 leak confirmations: - Tribrid Apex (the next Ascend + IRMPD) - Orbitrap Excedion is the downgraded version (240k max res) of the Orbitrap Excedion Pro. The name is going to cause a lot of confusion. Thanks go to my wonderful sources.
Once again, @keribackus.bsky.social and I are coordinating the chemoproteomics evening workshop at #ASMS2026. And being in San Diego, we have quite the panel depth! Join us Tuesday June 2 at 5:45pm! 🧪💊
Announcing the Women in Top-Down Proteomics (WiTDP), a new committee dedicated to fostering networking, mentorship, professional development, and community among women scientists in top-down proteomics. Go here to JOIN >> ctdp.org/about-the-co... #proteomics #ASMS2026 #proteoforms #teammassspec
The next generation of mass spectrometrists is here in San Diego! Undergrads at #ASMS2026: your community is waiting. Jump into the poster competition, the networking sessions, the evening workshops. Check the reposted material for details. Ask the question you think is “too basic.” It never is. 💪
Looking for a burrito at #ASMS2026? Definitely hit up The Taco Stand: maps.app.goo.gl/fSYTwvyUCs57...
maps.app.goo.gl
If you're in town for #ASMS2026 and want to talk chemoproteomics, computational proteomics, or generating high-throughput data for training ML models - hit me up!
