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Mouse lemur cell atlas informs primate genes, physiology and disease

Together with an accompanying paper presenting a transcriptomic atlas of the mouse lemur, interrogation of the atlas provides a rich body of data to support the use of the organism as a model for primate biology and health.

Camille Ezran
Shixuan Liu
Mark A. Krasnow
ResearchOpen Access30 Jul 2025
Nature

Volume: 644, P: 185-196
A molecular cell atlas of mouse lemur, an emerging model primate

Together with a companion paper, the generation of a transcriptomic atlas for the mouse lemur and analyses of example cell types establish this animal as a molecularly tractable primate model organism.

Antoine de Morree
Iwijn De Vlaminck
Mark A. Krasnow
ResearchOpen Access30 Jul 2025
Nature

Volume: 644, P: 173-184
Spatiotemporal expression and control of haemoglobin in space

Here the authors analyse the impact of space on haemoglobin gene regulation using data from NASA, JAXA and SpaceX i4 missions. They find that globin gene down-regulation leads to space anaemia with post-flight recovery, and reveal an adult-to-foetal globin switch activation.

Josef Borg
Conor Loy
Joseph Borg
ResearchOpen Access11 Jun 2024
Nature Communications

Volume: 15, P: 1-15
Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract

Urinary tract infections are one of the most common infections in humans. Here, the authors use urinary cell-free DNA (cfDNA) to comprehensively monitor host and pathogen dynamics in bacterial and viral urinary tract infections, and show that it is a versatile analyte for monitoring urinary tract infections.

Philip Burnham
Darshana Dadhania
Iwijn De Vlaminck
ResearchOpen Access20 Jun 2018
Nature Communications

Volume: 9, P: 1-10
Spatial mapping of the total transcriptome by in situ polyadenylation

Spatial RNA sequencing is extended beyond poly-A transcripts to capture the full transcriptome.

David W. McKellar
Madhav Mantri
Iwijn De Vlaminck
ResearchOpen Access03 Nov 2022
Nature Biotechnology

Volume: 41, P: 513-520
Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis

Using single-cell and spatial transcriptomics in chicken hearts, here, the authors generate a census of cellular interactions from early to late four-chambered heart stage, identifying a distinct epicardial-mesenchymal cell population with a migratory phenotype.

Madhav Mantri
Gaetano J. Scuderi
Iwijn De Vlaminck
ResearchOpen Access19 Mar 2021
Nature Communications

Volume: 12, P: 1-13
Circulating cell-free RNA in blood as a host response biomarker for detection of tuberculosis

Whole blood signatures have served as the potential biomarkers for TB but failed to meet World Health Organization’s (WHO) optimal target product profiles (TPP). By employing cohorts from multiple countries, the authors identify a diagnostic 6-gene signature from cell free RNA which outperforms TPP requirement in distinguishing TB from non-TB.

Adrienne Chang
Conor J. Loy
Iwijn De Vlaminck
ResearchOpen Access10 Jun 2024
Nature Communications

Volume: 15, P: 1-8
Spatial methods for microbiome–host interactions

Spatial transcriptomics offers a glimpse of how microbiomes interact with their hosts.

Ioannis Ntekas
Iwijn De Vlaminck
News & Views20 Nov 2023
Nature Biotechnology

Volume: 42, P: 1359-1360
Molecular characterization of Kawasaki disease subgroups using cell-free RNA profiling

Conor J. Loy
Hao Wang
Iwijn De Vlaminck
ResearchOpen Access14 Aug 2025
Scientific Reports

Volume: 15, P: 1-9
Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis

Conventional single-cell RNA sequencing analysis rely on genome annotations that may be incomplete or inaccurate especially for understudied organisms. Here the authors present a bioinformatic tool that leverages single-cell data to uncover biologically relevant transcripts beyond the best available genome annotation.

Michael F. Z. Wang
Madhav Mantri
Iwijn De Vlaminck
ResearchOpen Access12 Apr 2021
Nature Communications

Volume: 12, P: 1-10
Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes

Simultaneous DNA-FISH and multiplexed rRNA-FISH spatially map antimicrobial resistance plasmids and phage with their host taxa in polyspecies human oral biofilm samples, revealing hotspots of genetic exchange or amplification.

Benjamin Grodner
Hao Shi
Iwijn De Vlaminck
ResearchOpen Access25 Jun 2024
Nature Microbiology

Volume: 9, P: 2262-2277
An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome

Endocrinologists have traditionally focused on studying one hormone or organ system at a time. Here the authors use transcriptomic data from the mouse lemur to globally characterize primate hormonal signaling, describing hormone sources and targets, identifying conserved and primate specific regulation, and elucidating principles of the network.

Shixuan Liu
Camille Ezran
James E. Ferrell Jr.
ResearchOpen Access11 Mar 2024
Nature Communications

Volume: 15, P: 1-27
Electrical detection of confined gap plasmons in metal–insulator–metal waveguides

Electrical detection and characterization of gap plasmons is achieved by means of an integrated metal–semiconductor–metal photodetector. Integration of electro–optical components in metallic waveguides may lead to active high-bandwidth on-chip nano-optical circuits.

Pieter Neutens
Pol Van Dorpe
Gustaaf Borghs
Research19 Apr 2009
Nature Photonics

Volume: 3, P: 283-286
A quantitative comparison of urine centrifugation and filtration for the isolation and analysis of urinary nucleic acid biomarkers

Liz-Audrey Kounatse Djomnang
Carol Li
Iwijn De Vlaminck
ResearchOpen Access13 May 2024
Scientific Reports

Volume: 14, P: 1-8
Tunable optical forces between nanophotonic waveguides

The optical-gradient force between two nanophotonic waveguides can be tuned from attractive to repulsive by controlling the relative phase of the optical fields injected into the waveguides.

Joris Roels
Iwijn De Vlaminck
Roel Baets
Research13 Jul 2009
Nature Nanotechnology

Volume: 4, P: 510-513
A metagenomic DNA sequencing assay that is robust against environmental DNA contamination

The accuracy of metagenomic DNA sequencing is limited by environmental DNA contamination. Here, the authors develop and test SIFT-seq, a metagenomic DNA sequencing assay that allows to identify and remove environmental DNA contamination introduced during sample preparation.

Omary Mzava
Alexandre Pellan Cheng
Iwijn De Vlaminck
ResearchOpen Access21 Jul 2022
Nature Communications

Volume: 13, P: 1-10
Highly multiplexed spatial mapping of microbial communities

High-phylogenetic-resolution microbiome mapping by fluorescence in situ hybridization (HiPR-FISH) enables the spatial mapping of hundreds of species of microorganisms and shows how microbial networks in the mouse gut are affected by antibiotic treatment.

Hao Shi
Qiaojuan Shi
Iwijn De Vlaminck
Research02 Dec 2020
Nature

Volume: 588, P: 676-681
Precision run-on sequencing (PRO-seq) for microbiome transcriptomics

PRO-seq, which does not need antibodies or epitope tags on RNAP, is adapted to report nascent transcription in bacteria including human gut microbiome samples.

Albert C. Vill
Edward J. Rice
Ilana L. Brito
Research03 Jan 2024
Nature Microbiology

Volume: 9, P: 241-250
Single-cell multi-ome and immune profiles of the Inspiration4 crew reveal conserved, cell-type, and sex-specific responses to spaceflight

Multiple omics platforms and deep single-cell profiling in the I4 astronauts reveal both conserved and distinct immune system disruptions across missions, provide a single-cell immune reference for future missions.

JangKeun Kim
Braden T. Tierney
Christopher E. Mason
ResearchOpen Access11 Jun 2024
Nature Communications

Volume: 15, P: 1-18
Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis

Mantri et al. used spatial transcriptomics and scRNA-seq combined with smFISH to characterize the pathogenesis of reovirus-induced myocarditis in neonatal mice. They report a key role for endothelial cells in modulating the inflammatory response to the virus and a role for cytotoxic T-cell-induced pyroptosis in the cardiac pathology.

Madhav Mantri
Meleana M. Hinchman
Iwijn De Vlaminck
ResearchOpen Access10 Oct 2022
Nature Cardiovascular Research

Volume: 1, P: 946-960
Gut uropathogen abundance is a risk factor for development of bacteriuria and urinary tract infection

Urinary tract infections (UTIs) are associated with changes in the gut microbiome. Here, the authors evaluate the relationship between the gut microbiome and development of UTI in kidney transplant patients and show that uropathogenic gut abundance might represent a risk factor for development of bacteriuria and UTI.

Matthew Magruder
Adam N. Sholi
John Richard Lee
ResearchOpen Access04 Dec 2019
Nature Communications

Volume: 10, P: 1-9
The Space Omics and Medical Atlas (SOMA) and international astronaut biobank

An integrated data and sample repository for clinical, cellular and multi-omics research from diverse spaceflight missions known as Space Omics and Medical Atlas (SOMA) is presented.

Eliah G. Overbey
JangKeun Kim
Christopher E. Mason
ResearchOpen Access11 Jun 2024
Nature

Volume: 632, P: 1145-1154
Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells

DART-seq alters droplet sequencing in a simple and flexible way to simultaneously profile the transcriptome and multiplexed targeted RNAs, such as viral transcripts and immunoglobulin chains, in single cells.

Mridusmita Saikia
Philip Burnham
Iwijn De Vlaminck
Research17 Dec 2018
Nature Methods

Volume: 16, P: 59-62
Transcriptomic analysis of skeletal muscle regeneration across mouse lifespan identifies altered stem cell states

Skeletal muscle regeneration declines during aging but the underlying processes are incompletely understood. Here the authors generated single-cell and spatial transcriptomics data from uninjured and injured muscles across mouse lifespan and observed age-specific immune cell dynamics and an elevation of senescent-like muscle stem cells in aged muscles.

Lauren D. Walter
Jessica L. Orton
Benjamin D. Cosgrove
ResearchOpen Access22 Nov 2024
Nature Aging

Volume: 4, P: 1862-1881
Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration

David McKellar et al. integrate single-cell and -nuclear transcriptomic analyses of mouse skeletal muscle in homeostatic conditions or following injury. The resulting transcriptomic model of myogenesis identified rare, transitional states and cell subtypes that are poorly represented in individual datasets, providing a valuable resource for the field.

David W. McKellar
Lauren D. Walter
Benjamin D. Cosgrove
ResearchOpen Access12 Nov 2021
Communications Biology

Volume: 4, P: 1-12
A second space age spanning omics, platforms and medicine across orbits

The current ‘second space age’ has enabled multiple studies on the effects of spaceflight on human physiology and health, which are contributing to the development of measures that will be needed to maintain astronaut health in future space missions.

Christopher E. Mason
James Green
Afshin Beheshti
Reviews11 Jun 2024
Nature

Volume: 632, P: 995-1008
Metagenomic DNA sequencing to quantify Mycobacterium tuberculosis DNA and diagnose tuberculosis

Adrienne Chang
Omary Mzava
Iwijn De Vlaminck
ResearchOpen Access10 Oct 2022
Scientific Reports

Volume: 12, P: 1-8
Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets

An adversarial domain translation framework is presented for scalable integration of single-cell atlases across samples, technical platforms, data modalities and species.

Jia Zhao
Gefei Wang
Can Yang
Research30 May 2022
Nature Computational Science

Volume: 2, P: 317-330
Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma

Philip Burnham
Min Seong Kim
Iwijn De Vlaminck
ResearchOpen Access14 Jun 2016
Scientific Reports

Volume: 6, P: 1-9

Search

Mouse lemur cell atlas informs primate genes, physiology and disease

A molecular cell atlas of mouse lemur, an emerging model primate

Spatiotemporal expression and control of haemoglobin in space

Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract

Spatial mapping of the total transcriptome by in situ polyadenylation

Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis

Circulating cell-free RNA in blood as a host response biomarker for detection of tuberculosis

Spatial methods for microbiome–host interactions

Molecular characterization of Kawasaki disease subgroups using cell-free RNA profiling

Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis

Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes

An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome

Electrical detection of confined gap plasmons in metal–insulator–metal waveguides

A quantitative comparison of urine centrifugation and filtration for the isolation and analysis of urinary nucleic acid biomarkers

Tunable optical forces between nanophotonic waveguides

A metagenomic DNA sequencing assay that is robust against environmental DNA contamination

Highly multiplexed spatial mapping of microbial communities

Precision run-on sequencing (PRO-seq) for microbiome transcriptomics

Single-cell multi-ome and immune profiles of the Inspiration4 crew reveal conserved, cell-type, and sex-specific responses to spaceflight

Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis

Gut uropathogen abundance is a risk factor for development of bacteriuria and urinary tract infection

The Space Omics and Medical Atlas (SOMA) and international astronaut biobank

Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells

Transcriptomic analysis of skeletal muscle regeneration across mouse lifespan identifies altered stem cell states

Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration

A second space age spanning omics, platforms and medicine across orbits

Metagenomic DNA sequencing to quantify Mycobacterium tuberculosis DNA and diagnose tuberculosis

Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets

Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma

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