Nature Search

Humoral determinants of checkpoint immunotherapy

Rapid extracellular antibody profiling reveals a contribution of autoantibodies to the effectiveness of checkpoint immunotherapy for cancer.

Yile Dai
Lilach Aizenbud
Aaron M. Ring
Research23 Jul 2025
Nature

Volume: 644, P: 527-536
Nerve-associated macrophages control adipose homeostasis across lifespan and restrain age-related inflammation

Gonzalez-Hurtado, Leveau and colleagues characterize adipose resident tissue macrophages across lifespan in mice, finding that nerve-associated macrophages, which mitigate inflammation and control lipolysis and catecholamine resistance, are lost during aging.

Elsie Gonzalez-Hurtado
Claire Leveau
Vishwa Deep Dixit
ResearchOpen Access02 Sept 2025
Nature Aging

Volume: 5, P: 1828-1843
SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data

Dissecting cellular intrinsic properties and spatial interactions is crucial for understanding biological processes. Here, authors develop a theoretically grounded deep learning framework SIMVI, that disentangles the two factors from spatial omics data.

Mingze Dong
David G. Su
Yuval Kluger
ResearchOpen Access27 Mar 2025
Nature Communications

Volume: 16, P: 1-17
Gene trajectory inference for single-cell data by optimal transport metrics

Gene dynamics of concurrent biological processes are unraveled by considering gene trajectories instead of cell trajectories.

Rihao Qu
Xiuyuan Cheng
Yuval Kluger
Research05 Apr 2024
Nature Biotechnology

Volume: 43, P: 258-268
Cluster-independent multiscale marker identification in single-cell RNA-seq data using localized marker detector (LMD)

LMD identifies genes localized in high-dimensional transcriptomic neighborhoods, detecting subpopulations missed by clustering. Per-gene analysis reveals condition-specific or shared localization patterns without requiring batch correction.

Ruiqi Li
Rihao Qu
Yuval Kluger
ResearchOpen Access16 Jul 2025
Communications Biology

Volume: 8, P: 1-15
Circulating tumor-reactive KIR⁺CD8⁺ T cells suppress anti-tumor immunity in patients with melanoma

Tumor-antigen-specific CD8⁺ T cells are generally thought to help fight against cancer, but here the authors identify a subpopulation of CD8⁺ T cells that are associated with a poor clinical outcome in melanoma. Although these cells can recognize tumor antigens, they suppress cancer immunity.

Benjamin Y. Lu
Liliana E. Lucca
David A. Hafler
Research28 Nov 2024
Nature Immunology

Volume: 26, P: 82-91
Zero-preserving imputation of single-cell RNA-seq data

Missing values in scRNA-seq datasets can bias their analysis. Here, the authors threshold the low rank approximation of the expression matrix, so false zeros can be imputed while true zeros are preserved.

George C. Linderman
Jun Zhao
Yuval Kluger
ResearchOpen Access11 Jan 2022
Nature Communications

Volume: 13, P: 1-11
Author Correction: Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function

Will Bailis
Justin A. Shyer
Richard A. Flavell
Amendments and Corrections26 Aug 2019
Nature

Volume: 573, P: E2
IL-10 constrains sphingolipid metabolism to limit inflammation

IL-10 exerts its anti-inflammatory activity in macrophages by increasing the expression of enzymes that promote fatty acid desaturation and downstream regulation of the transcription factor REL.

Autumn G. York
Mathias H. Skadow
Richard A. Flavell
ResearchOpen Access21 Feb 2024
Nature

Volume: 627, P: 628-635
Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden

Germline variants that affect the expression or function of protein-coding regions of cancer genes are associated with cancer susceptibility. Here, the authors show that a larger number of germline variants are present in early-onset cancers, while acquired somatic mutations are prevalent in cancers that develop at older age.

Tao Qing
Hussein Mohsen
Lajos Pusztai
ResearchOpen Access15 May 2020
Nature Communications

Volume: 11, P: 1-8
A highly efficient and faithful MDS patient-derived xenotransplantation model for pre-clinical studies

Myelodyplastic hematopoietic stem cells (MDS HSC) have eluded in vivo modeling. Here the authors present a highly efficient MDS patient-derived xenotransplantation model in cytokine-humanized mice with replication of the donors’ genetic complexity and myeloid, erythroid, and megakaryocytic lineage dysplasia.

Yuanbin Song
Anthony Rongvaux
Stephanie Halene
ResearchOpen Access21 Jan 2019
Nature Communications

Volume: 10, P: 1-14
Spatial epigenome–transcriptome co-profiling of mammalian tissues

The authors present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications and gene expression on the same tissue section at near-single-cell resolution.

Di Zhang
Yanxiang Deng
Rong Fan
ResearchOpen Access15 Mar 2023
Nature

Volume: 616, P: 113-122
The age of bone marrow dictates the clonality of smooth muscle-derived cells in atherosclerotic plaques

Kabir et al. show that aged bone marrow induces smooth muscle cell (SMC) polyclonality in atherosclerosis. Decreased TET2 levels in aged myeloid cells lead to silenced integrin β₃, resulting in increased TNFα signaling and the expansion of multiple SMC progenitors.

Inamul Kabir
Xinbo Zhang
Daniel M. Greif
Research09 Jan 2023
Nature Aging

Volume: 3, P: 64-81
Inflammasome activation in infected macrophages drives COVID-19 pathology

A new humanized mouse model for COVID-19 demonstrates SARS-CoV-2 infection and subsequent activation of inflammasomes in human macrophages as a critical driver of disease.

Esen Sefik
Rihao Qu
Richard A. Flavell
Research28 Apr 2022
Nature

Volume: 606, P: 585-593
A humanized mouse model of chronic COVID-19

A mouse model of chronic COVID-19 facilitates the study of disease mechanisms and therapies.

Esen Sefik
Benjamin Israelow
Richard A. Flavell
Research17 Dec 2021
Nature Biotechnology

Volume: 40, P: 906-920
Paracrine orchestration of intestinal tumorigenesis by a mesenchymal niche

Single-cell RNA-sequencing analysis of intestinal mesenchyme identified a population of fibroblasts that produce prostaglandin E₂, which, when disrupted, prevented initiation of intestinal tumours.

Manolis Roulis
Aimilios Kaklamanos
Richard A. Flavell
Research01 Apr 2020
Nature

Volume: 580, P: 524-529
Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data

FIt-SNE, a sped-up version of t-SNE, enables visualization of rare cell types in large datasets by obviating the need for downsampling. One-dimensional t-SNE heatmaps allow simultaneous visualization of expression patterns from thousands of genes.

George C. Linderman
Manas Rachh
Yuval Kluger
Research11 Feb 2019
Nature Methods

Volume: 16, P: 243-245
A Molecular Chipper technology for CRISPR sgRNA library generation and functional mapping of noncoding regions

The interrogation of noncoding regions of the genome with CRISPR strategies requires dense and, ideally, inexpensive libraries to ensure coverage and customisation. Here the authors present 'Molecular Chipper' that uses fragmentation to generate guide RNAs from input DNA.

Jijun Cheng
Christine A. Roden
Jun Lu
ResearchOpen Access30 Mar 2016
Nature Communications

Volume: 7, P: 1-10
Structural proteomics of an archaeon

Dinesh Christendat
Adelinda Yee
Cheryl H. Arrowsmith
Research01 Oct 2000
Nature Structural Biology

Volume: 7, P: 903-909
The RAG2 C-terminus and ATM protect genome integrity by controlling antigen receptor gene cleavage

Mice lacking the C-terminal non-core domain of RAG2 and ATM mutant mice develop thymic lymphomas harbouring recurrentTcra/d–Ightranslocations. Here the authors show that ATM and the non-core domain of RAG2 prevent bi-locus recombination by modulating higher-order chromatin structure.

Julie Chaumeil
Mariann Micsinai
Jane A. Skok
Research31 Jul 2013
Nature Communications

Volume: 4, P: 1-10
FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

Screening of cells transduced with a lentivirus library harboring nucleosome-free regions of mammalian genomes identifies cis elements that regulate transcription.

Matthew Murtha
Zeynep Tokcaer-Keskin
Lisa Dailey
Research23 Mar 2014
Nature Methods

Volume: 11, P: 559-565
Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function

Genetic, pharmacological and metabolomics experiments reveal that the malate–aspartate shuttle and mitochondrial citrate export support the differentiation of mouse T helper 1 cells, whereas succinate dehydrogenase enforces their terminal effector function.

Will Bailis
Justin A. Shyer
Richard A. Flavell
Research19 Jun 2019
Nature

Volume: 571, P: 403-407
m⁶A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways

The authors assess the role of N⁶-methyladenosine in T cell development and function, and show that RNA methylation controls T cell homeostasis by regulating IL-7-mediated STAT5 activation.

Hua-Bing Li
Jiyu Tong
Richard A. Flavell
Research09 Aug 2017
Nature

Volume: 548, P: 338-342
Nlrp9b inflammasome restricts rotavirus infection in intestinal epithelial cells

The inflammasome receptor Nlrp9b defends against enteric viruses by interacting with double-stranded viral RNA-bound helicase Dhx9, triggering gasdermin-D-dependent pyroptotic cell death of infected cells and secretion of Il-18.

Shu Zhu
Siyuan Ding
Richard A. Flavell
Research21 Jun 2017
Nature

Volume: 546, P: 667-670
Computation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome

Micha Sam Brickman Raredon
Junchen Yang
Laura E. Niklason
ResearchOpen Access09 Mar 2022
Scientific Reports

Volume: 12, P: 1-12
A tissue quality index: an intrinsic control for measurement of effects of preanalytical variables on FFPE tissue

Veronique M Neumeister
Fabio Parisi
David L Rimm
Research17 Feb 2014
Laboratory Investigation

Volume: 94, P: 467-474
cDNA microarray analysis of invasive and tumorigenic phenotypes in a breast cancer model

Harriet M Kluger
Yuval Kluger
Eva Sapi
Research19 Jan 2004
Laboratory Investigation

Volume: 84, P: 320-331
NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health

This Perspective lays out the impetus and goals of the Cellular Senescence Network established to comprehensively identify and characterize senescent cells (SnCs) across tissues and lifespan, providing a publicly available SnC atlas.

Patty J. Lee
Christopher C. Benz
Mingyu Yang
Reviews20 Dec 2022
Nature Aging

Volume: 2, P: 1090-1100
The single-cell opioid responses in the context of HIV (SCORCH) consortium

Seth A. Ament
Rianne R. Campbell
Hongkui Zeng
ReviewsOpen Access15 Jun 2024
Molecular Psychiatry

Volume: 29, P: 3950-3961
Insulin receptor alternative splicing is regulated by insulin signaling and modulates beta cell survival

Pushkar Malakar
Lital Chartarifsky
Rotem Karni
ResearchOpen Access16 Aug 2016
Scientific Reports

Volume: 6, P: 1-14
Preanalytical variables and phosphoepitope expression in FFPE tissue: quantitative epitope assessment after variable cold ischemic time

Maria Vassilakopoulou
Fabio Parisi
Veronique M Neumeister
Research24 Nov 2014
Laboratory Investigation

Volume: 95, P: 334-341

Search

Humoral determinants of checkpoint immunotherapy

Nerve-associated macrophages control adipose homeostasis across lifespan and restrain age-related inflammation

SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data

Gene trajectory inference for single-cell data by optimal transport metrics

Cluster-independent multiscale marker identification in single-cell RNA-seq data using localized marker detector (LMD)

Circulating tumor-reactive KIR⁺CD8⁺ T cells suppress anti-tumor immunity in patients with melanoma

Zero-preserving imputation of single-cell RNA-seq data

Author Correction: Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function

IL-10 constrains sphingolipid metabolism to limit inflammation

Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden

A highly efficient and faithful MDS patient-derived xenotransplantation model for pre-clinical studies

Spatial epigenome–transcriptome co-profiling of mammalian tissues

The age of bone marrow dictates the clonality of smooth muscle-derived cells in atherosclerotic plaques

Inflammasome activation in infected macrophages drives COVID-19 pathology

A humanized mouse model of chronic COVID-19

Paracrine orchestration of intestinal tumorigenesis by a mesenchymal niche

Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data

A Molecular Chipper technology for CRISPR sgRNA library generation and functional mapping of noncoding regions

Structural proteomics of an archaeon

The RAG2 C-terminus and ATM protect genome integrity by controlling antigen receptor gene cleavage

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function

m⁶A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways

Nlrp9b inflammasome restricts rotavirus infection in intestinal epithelial cells

Computation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome

A tissue quality index: an intrinsic control for measurement of effects of preanalytical variables on FFPE tissue

cDNA microarray analysis of invasive and tumorigenic phenotypes in a breast cancer model

NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health

The single-cell opioid responses in the context of HIV (SCORCH) consortium

Insulin receptor alternative splicing is regulated by insulin signaling and modulates beta cell survival

Preanalytical variables and phosphoepitope expression in FFPE tissue: quantitative epitope assessment after variable cold ischemic time

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