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Interpretable inflammation landscape of circulating immune cells

Including data from 1,047 patients across 19 inflammatory diseases, a new atlas presents a comprehensive model of inflammation in circulating immune cells.

Laura Jiménez-Gracia
Davide Maspero
Holger Heyn
ResearchOpen Access12 Jan 2026
Nature Medicine

Volume: 32, P: 633-644
Publisher Correction: Interpretable inflammation landscape of circulating immune cells

Laura Jiménez-Gracia
Davide Maspero
Holger Heyn
Amendments and CorrectionsOpen Access26 Jan 2026
Nature Medicine

Volume: 32, P: 765
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

An integrated analysis of over 100 single-cell and single-nucleus transcriptomics studies illustrates severe acute respiratory syndrome coronavirus 2 viral entry gene coexpression patterns across different human tissues, and shows association of age, smoking status and sex with viral entry gene expression in respiratory cell populations.

Christoph Muus
Malte D. Luecken
Xiaohui Zhang
Research02 Mar 2021
Nature Medicine

Volume: 27, P: 546-559
Brain change trajectories in healthy adults correlate with Alzheimer’s related genetic variation and memory decline across life

This study shows that among healthy adults tracked across their lives, brain atrophy rates correlate with genetic risk for Alzheimer’s and memory decline, and that degeneration in Alzheimer’s-vulnerable brain regions is a continuous phenomenon.

James M. Roe
Didac Vidal-Piñeiro
Yunpeng Wang
ResearchOpen Access17 Dec 2024
Nature Communications

Volume: 15, P: 1-19
Spatial single-cell atlas reveals regional variations in healthy and diseased human lung

Using multiplexed spatially resolved transcriptomic approaches, the authors generate a topographic atlas of the healthy adult lung with location-related gene expression variability or neighbourhood changes as exemplified by COPD patient sample analysis.

Alexandra B. Firsova
Sergio Marco Salas
Christos Samakovlis
ResearchOpen Access05 Nov 2025
Nature Communications

Volume: 16, P: 1-17
A cellular census of human lungs identifies novel cell states in health and in asthma

Single-cell transcriptomics reveals immune and stromal compartment remodeling, including the enrichment of unique populations of epithelial cells and CD4⁺ T cells, in asthmatic lungs

Felipe A. Vieira Braga
Gozde Kar
Sarah A. Teichmann
Research17 Jun 2019
Nature Medicine

Volume: 25, P: 1153-1163
An integrated cell atlas of the lung in health and disease

A single-cell atlas of the human lungs, integrating data from 2.4 million cells from 486 individuals and including samples from healthy and diseased lungs, provides a roadmap for the generation of organ-scale cell atlases.

Lisa Sikkema
Ciro Ramírez-Suástegui
Fabian J. Theis
ResearchOpen Access08 Jun 2023
Nature Medicine

Volume: 29, P: 1563-1577
Variant-specific local tissue response to SARS-CoV-2 in the nasal mucosa

Cell-type-specific SARS-CoV-2-induced responses in nasal mucosa differ largely between ancestral, Delta and Omicron cases, including the association with severe disease and the cellular and immunological effects of prior vaccination.

Debbie van Baarle
Martijn C. Nawijn
News & Views29 Jan 2025
Nature Immunology

Volume: 26, P: 152-154
Nasal DNA methylation at three CpG sites predicts childhood allergic disease

Accurate prediction of the onset of childhood allergy is important to clarify the difference between various respiratory diseases. Here the authors propose that the methylation status of three sites in nasal DNA predicts the onset of childhood allergy which may aid diagnosis and monitoring.

Merlijn van Breugel
Cancan Qi
Cheng-Jian Xu
ResearchOpen Access01 Dec 2022
Nature Communications

Volume: 13, P: 1-13
Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19

Here the authors characterise the cellular and molecular progression of lung alveolar damage in severe COVID-19 patients using integrated histopathology and cell atlassing, pinpointing a role for macrophage SPP1 signalling to vasculature in this process.

Jimmy Tsz Hang Lee
Sam N. Barnett
Omer Ali Bayraktar
ResearchOpen Access10 Mar 2025
Nature Communications

Volume: 16, P: 1-16
SARS-CoV-2-specific hotspots in virus–host interaction networks

A multimodal proteomic analysis of the perturbations that SARS-CoV-2 and SARS-CoV induce in infected human lung epithelial cells reveals common and distinct immune-evasive and pathobiological mechanisms used by these coronaviruses.

Herbert B. Schiller
Merlijn van Breugel
Martijn C. Nawijn
News & Views21 Jun 2021
Nature Immunology

Volume: 22, P: 806-808
Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity

Patients with chronic lung disease (CLD) have an increased risk for severe coronavirus disease-19 and poor outcomes. Here the authors compare the transcriptomes of single cells isolated from healthy and CLD lungs to identify molecular characteristics of lung cells that may account for worse COVID-19 outcomes in these patients.

Linh T. Bui
Nichelle I. Winters
Laure Emmanuelle Zaragosi
ResearchOpen Access14 Jul 2021
Nature Communications

Volume: 12, P: 1-13
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage

This Resource describes data, code and tools developed for the Human Reference Atlas and the Human BioMolecular Atlas Program for building and navigating a multiscale human atlas.

Katy Börner
Philip D. Blood
Bruce W. Herr II
ResearchOpen Access13 Mar 2025
Nature Methods

Volume: 22, P: 845-860
Variants and vaccines impact nasal immunity over three waves of SARS-CoV-2

Ordovas-Montanes and colleagues describe the composition of the nasal cellular ecosystem and signatures of disease severity in vaccinated and unvaccinated adults during infection with the ancestral, Delta and Omicron variants of SARS-CoV-2.

Jaclyn M. L. Walsh
Vincent N. Miao
Jose Ordovas-Montanes
Research20 Jan 2025
Nature Immunology

Volume: 26, P: 294-307
Correction: Brain structural abnormalities in obesity: relation to age, genetic risk, and common psychiatric disorders

Nils Opel
Anbupalam Thalamuthu
Udo Dannlowski
Amendments and CorrectionsOpen Access22 Jun 2021
Molecular Psychiatry

Volume: 26, P: 7854
1,25(OH)₂VitD3 supplementation enhances suppression of grass pollen-induced allergic asthma by subcutaneous and sublingual immunotherapy in a mouse model

Laura Hesse
Arjen H. Petersen
Martijn C. Nawijn
ResearchOpen Access02 Jun 2020
Scientific Reports

Volume: 10, P: 1-13
High dose vitamin D₃ empowers effects of subcutaneous immunotherapy in a grass pollen-driven mouse model of asthma

Laura Hesse
N. van Ieperen
Martijn C. Nawijn
ResearchOpen Access30 Nov 2020
Scientific Reports

Volume: 10, P: 1-14
For better or for worse: the role of Pim oncogenes in tumorigenesis

The Pim family of kinases actively collaborate with MYC in driving tumorigenesis. However, in several cancers the expression levels of PIMs can correlate with favourable prognostic outcome. This Review analyses the physiological and oncogenic activities of Pim kinases and their synergistic marriage with MYC, for better or for worse.

Martijn C. Nawijn
Andrej Alendar
Anton Berns
Reviews09 Dec 2010
Nature Reviews Cancer

Volume: 11, P: 23-34
Characterization of a lung epithelium specific E-cadherin knock-out model: Implications for obstructive lung pathology

S. Post
I. H. Heijink
M. C. Nawijn
ResearchOpen Access05 Sept 2018
Scientific Reports

Volume: 8, P: 1-12
Benchmarking atlas-level data integration in single-cell genomics

This benchmarking study compares 16 methods for integrating complex single-cell RNA and ATAC datasets and provides a guide to method choice.

Malte D. Luecken
M. Büttner
Fabian J. Theis
ResearchOpen Access23 Dec 2021
Nature Methods

Volume: 19, P: 41-50
Genetic variant in CACNA1C is associated with PTSD in traumatized police officers

Izabela M. Krzyzewska
Judith B. M. Ensink
Peter Henneman
ResearchOpen Access23 Jan 2018
European Journal of Human Genetics

Volume: 26, P: 247-257
Optimized summary-statistic-based single-cell eQTL meta-analysis

Maryna Korshevniuk
Harm-Jan Westra
Marc Jan Bonder
ResearchOpen Access04 Aug 2025
Scientific Reports

Volume: 15, P: 1-13
Mutation of GATA3 in human breast tumors

Jerry Usary
Victor Llaca
Charles M Perou
Research13 Sept 2004
Oncogene

Volume: 23, P: 7669-7678
The proto-oncogene Pim-1 is a target of miR-33a

M Thomas
K Lange-Grünweller
R K Hartmann
Research11 Jul 2011
Oncogene

Volume: 31, P: 918-928
SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

An analysis of single-cell transcriptomics datasets from different tissues shows that ACE2 and TMPRSS2 are co-expressed in respiratory, corneal and intestinal epithelial cell populations, and that respiratory expression of ACE2 is associated with genes involved in innate immunity.

Waradon Sungnak
Ni Huang
Francisco Figueiredo
Research23 Apr 2020
Nature Medicine

Volume: 26, P: 681-687
Examining the association between posttraumatic stress disorder and disruptions in cortical networks identified using data-driven methods

Jin Yang
Ashley A. Huggins
Aristeidis Sotiras
Research28 Nov 2023
Neuropsychopharmacology

Volume: 49, P: 609-619
Smooth-muscle-derived WNT5A augments allergen-induced airway remodelling and Th2 type inflammation

Tim Koopmans
Laura Hesse
Reinoud Gosens
ResearchOpen Access21 Apr 2020
Scientific Reports

Volume: 10, P: 1-14
Altered white matter microstructural organization in posttraumatic stress disorder across 3047 adults: results from the PGC-ENIGMA PTSD consortium

Emily L. Dennis
Seth G. Disner
Rajendra A. Morey
Research19 Dec 2019
Molecular Psychiatry

Volume: 26, P: 4315-4330
Cortical volume abnormalities in posttraumatic stress disorder: an ENIGMA-psychiatric genomics consortium PTSD workgroup mega-analysis

Xin Wang
Hong Xie
Israel Liberzon
Research07 Dec 2020
Molecular Psychiatry

Volume: 26, P: 4331-4343
Brain structural abnormalities in obesity: relation to age, genetic risk, and common psychiatric disorders

Nils Opel
Anbupalam Thalamuthu
Udo Dannlowski
ResearchOpen Access28 May 2020
Molecular Psychiatry

Volume: 26, P: 4839-4852
Frat oncoproteins act at the crossroad of canonical and noncanonical Wnt-signaling pathways

R van Amerongen
M C Nawijn
A Berns
Research05 Oct 2009
Oncogene

Volume: 29, P: 93-104
DAMPs activating innate and adaptive immune responses in COPD

S D Pouwels
I H Heijink
A JM van Oosterhout
Reviews23 Oct 2013
Mucosal Immunology

Volume: 7, P: 215-226

Search

Interpretable inflammation landscape of circulating immune cells

Publisher Correction: Interpretable inflammation landscape of circulating immune cells

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Brain change trajectories in healthy adults correlate with Alzheimer’s related genetic variation and memory decline across life

Spatial single-cell atlas reveals regional variations in healthy and diseased human lung

A cellular census of human lungs identifies novel cell states in health and in asthma

An integrated cell atlas of the lung in health and disease

Variant-specific local tissue response to SARS-CoV-2 in the nasal mucosa

Nasal DNA methylation at three CpG sites predicts childhood allergic disease

Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19

SARS-CoV-2-specific hotspots in virus–host interaction networks

Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage

Variants and vaccines impact nasal immunity over three waves of SARS-CoV-2

Correction: Brain structural abnormalities in obesity: relation to age, genetic risk, and common psychiatric disorders

1,25(OH)₂VitD3 supplementation enhances suppression of grass pollen-induced allergic asthma by subcutaneous and sublingual immunotherapy in a mouse model

High dose vitamin D₃ empowers effects of subcutaneous immunotherapy in a grass pollen-driven mouse model of asthma

For better or for worse: the role of Pim oncogenes in tumorigenesis

Characterization of a lung epithelium specific E-cadherin knock-out model: Implications for obstructive lung pathology

Benchmarking atlas-level data integration in single-cell genomics

Genetic variant in CACNA1C is associated with PTSD in traumatized police officers

Optimized summary-statistic-based single-cell eQTL meta-analysis

Mutation of GATA3 in human breast tumors

The proto-oncogene Pim-1 is a target of miR-33a

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

Examining the association between posttraumatic stress disorder and disruptions in cortical networks identified using data-driven methods

Smooth-muscle-derived WNT5A augments allergen-induced airway remodelling and Th2 type inflammation

Altered white matter microstructural organization in posttraumatic stress disorder across 3047 adults: results from the PGC-ENIGMA PTSD consortium

Cortical volume abnormalities in posttraumatic stress disorder: an ENIGMA-psychiatric genomics consortium PTSD workgroup mega-analysis

Brain structural abnormalities in obesity: relation to age, genetic risk, and common psychiatric disorders

Frat oncoproteins act at the crossroad of canonical and noncanonical Wnt-signaling pathways

DAMPs activating innate and adaptive immune responses in COPD

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