#metabolomics — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #metabolomics, aggregated by home.social.
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It's always fun meeting with high-school lab assistants and getting to explain PCA (draw a banana!), where additive and proportional error come from (measure lots of times!), and that -omics data in general have these, regardless of technology.
Which reminded me of two of my favorite posters.
Visualization of error in omics technologies
https://figshare.com/articles/poster/Characterization_and_Visualization_of_Error_in_Omics_Technologies/1431927?file=2191588Visualizing the effects of data transformations
https://figshare.com/articles/poster/Visualizing_the_Effects_of_Data_Transformations_on_Errors/3168775?file=4933519 -
new paper: "Computational metabolomics at scale: from open data to insight" https://doi.org/10.1016/j.copbio.2026.103557 #metabolomics
"Metabolomics stands at a pivotal moment where the volume, diversity, and richness of publicly available data offer unprecedented opportunities for discovery"
It describes the results from a series of Dagstuhl meeting. I attended a few (not this year). It gives a good overview of where the field may be going, and perhaps should be going. Happy to have been part of this community!
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Metabolomics of single-strain & co-cultures of 7 Fusarium strains causing #metabolome head blight reveals metabolic modifications induced by strain co-occurrence.
FHB #metabolomics reveals species‑specific biomarkers & interaction‑driven shifts in co‑cultures
#microbiology #agriculture #metabolome #Ag
https://davidojcius.blogspot.com/2026/08/how-fusarium-strain-co-occurrence.html
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New lab publication:
High-Quality Predicted Metabolite-Pathway Annotations Expand Pathway Coverage and Increase Enriched Pathway Detection Across Metabolomics Datasets, by Huckvale et al
https://www.mdpi.com/2218-1989/16/8/545
We show that the metabolite pathway annotation pipeline we've been building improves annotation enrichment results using GSEA on 990 datasets from Metabolomics Workbench.
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Want to participate in a remote #Metabolomics conference?
Deadline for abstract submission to the International Electronic Conference on Metabolomics 2026 is July 17th.
Yes, it's funded by MDPI. I understand if you don't register because of that. But there are many genuinely good speakers who will be there, and yours truly will hopefully be presenting their work on trying to do QC/QA of the entirety of Metabolomics Workbench!
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New co-authored manuscript on liver cancer multi-omics:
Integrated Multi-omic Analyses Reveal Novel Gene-Metabolite Relationships in Human Steatohepatitic Hepatocellular Carcinoma
Anspach et al., https://www.jlr.org/article/S0022-2275(26)00107-0/fulltext8 patients, *paired samples* of cancer and adjacent normal!! (made the statistics so nice to work with and look for correlations between rna-seq and metabolomics).
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Everytime I think that uploaded #metabolomics data can't get any weirder, I find something else.
Today, it's 1 sample out of 64 that has negative values. ONE out of 64 that has negative values. Unless something weird was done in processing, either all of them should contain negative values or none of them should. 🤦♂️
All missing for one sample, that sort of, might make sense. But 1 of 64 has negatives? WTF. And it's not just one value, it's 64 of 407.
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📢 Call for Papers: Computational Spatial Omics - Multimodal Strategies for Systems Biology and Biomedical Discovery
⏳ Submission Deadline: 31 December 2026
🔗 Submit your work: https://spj.science.org/journal/csbj/si/computational-spatial-omics
#CallForPapers #SpatialOmics #SpatialTranscriptomics #SpatialProteomics #Metabolomics #Lipidomics #Multiomics #ComputationalBiology #SystemsBiology #Bioinformatics #AIinHealthcare #DigitalPathology #GraphNeuralNetworks #PrecisionMedicine
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UC San Diego: From Molecules to Meaning: A Search Engine for the Chemistry of Life. “An international team led by researchers at University of California San Diego and University of California, Riverside has developed a free, web-based platform designed to make public metabolomics data more accessible.”
https://rbfirehose.com/2026/05/14/from-molecules-to-meaning-a-search-engine-for-the-chemistry-of-life-uc-san-diego/ -
Working with data from Metabolomics Workbench again, and it always feels like the data is yelling at me with the fields in all caps.
Now that I've double checked, the Protein Data Bank file format was like this too, all caps everywhere (even more so).
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Researchers have identified composite blood biomarkers—specific combinations of proteins and metabolites—that can reliably detect early stages of colorectal, lung, and ovarian cancers.
#Oncology #Proteomics #Metabolomics #Pathology #sflorg
https://www.sflorg.com/2026/04/ongy04202601.html -
Why has GC-MS (gas chromatography- electron impact ioniation- mass spectrometry) had such enduring value for the field of metabolomics? How do we identify metabolites based on mass spectrometry data?
I hope you'll enjoy this video explaining the basics of GC-MS and the spectral library methods we use for explaining these spectra!
https://www.youtube.com/watch?v=vTWXkHPHEI0
#bioinformatics
#metabolomics #GCMS -
Why would we choose to measure just a few metabolites instead of doing a broad untargeted survey? In two words: "quantitative precision"
This is the first lecture recording I have produced with my new home video setup!
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📢 Call for Papers: Metabolome-Microbiome in Health and Diseases for One Health
⏳ Submission Deadline: 31 May 2026
🔗 Submit your work: https://spj.science.org/journal/csbj/si/metabolome-microbiome-health-diseases
#CallForPapers #Metabolomics #Microbiome #SystemsBiology #OneHealth #DiseaseBiology #MedicalInformatics #Phenomics
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I really appreciated this detailed post from Nicola Zamboni on #bioinformatics for #metabolomics !
https://metabolomics.blog/2026/03/how-we-analyze-untargeted-metabolomics-data/
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Researchers discovered that a metabolite known as pTOS, which drastically elevates in #pythons after large meals, successfully reduces food intake and drives weight loss in #obese laboratory mice.
#Endocrinology #Pathology #Metabolomics #Zoology #sflorg
https://www.sflorg.com/2026/03/bio03192602.html -
New preprint!
An Integrated Multi-omic Analysis Reveals Novel Gene-Metabolite Relationships in Human Steatohepatitic Hepatocellular Carcinoma
https://www.medrxiv.org/content/10.64898/2026.01.28.26344977v1Colleagues took paired samples of hepatocellularcarcinoma from several patients (8), and did bulk RNA-Seq, lipidomics, and metabolomics on the samples.
We analyzed the data to see what was different in each modality, as well as what correlations could be found between RNA-Seq and metabolomics.
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Y'all. I was having a full on Pikachu face today when I found discrepancies in what metabolites were included in my datasets and what were included in a colleagues datasets when we processed identical experiments from Metabolomics Workbench (I am borrowing some stuff they did with the exact same experiments to supplement my own work).
Digging into it, I'm removing things that are missing across more than X number of samples, the colleague kept everything. 😮💨
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New lab paper is out! We've released our python package mwtab v2 for interacting with the Metabolomics Workbench (MW) website, and updated the file status website with some measures of issues with the data available from MW!
A Major Update and Improved Validation Functionality in the mwtab Python Library and the Metabolomics Workbench File Status Website
https://doi.org/10.3390/metabo16010076If you want a programmatic way to get data from MW, this might be useful.
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#metabolomics postdoc "The exact focus will be tailored to the candidate’s strengths and evolving opportunities in the field." https://jobs.ethz.ch/job/view/JOPG_ethz_1gSP4dmYD54u5EqbLs
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#Cancer immunotherapy is a type of cancer treatment that harnesses the #immune system to fight cancer cells. The treatment involves #CD8⁺ T cells, also known as killer T cells, which play a crucial role in attacking #tumors
#Immunology #Oncology #Metabolomics #sflorg
https://www.sflorg.com/2026/01/imgy01212601.html -
This year's @bioconductor Biological Data Science Summer School in Brixen, South Tyrol (the 22nd edition!) takes place 24-29 May 2026.
We cover (sc)-RNA-seq and #spatial #omics analysis, underlying (bio)statistical topics, #multiomics, #proteomics and #metabolomics, and also programmatic interaction from #Rstats :rstats: with LLMs, all very hands-on using R/Bioconductor tools.
https://csama2026.bioconductor.eu/
Registration opens on 1 Feb.