Nature Search

Systematic analyses of lipid mobilization by human lipid transfer proteins

Kevin Titeca
Antonella Chiapparino
Anne-Claude Gavin
Research07 Jan 2026
Nature

P: 1-3
SpaceM reveals metabolic states of single cells

SpaceM combines light microscopy and MALDI-imaging mass spectrometry to enable single-cell metabolic profiling of cultured cells. SpaceM reveals coexisting metabolic states of hepatocytes and aims to democratize single-cell metabolomics.

Luca Rappez
Mira Stadler
Theodore Alexandrov
Research05 Jul 2021
Nature Methods

Volume: 18, P: 799-805
FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

The authors present a computational framework for false-discovery-rate-controlled metabolite annotation from high-resolution imaging mass spectrometry data.

Andrew Palmer
Prasad Phapale
Theodore Alexandrov
Research14 Nov 2016
Nature Methods

Volume: 14, P: 57-60
Spatial metabolomics: from a niche field towards a driver of innovation

Spatial metabolomics has matured and is driving innovation in mass spectrometry, metabolomics and spatial omics. With exciting discoveries, complementary capabilities and increasing accessibility, it has secured its place in the spatial biology toolbox, showing promise in biology, medicine and pharmacology.

Theodore Alexandrov
Comments & Opinion07 Sept 2023
Nature Metabolism

Volume: 5, P: 1443-1445
METASPACE-ML: Context-specific metabolite annotation for imaging mass spectrometry using machine learning

Imaging mass spectrometry has revolutionised spatial metabolomics, but metabolites are annotated for only a fraction of the data. Here, authors show that METASPACE-ML enhances precision, increases throughput, and improves the identification of low-intensity and biologically relevant metabolites.

Bishoy Wadie
Lachlan Stuart
Theodore Alexandrov
ResearchOpen Access22 Oct 2024
Nature Communications

Volume: 15, P: 1-16
Spatial single-cell isotope tracing reveals heterogeneity of de novo fatty acid synthesis in cancer

Buglakova et al. present ¹³C-SpaceM, a method that combines stable isotope tracing with imaging mass spectrometry thus enabling spatial analysis of lipid dynamics with near-single-cell resolution in tissues.

Elena Buglakova
Måns Ekelöf
Theodore Alexandrov
ResearchOpen Access09 Sept 2024
Nature Metabolism

Volume: 6, P: 1695-1711
Rapid response of fly populations to gene dosage across development and generations

While developmental phenotypes are often multigenic and involve environmental inputs, most research approaches involve perturbation of small numbers of genes. Here they use a synthetic evolution approach in Drosophila to show that adding extra copies of bicoid leads to rapid, system-wide phenotypic responses, potentiated by highly polygenic traits such as embryo size.

Xueying C. Li
Lautaro Gandara
Justin Crocker
ResearchOpen Access29 May 2024
Nature Communications

Volume: 15, P: 1-14
Spatial metabolomics and multiomics integration for breakthroughs in precision medicine for kidney disease

Here, the authors discuss how spatial metabolomics could contribute to better understanding of cellular mechanisms in kidney health and disease, as well as the discovery of blood and urine biomarkers and drug targets for new therapies to halt kidney disease progression.

Kumar Sharma
Jens Hansen
Ravi Iyengar
Reviews09 Oct 2025
Nature Reviews Nephrology

Volume: 22, P: 152-164
HERMES: a molecular-formula-oriented method to target the metabolome

HERMES is a molecular-formula-oriented and peak-detection-free method that uses LC/MS1 information to optimize MS2 acquisition for LC/MS-based metabolomic analysis.

Roger Giné
Jordi Capellades
Oscar Yanes
Research01 Nov 2021
Nature Methods

Volume: 18, P: 1370-1376
FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy

van der Weijden et al. perform genomic, proteomic and metabolic analyses and find that FOXO1-mediated fatty acid oxidation maintains mouse embryos in diapause.

Vera A. van der Weijden
Maximilian Stötzel
Aydan Bulut-Karslioglu
ResearchOpen Access04 Jan 2024
Nature Cell Biology

Volume: 26, P: 181-193
A call for accessible tools to unlock single-cell immunometabolism research

Recent technological advances permit the profiling of metabolic changes in single cells, which sheds light on how metabolism regulates immune responses. We advocate for accessible and standardized tools to reduce the barrier of entry to immunometabolism studies and facilitate the translation of fundamental findings towards clinical applications.

Jason Cosgrove
Antoine Marçais
Jan Van den Bossche
Comments & Opinion11 Apr 2024
Nature Metabolism

Volume: 6, P: 779-782
An atlas of healthy and injured cell states and niches in the human kidney

A high-resolution kidney cellular atlas of 51 main cell types, including rare and previously undescribed cell populations, represents a comprehensive benchmark of cellular states, neighbourhoods, outcome-associated signatures and publicly available interactive visualizations.

Blue B. Lake
Rajasree Menon
Sanjay Jain
ResearchOpen Access19 Jul 2023
Nature

Volume: 619, P: 585-594
Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states

Haas, Velten and colleagues use single-cell multiomics of human blood and bone marrow to generate a reference map allowing the quantitative linking of cytometry and proteo-genomic information.

Sergio Triana
Dominik Vonficht
Simon Haas
ResearchOpen Access22 Nov 2021
Nature Immunology

Volume: 22, P: 1577-1589
Feature-based molecular networking in the GNPS analysis environment

Feature-based molecular networking allows the generation of molecular networks for mass spectrometry data that can recognize isomers, incorporate relative quantification and integrate ion mobility data.

Louis-Félix Nothias
Daniel Petras
Pieter C. Dorrestein
Research24 Aug 2020
Nature Methods

Volume: 17, P: 905-908
Creating a 3D microbial and chemical snapshot of a human habitat

Clifford A. Kapono
James T. Morton
Pieter C. Dorrestein
ResearchOpen Access27 Feb 2018
Scientific Reports

Volume: 8, P: 1-12
Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

Ontologies are powerful tools that facilitate the integration of large and disparate data sets. Here, researchers from the Kidney Precision Medicine Project provide an introduction to ontologies, including those developed by the consortium, describing how these will be used to improve the annotation of kidney-relevant data, eventually leading to new definitions of kidney disease in support of precision medicine.

Edison Ong
Lucy L. Wang
Yongqun He
Reviews16 Sept 2020
Nature Reviews Nephrology

Volume: 16, P: 686-696
3D molecular cartography using LC–MS facilitated by Optimus and 'ili software

3D molecular cartography is used for mapping of metabolites in our environment. This protocol describes the procedures for sample collection and processing, mass spectrometry analysis, and data processing and visualization.

Ivan Protsyuk
Alexey V Melnik
Theodore Alexandrov
Protocols21 Dec 2017
Nature Protocols

Volume: 13, P: 134-154
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

GNPS is an open-access community-curated analysis platform for sharing natural product mass spectrometry data that enables continuous, automatic reanalysis of deposited 'living' data sets.

Mingxun Wang
Jeremy J Carver
Nuno Bandeira
Reviews09 Aug 2016
Nature Biotechnology

Volume: 34, P: 828-837
A model for network-based identification and pharmacological targeting of aberrant, replication-permissive transcriptional programs induced by viral infection

Master Regulator proteins, controlling the transcriptional identity of infected cells, can serve as drug targets for inhibiting virus replication, here demonstrated in a SARSCoV-2 infection model.

Pasquale Laise
Megan L. Stanifer
Mariano J. Alvarez
ResearchOpen Access19 Jul 2022
Communications Biology

Volume: 5, P: 1-12
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways

Martina Poletti
Agatha Treveil
Tamas Korcsmaros
ResearchOpen Access02 May 2022
npj Systems Biology and Applications

Volume: 8, P: 1-19
Molecular and chemical dialogues in bacteria-protozoa interactions

Chunxu Song
Mark Mazzola
Jos M. Raaijmakers
ResearchOpen Access06 Aug 2015
Scientific Reports

Volume: 5, P: 1-13
Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine

Nikolaus Rajewsky
Geneviève Almouzni
Frauke Zipp
Amendments and CorrectionsOpen Access17 Mar 2021
Nature

Volume: 592, P: E8
LifeTime and improving European healthcare through cell-based interceptive medicine

The LifeTime initiative is an ambitious, multidisciplinary programme that aims to improve healthcare by tracking individual human cells during disease processes and responses to treatment in order to develop and implement cell-based interceptive medicine in Europe.

Nikolaus Rajewsky
Geneviève Almouzni
Frauke Zipp
Reviews07 Sept 2020
Nature

Volume: 587, P: 377-386
Microbial metabolic exchange in 3D

Jeramie D Watrous
Vanessa V Phelan
Pieter C Dorrestein
Research03 Jan 2013
The ISME Journal

Volume: 7, P: 770-780
A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology

Lutnick et al. develop a cloud-based deep learning tool for whole slide image segmentation. The authors provide several examples of its application in renal pathology, for segmenting glomeruli, interstitial fibrosis and other features of interest.

Brendon Lutnick
David Manthey
Angela Victoria-Castro
ResearchOpen Access19 Aug 2022
Communications Medicine

Volume: 2, P: 1-15
Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline

Tissue cytometry is a promising new microscopy technique that can be used to enumerate and characterize each cell in a tissue. Here the authors describe a complete and accessible pipeline, including methods of sample preparation, microscopy, image analysis, and data analysis for large-scale three-dimensional tissue cytometry of human kidney tissues.

Michael J. Ferkowicz
Seth Winfree
Francis Perry Wilson
Research06 Jan 2021
Laboratory Investigation

Volume: 101, P: 661-676

Search

Systematic analyses of lipid mobilization by human lipid transfer proteins

SpaceM reveals metabolic states of single cells

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

Spatial metabolomics: from a niche field towards a driver of innovation

METASPACE-ML: Context-specific metabolite annotation for imaging mass spectrometry using machine learning

Spatial single-cell isotope tracing reveals heterogeneity of de novo fatty acid synthesis in cancer

Rapid response of fly populations to gene dosage across development and generations

Spatial metabolomics and multiomics integration for breakthroughs in precision medicine for kidney disease

HERMES: a molecular-formula-oriented method to target the metabolome

FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy

A call for accessible tools to unlock single-cell immunometabolism research

An atlas of healthy and injured cell states and niches in the human kidney

Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states

Feature-based molecular networking in the GNPS analysis environment

Creating a 3D microbial and chemical snapshot of a human habitat

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

3D molecular cartography using LC–MS facilitated by Optimus and 'ili software

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

A model for network-based identification and pharmacological targeting of aberrant, replication-permissive transcriptional programs induced by viral infection

Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways

Molecular and chemical dialogues in bacteria-protozoa interactions

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine

LifeTime and improving European healthcare through cell-based interceptive medicine

Microbial metabolic exchange in 3D

A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology

Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline

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