Updated reference panel improved imputation accuracy in East Asians to find population-specific association signals.

Nature Biotechnology - MultiVelo extends the concept of RNA velocity to multimodal single-cell measurements.

Nature Biotechnology - Visium spatial transcriptomics is combined with markers for more than 30 proteins.

A next step for cell atlases should be to chart perturbations in human model systems

Salcher et al. integrate non-small cell lung cancer (NSCLC) single-cell datasets, refine patient stratification, and reveal histological and genotypic associations with tumor microenvironment (TME)...

Nature Communications - Here the authors introduce a new method to study DNA in single cells by long-read sequencing. Their method gives a more complete view of the genomic structure of individual...

Nature - Temporarily disrupting epigenetic silencing causes flies to grow tumours.

Nature Genetics - Analysis of enhancer–promoter (E–P) interactions during Drosophila embryogenesis suggests that the relationship between E–P proximity and activity depends on the...

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

Nature Communications - Intratumoural heterogeneity in high-grade serous ovarian carcinoma (HGSOC) remains to be explored. Here, the authors perform spatial transcriptomics and reveal a high degree...

Nature Methods - This study presents a significance analysis framework for evaluating single-cell clusters. Application of the method detects cases of over-clustering in reported single-cell...

Nature - 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...

Nature Communications - Here, the authors apply the Activity-by-Contact (ABC) model to infer enhancer-gene regulation and the effect of associated variants across multiple cancer types, integrating...

Nature - The JAK2V617F mutation leads to epigenetic rewiring in a cell-intrinsic and cell-type-specific manner, influencing inflammation states and differentiation trajectories in patients with...

Nature Methods - Pretrained using over 33 million single-cell RNA-sequencing profiles, scGPT is a foundation model facilitating a broad spectrum of downstream single-cell analysis tasks by transfer...

Nature Genetics - SCENT is a nonparametric method that models association between chromatin accessibility and gene expression in single-cell multimodal datasets, enabling construction of...

Li et al. use single-cell and spatial sequencing to examine the cellular features of kidney tumors and classify cancer cells according to function. They find a more invasive phenotype at the interf...

Nature Genetics - Single-cell multiomic and functional characterization of human pancreatic islets identifies two beta cell subtypes correlated with type 2 diabetes progression that exhibit...

Nature Methods - Communication between cells is crucial for coordinated cellular functions in multicellular organisms. We present an optimal transport theory-based tool to infer cell–cell...

Jiang et al. use scRNA-seq and scATAC-seq to profile gene expression and chromatin accessibility in mouse embryos. By integrated analysis, they provide a cis-regulatory atlas and inferred spatially...

Nature Biotechnology - Single-cell nanobody-tethered transposition followed by sequencing (scNTT-seq) is a new assay that measures the genome-wide presence of multiple histone modifications and...

Nature - Combining single-cell RNA-sequencing with high-resolution multiplexed error-robust fluorescence in situ hybridization reveals in detail the cellular interactions and specialization of...

Nature Reviews Genetics - In this Review, the authors discuss our latest understanding of the spatial aspects of cancer evolution, including the roles of cancer subclonal structure, tissue...

Nature Biotechnology - Metabolites and RNA in a tissue section are profiled simultaneously.

Nature Cell Biology - Bravo González-Blas et al. uncover enhancer-gene regulatory networks underlying hepatocyte identity and their zonation state by combining single-cell and spatial...

A deep-learning model reveals the rules that define transcription initiation

Nature Methods - napari-imagej: ImageJ ecosystem access from napari

Nature - We present the ‘zebrafish single-cell atlas of perturbed embryos’, single-cell trancriptomic data of developing zebrafish embryos across various timepoints and with genetic...

Nature Communications - Sleep deprivation impacts molecular changes across brain regions. Here, the authors utilize a spatial. transcriptomics approach to elucidate acute sleep deprivation-induced...

Nature Genetics - Genomic, transcriptomic and epigenetic analyses of malignant pleural mesothelioma identify molecular axes and specialized tumor profiles underlying intertumoral heterogeneity.

Nature Biotechnology - The Iniquitate pipeline assessed the impacts of cell-type imbalance on single-cell RNA sequencing integration through perturbations to dataset balance. The results indicated...

Nature Genetics - Multi-omic analysis of single nuclei from 12 human placentas collected during early-stage and late-stage pregnancy characterizes syncytiotrophoblast diversity. Gene regulatory...

AbstractMotivation. Transcriptional dynamics are governed by the action of regulatory proteins and are fundamental to systems ranging from normal developme

Nature - A study identifies 41 consensus gene expression meta-programs that are coordinately upregulated in subpopulations of malignant cells across tumour types, providing a comprehensive picture...

Nature Communications - Oral squamous cell carcinoma is known to contain altered tumour cells within both the tumour core and leading edge. Here, the authors utilise spatial transcriptomics to...

Nature - An extensive global transcriptomics analysis of in vivo responses to 86 cytokines across more than 17 immune cell types reveals enormous complexity of cellular responses to cytokines,...

Nature Biotechnology - Chromatin accessibility profiles are spatially resolved in tissue sections.

Nature Medicine - This Perspective outlines how cell atlases can provide the missing links between genes, diseases and therapies, with advances already being made in several fields, including...

Nature - We present the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base...

Nature - We develop a high-throughput CRISPR screening system in cerebral organoids and identify vulnerable cell types and gene regulatory networks associated with autism spectrum disorder from...

Nature Genetics - A high-throughput reporter gene assay for use in living tissues has been developed. The assay allows investigators to quantify, in parallel, the activities of reporter genes in...

Nature Cell Biology - Sountoulidis et al. provide a spatial gene expression atlas of human embryonic lung during the first trimester of gestation and identify 83 cell identities corresponding to...

Nature Methods - The nanopore community is stepping toward a new frontier of single-molecule protein sequencing. Here, we offer our opinions on the unique potential for this emerging technology,...

Transcription factors directly bind repetitive sequences that need not resemble known motifs.

Technologies called transcriptomics that study sets of RNA within organisms enable scientists to understand what each cell does. However, the question of how particular genes work within a solo cell,...

FucoID is a platform that can be used to discover and quantify cell-cell interactions mediated by diverse molecular pairs.

Nature Communications - Spatial genomics offers insights into cellular interactions within tissues. Here, the authors develop barcoded multiple displacement amplification, achieving high-coverage...

Nature Communications - Most RNA velocity models extract dynamics from the phase delay between unspliced and spliced mRNA for each gene. Here, authors propose TFvelo, broadening RNA velocity beyond...

Nature Communications - Qu et al. present a detailed three-dimensional spatial transcriptome atlas of all major organs in the mouse embryo at E13.5, providing a better understanding of organ...

Nature Biotechnology - We have designed a method, binding affinities to native chromatin by sequencing (BANC-seq), to determine the transcription factor concentrations required for binding to...

Nature Methods - SATURN performs cross-species integration and analysis using both single-cell gene expression and protein representations generated by protein language models.

Nature - Pretraining on a large data set gives model insight into how genes interact.

Nature - A study reports single-cell RNA-sequencing profiles for more than 1.6 million cell nuclei from 101 whole mouse embryos including 22 mutant and 4 wild-type genotypes, from one experiment.

Nature Biotechnology - Annotation transfer from reference to new datasets is improved with a probabilistic approach.

(Cell Reports 35, 109286; June 22, 2021)

Spatially resolved scRNA-seq deconvolutes positional and cell type-specific components of cell identity in the mouse limb bud.

Nature Genetics - A single-cell massively parallel reporter assay is used to compare cis-regulatory sequence activities in cell line models and mouse retinal tissue ex vivo, identifying cell state-...

Deshpande, Loth, et al. present SpaceMarkers as an algorithm to identify molecular changes resulting from cell-cell interactions using latent space analysis of spatial transcriptomics. SpaceMarkers...

Nature Biotechnology - Single-cell data from RNA-seq, chromatin accessibility, DNA methylation and other modalities can be readily integrated using two new methods.

Nature Genetics - Single-nucleus RNA sequencing from the dorsolateral prefrontal cortex of 424 aging individuals, and mapping the effect of genetic variation on gene expression, identified a large...

Nature Protocols - This tutorial outlines common strategies for analysis of bulk RNA-sequencing (RNA-seq) data in the context of tumor immunity and immunotherapy response and presents a...

Xu et al. develop an interpretable deep learning framework (termed NETTAG) to identify Alzheimer’s disease (AD) risk genes and drug targets through leveraging GWAS, multimodal genomics, and human...

Nature Reviews Genetics - Regulatory circuits of gene expression can be represented as gene regulatory networks (GRNs) that are useful to understand cellular identity and disease. Here, the authors...

Single-cell RNA-sequencing (scRNA-seq) measures gene expression in single cells, while single-nucleus ATAC-sequencing (snATAC-seq) quantifies chromatin accessibility in single nuclei. These two data...

Nature Genetics - Multiomic analysis of cervical squamous cell carcinoma identifies distinct cellular ecosystems characterized by immune cell infiltration, heterotypic signaling and patient outcomes.

Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods, together with associated computational tools and the growing availability of public data resources, are transf...

Nature Biotechnology - Cell–cell communication pathways are dissected at the level of individual cells.

Nature Methods - This Review provides an overview of bioinformatic approaches that enable immune repertoire analyses at the single-cell level.

Nature Reviews Genetics - In this Review, the authors discuss the latest advances in profiling multiple molecular modalities from single cells, including genomic, transcriptomic, epigenomic and...

Nature Methods - By learning to embed DNA k-mers and cells into a joint space, CellSpace improves single-cell ATAC-seq analysis in multiple tasks such as latent structure discovery, transcription...

Zeng et al. illustrate the transcriptional profiles and spatial organization of different cell types during human gastrulation and early nervous system development. They reveal the spatial patterning...

Bibby et al. develop a single-cell pathway analysis tool that assesses changes in multivariate distributions of pathways. They apply it to characterize pathways that are critical for human T cell...

Nature Communications - Researchers used single-nucleus RNA and ATAC sequencing to create an atlas of skeletal muscle development. They identified the gene programs and transcription factors that...

Nature Communications - Alzheimer’s disease genetic risk is enriched in glial genes. Here, the authors derive cell-type-specific polygenic risk scores and link astrocytic genes with Aβ,...

Nature Methods - Recently proposed computational approaches explore casual links between chromatin and transcriptional changes that are provided by single-cell multimodal sequencing to bridge the...

Nature - A multiomics single-cell atlas of the human maternal–fetal interface including the myometrium, combining spatial transcriptomics data with chromatin accessibility, provides a...

Nature Protocols - This protocol presents an optimized version of the single-cell combinatorial indexing RNA sequencing protocol that is faster, less expensive and suitable for profiling tissues...

IKAROS mediates long-distance interactions both within and across domains and compartments to assemble a lineage-specific 3D genome organization required for immune cell development and function.

Nature Genetics - As part of the enhanced GTEx (eGTEx) project, 987 human samples from 9 tissue types and 424 donors are assayed using DNA methylation microarrays. Colocalization of GWAS variants,...

Nature Biotechnology - Single-cell, multiomic datasets are integrated using dimensionality reduction, imputation and batch correction.

Nature Genetics - Brain expression quantitative trait locus (eQTL) and network analyses encompassing 8,613 RNA-sequencing samples from 14 eQTL datasets reveal downstream effects and putative...

Nature Genetics - Single-cell analyses of immune cells from patients with pathogenic, single large-scale mitochondrial DNA (mtDNA) deletions including Pearson syndrome describe heteroplasmy...

Nature Genetics - Single-cell RNA- and ATAC-seq analysis of human scalp biopsies characterizes the regulatory programs of heterogeneous cell types. Integration with genome-wide association studies...

An intercellular genetic technology monitors cell-cell contact and traces cell contact histories by permanently marking contact between cells.

Nature Medicine - Single-cell multi-omic analysis of 300,000 cells from 29 patients representing peripheral immune cells and colon mucosal immune, epithelial and mesenchymal cells reveals crosstalk...