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This study maps chromatin accessibility at single-cell resolution in rice and related grasses, revealing how regulatory DNA elements evolve across cell types and species and identifying potential silencers that control gene expression.

Current developmental brain atlases are limited in the number of stages they represent. Here authors generate the Developmental Mouse Brain Atlas, a 4D atlas representing every postnatal day from 4 to 56.

Zhao et al. used single-cell and spatial multiomics data analysis of human and mouse lung adenocarcinoma tumors and cell lines to reveal TP53 mutation-associated changes in cancer cells and their microenvironment.

The authors introduce the Neurolipid Atlas, a dynamic resource for the community to gain insight into lipid alterations in neurodegenerative disease, and they leverage the platform to show how cholesterol alterations in astrocytes can dysregulate neuroinflammatory pathways in Alzheimer disease.

This study introduces the Cattle Cell Atlas, a single-cell expression resource including 1,793,854 cells from 59 tissues. Integrative analyses leveraging this atlas provide insights into the biology underlying bovine monogenic and complex traits.

Non-covalent interactions are very diverse, and they are generally difficult to investigate through experimental methods. Here tailored metal–organic frameworks serve as a platform for the systematic generation of a variety of non-covalent interactions, which can be studied through the electric fields produced by the charges and dipoles involved in the interactions.

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.

Steele et al. use single-cell RNA sequencing and spatial transcriptomics to provide an atlas of adult human skin fibroblasts in healthy and diseased human skin.

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.

The cause of abnormal alveolar regeneration in idiopathic pulmonary fibrosis is unknown. Here, the authors generated a temporo-spatial cellular map of the regenerating niche and, using unbiased mathematical methods, identified a spatial interaction between a subset of macrophages and aberrant alveolar epithelial cells across all stages of the disease.

ATLAS is a tool for circuit tracing, demonstrated here in rodents. It allows anterograde transsynaptic tracing, starting from genetically defined neurons.

The Biodiversity Cell Atlas aims to create comprehensive single-cell molecular atlases across the eukaryotic tree of life, which will be phylogenetically informed, rely on high-quality genomes and use shared standards to facilitate comparisons across species.

GIANT, a genetically informed brain atlas, integrates genetic heritability with neuroanatomy. It shows strong neuroanatomical validity and surpasses traditional atlases in discovery power for brain imaging genomics.

In patients with advanced cancer, the development of brain metastasis (BM) often signals a worsening prognosis with limited therapeutic options. Here, the authors assemble a large, open-source neuroimaging dataset of BM and perform spatial and morphological analysis which they use to develop a framework for function-sparing brain radiotherapy design.

This study presents an ultradeep analysis of the N-glycoproteome in mouse tissues, establishing the largest dataset to date. The resource enhances AI models for glycopeptide prediction, provides insights into tissue-specific glycosylation patterns, and reveals distinct pathological signatures in neurodegenerative diseases. To facilitate access to mouse and human N-glycoproteome, the authors establish a comprehensive database resource N-GlycoMiner.

This study presents an extensive single-nucleus and spatial transcriptomic atlas of the Arabidopsis life cycle that represents ten distinct developmental time points inclusive of six diverse organs.

Alatrakchi and colleagues profile immune cells from liver and blood obtained from patients with MASLD/MASH using single-cell sequencing. They note increased immunoregulatory programs that correlated with increased fibrogenesis and disease progression.

The human endoderm-derived organoid cell atlas (HEOCA) presents an integrative analysis of single-cell transcriptomes across different conditions, sources and protocols. It compares cell types and states between models, and harmonizes cell annotations through mapping to primary tissues.

Adult zebrafish possess the ability to regenerate injured hearts through a complex orchestration of molecular and cellular activities. Here, the authors present a single cell and spatially-resolved atlas of the regenerating zebrafish heart, which serves as a valuable resource for research on heart regeneration.

The connection between plasma proteomic and brain structure remains unclear. Here, the authors establish a comprehensive atlas of the patterns of associations between microscale proteome and brain structure, and demonstrate their potential value for studying brain disorders.

MicroRNAs regulate brain development and aging. Here, authors show that a spatio-temporal atlas of 15 mouse brain regions reveals sex- and region-specific microRNA patterns, including age-related microglial miR-155-5p increase targeting mTOR.

It has been proposed that language meaning is represented throughout the cerebral cortex in a distributed ‘semantic system’, but little is known about the details of this network; here, voxel-wise modelling of functional MRI data collected while subjects listened to natural stories is used to create a detailed atlas that maps representations of word meaning in the human brain.

Salmonella is a major cause of foodborne disease worldwide. Authors created a Salmonella database and present a genetic atlas of antimicrobial resistance, identifying some socioeconomic and environmental drivers for the rise of resistance globally.

Metabolic, immune and endocrine systems undergo seasonal changes in animals. Here the authors report the seasonal transcriptome of 80 tissues collected over 1 year from male and female rhesus macaques as well as sex differences in seasonally oscillating genes.

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.

The topographical organization of cells in the hippocampus reflects its ability to regulate mood and cognition. Here the authors generate a spatially resolved gene expression map in the human hippocampus to enable cross-species and functional interpretation.

Here they generate a cell type atlas of the colonial cnidarian Hydractinia symbiolongicarpus, which reveals that distinct colony parts are mostly made from unique combinations of shared cell types, and identify novel cell types involved in biomineralization, and self/non-self recognition.

Neurodegenerative diseases are linked to changes in the immune system and inflammation. Here, the authors studied immune cells from healthy individuals and neurodegenerative diseases and identified sex-specific disease-associated changes.

Shen et al. report a method for multiplexing isogenic iPSCs for single-cell RNA-seq. With it, they created an atlas of in vitro differentiation and identified TMEM88 as a regulator of cardiovascular development, impacting blood pressure in adult mice.

META-SiM brings foundation model power to single-molecule time traces, excelling across diverse analysis tasks. Paired with the web-based META-SiM Projector and entropy mapping, it rapidly reveals hidden molecular behaviors inaccessible by other means.

A cross-sectional study from four African countries shows the importance of investigating the gut microbiome in previously under-represented populations and provides a framework for equitable microbiome research.

Sydnor et al. developed a new tractography atlas of thalamocortical structural connections and applied it to three youth samples. They uncovered coordinated development between thalamic connectivity and hierarchical cortical plasticity in humans.

Brain gene regulation is key for neuropsychiatric disorders. Here, the authors show that profiling gene expression and chromatin states in 25 brain regions enables enhancer-promoter mapping at isoform resolution, improving genetic fine-mapping.

Single-cell transcriptomics of human lung tissue from individuals with tuberculosis identifies signatures of inflammation, apoptosis and senescence affecting immune, epithelial and endothelial cells linked with long-term pulmonary impairment.

A quantitative morphological framework for the human thymus reveals the establishment of the lobular cytokine network, canonical thymocyte trajectories and thymic epithelial cell distributions in fetal and paediatric thymic development.

A human neural organoid cell atlas integrating 36 single-cell transcriptomic datasets shows cell types and states and estimates transcriptomic similarity between primary and organoid counterparts, showing potential to assess organoid fidelity and facilitate protocol development.

Tan and colleagues conducted a single-cell multiomic analysis of T cell acute lymphoblastic leukemia and identified a treatment-resistant subpopulation of bone marrow progenitor-like blasts associated with poor outcomes.

Entanglement was observed in top–antitop quark events by the ATLAS experiment produced at the Large Hadron Collider at CERN using a proton–proton collision dataset with a centre-of-mass energy of √s  = 13 TeV and an integrated luminosity of 140 fb⁻¹.

This isoform-centric microglia genomic atlas includes 35,879 novel human microglia isoforms identified by long-read RNA sequencing. A multi-ancestry quantitative trait locus meta-analysis of known and novel isoforms in 555 samples from 391 donors finds associations with genetic risk loci in Alzheimer’s and Parkinson’s diseases.

The affected cellular populations during Alzheimer’s disease progression remain understudied. Here the authors use a cohort of 84 donors, quantitative neuropathology and multimodal datasets from the BRAIN Initiative. Their pseudoprogression analysis revealed two disease phases.

Single cell sequencing can be used to examine tumour associated macrophages (TAM) and comparison between studies has been a challenge. Here the authors show a comparison tool to compare and contrast TAMs from different human tumour types and how these cells associate with T cells exploring further macrophage heterogeneity.

In this Review, Roden and co-workers describe how multiplexed assays of variant effects can be used for high-throughput functional assessment of nearly all coding variants in a target sequence to improve variant annotation for cardiovascular-related genes and to resolve the problem of classification as variants of uncertain significance. They also discuss how variant effect predictors can be integrated with multiplexed methods to inform cardiovascular genomic medicine.

This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells.

A modeling approach to assess the global risk of Plasmodium falciparum histidine-rich protein 2 and 3 gene deletions identifies ten priority African countries for surveillance and could inform malaria control policies.

The Human Microglia Atlas includes 91,716 brain immune cells covering six neurologic pathologies. It characterizes the signatures of nine populations and describes the expansion of GPNMB-high microglia in Multiple Sclerosis and Alzheimer’s Disease.

Here, using human liver chimeric mice, the authors describe perturbation of the diurnal transcriptome and epigenome of human hepatocytes during hepatitis C virus infection, affecting pathways mediating metabolic alterations, fibrosis, and cancer, and further show that the pathways remain affected in patients with advanced liver disease.

A multi-modal analysis of pre-metastatic liver biopsies from patients with localized pancreatic cancer with a minimum of 3 years of follow-up shows that immunological, proliferative and metabolomic features distinguish patients who develop metastases from disease-free survivors and can be used to predict outcomes.

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.

A Stereo-seq and scRNA-seq atlas of mouse liver in homeostasis and regeneration after partial hepatectomy identifies zonated genes, pathways, cell–cell interactions and gene regulatory networks. Functional validation finds that cooperation between TBL1XR1 and β-catenin activates hepatocyte proliferation.