- Home
- Publications
- Publication Search
- Publication Details
Title
Methods and applications for single-cell and spatial multi-omics
Authors
Keywords
-
Journal
NATURE REVIEWS GENETICS
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2023-03-02
DOI
10.1038/s41576-023-00580-2
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- scONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors
- (2023) Lei Yu et al. Science Advances
- Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
- (2022) Martin Guilliams et al. CELL
- Seven technologies to watch in 2022
- (2022) Michael Eisenstein NATURE
- Cell2location maps fine-grained cell types in spatial transcriptomics
- (2022) Vitalii Kleshchevnikov et al. NATURE BIOTECHNOLOGY
- Squidpy: a scalable framework for spatial omics analysis
- (2022) Giovanni Palla et al. NATURE METHODS
- Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO
- (2022) Britta Velten et al. NATURE METHODS
- Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level
- (2022) Yanxiang Deng et al. SCIENCE
- SM-Omics is an automated platform for high-throughput spatial multi-omics
- (2022) S. Vickovic et al. Nature Communications
- Advances in MALDI Mass Spectrometry Imaging Single Cell and Tissues
- (2022) Xiaoping Zhu et al. Frontiers in Chemistry
- Recent advances in single-cell sequencing technologies
- (2022) Lu Wen et al. Precision Clinical Medicine
- Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
- (2022) Ao Chen et al. CELL
- Single-cell profiling of transcriptome and histone modifications with EpiDamID
- (2022) Franka J. Rang et al. MOLECULAR CELL
- Somatic genomic changes in single Alzheimer’s disease neurons
- (2022) Michael B. Miller et al. NATURE
- Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro
- (2022) Bingjie Zhang et al. NATURE BIOTECHNOLOGY
- Integrative spatial analysis of cell morphologies and transcriptional states with MUSE
- (2022) Feng Bao et al. NATURE BIOTECHNOLOGY
- Museum of spatial transcriptomics
- (2022) Lambda Moses et al. NATURE METHODS
- Alignment and integration of spatial transcriptomics data
- (2022) Ron Zeira et al. NATURE METHODS
- NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells
- (2022) Amy F. Chen et al. NATURE METHODS
- Single-cell atlases: shared and tissue-specific cell types across human organs
- (2022) Rasa Elmentaite et al. NATURE REVIEWS GENETICS
- Genetic mosaicism in the human brain: from lineage tracing to neuropsychiatric disorders
- (2022) Sara Bizzotto et al. NATURE REVIEWS NEUROSCIENCE
- CRISPR/Cas gene editing in the human germline
- (2022) B. Bekaert et al. SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
- Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma
- (2022) Vidhya M. Ravi et al. CANCER CELL
- Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq
- (2022) Joseph M. Replogle et al. CELL
- Unbiased spatial proteomics with single-cell resolution in tissues
- (2022) Andreas Mund et al. MOLECULAR CELL
- Live-seq enables temporal transcriptomic recording of single cells
- (2022) Wanze Chen et al. NATURE
- Spatial profiling of chromatin accessibility in mouse and human tissues
- (2022) Yanxiang Deng et al. NATURE
- Recording gene expression order in DNA by CRISPR addition of retron barcodes
- (2022) Santi Bhattarai-Kline et al. NATURE
- A time-resolved, multi-symbol molecular recorder via sequential genome editing
- (2022) Junhong Choi et al. NATURE
- The emerging landscape of spatial profiling technologies
- (2022) Jeffrey R. Moffitt et al. NATURE REVIEWS GENETICS
- Characterizing cis-regulatory elements using single-cell epigenomics
- (2022) Sebastian Preissl et al. NATURE REVIEWS GENETICS
- The era of 3D and spatial genomics
- (2022) Britta A.M. Bouwman et al. TRENDS IN GENETICS
- scPCOR-seq enables co-profiling of chromatin occupancy and RNAs in single cells
- (2022) Lixia Pan et al. Communications Biology
- High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging
- (2022) Shanshan He et al. NATURE BIOTECHNOLOGY
- ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells
- (2022) Wei Xu et al. NATURE METHODS
- Cell competition in development, homeostasis and cancer
- (2022) Sanne M. van Neerven et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation
- (2022) Wenqi Hu et al. Nature Communications
- Computational Methods for Single-cell Multi-omics Integration and Alignment
- (2022) Stefan Stanojevic et al. GENOMICS PROTEOMICS & BIOINFORMATICS
- Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing
- (2022) Jonathan Liu et al. Life Science Alliance
- Multi-domain translation between single-cell imaging and sequencing data using autoencoders
- (2021) Karren Dai Yang et al. Nature Communications
- Removal of optimal cutting temperature (O.C.T.) compound from embedded tissue for MALDI imaging of lipids
- (2021) Jacob X. M. Truong et al. ANALYTICAL AND BIOANALYTICAL CHEMISTRY
- Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics
- (2021) Michael J. Taylor et al. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
- Highly Multiplexed Immunohistochemical MALDI-MS Imaging of Biomarkers in Tissues
- (2021) Gargey Yagnik et al. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
- Integrated spatial genomics reveals global architecture of single nuclei
- (2021) Yodai Takei et al. NATURE
- ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
- (2021) Jeffrey M. Granja et al. NATURE GENETICS
- Joint profiling of histone modifications and transcriptome in single cells from mouse brain
- (2021) Chenxu Zhu et al. NATURE METHODS
- SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes
- (2021) Marc Elosua-Bayes et al. NUCLEIC ACIDS RESEARCH
- Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems
- (2021) Shahar Alon et al. SCIENCE
- Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos
- (2021) Yang Wang et al. Nature Communications
- Decoding dynamic epigenetic landscapes in human oocytes using single-cell multi-omics sequencing
- (2021) Rui Yan et al. Cell Stem Cell
- Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens
- (2021) Noa Liscovitch-Brauer et al. NATURE BIOTECHNOLOGY
- Computational principles and challenges in single-cell data integration
- (2021) Ricard Argelaguet et al. NATURE BIOTECHNOLOGY
- Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions
- (2021) Haiqing Xiong et al. NATURE METHODS
- BABEL enables cross-modality translation between multiomic profiles at single-cell resolution
- (2021) Kevin E. Wu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq
- (2021) Elliott Swanson et al. eLife
- Integrated analysis of multimodal single-cell data
- (2021) Yuhan Hao et al. CELL
- Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA
- (2021) Romualdas Vaisvila et al. GENOME RESEARCH
- Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells
- (2021) Eleni P. Mimitou et al. NATURE BIOTECHNOLOGY
- Smart-RRBS for single-cell methylome and transcriptome analysis
- (2021) Hongcang Gu et al. Nature Protocols
- CODEX multiplexed tissue imaging with DNA-conjugated antibodies
- (2021) Sarah Black et al. Nature Protocols
- Intricacies of single-cell multi-omics data integration
- (2021) Pia Rautenstrauch et al. TRENDS IN GENETICS
- High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer
- (2021) Sarah E. Pierce et al. Nature Communications
- A combined approach for single-cell mRNA and intracellular protein expression analysis
- (2021) Johan Reimegård et al. Communications Biology
- Simultaneous profiling of multiple chromatin proteins in the same cells
- (2021) Sneha Gopalan et al. MOLECULAR CELL
- Super-resolved spatial transcriptomics by deep data fusion
- (2021) Ludvig Bergenstråhle et al. NATURE BIOTECHNOLOGY
- Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin
- (2021) Martina Tedesco et al. NATURE BIOTECHNOLOGY
- Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC
- (2021) Evgenij Fiskin et al. NATURE BIOTECHNOLOGY
- Benchmarking atlas-level data integration in single-cell genomics
- (2021) Malte D. Luecken et al. NATURE METHODS
- Joint single-cell measurements of nuclear proteins and RNA in vivo
- (2021) Hattie Chung et al. NATURE METHODS
- Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram
- (2021) Tommaso Biancalani et al. NATURE METHODS
- Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2)
- (2021) Nongluk Plongthongkum et al. Nature Protocols
- Integrated spatial multiomics reveals fibroblast fate during tissue repair
- (2021) Deshka S. Foster et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Joint single-cell multiomic analysis in Wnt3a induced asymmetric stem cell division
- (2021) Zhongxing Sun et al. Nature Communications
- Computational methods for single-cell omics across modalities
- (2020) Mirjana Efremova et al. NATURE METHODS
- Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
- (2020) Anna S. E. Cuomo et al. Nature Communications
- Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration
- (2020) Michaela Asp et al. BIOESSAYS
- N6-methyladenine is incorporated into mammalian genome by DNA polymerase
- (2020) Xiaoling Liu et al. CELL RESEARCH
- Multiplex digital spatial profiling of proteins and RNA in fixed tissue
- (2020) Christopher R. Merritt et al. NATURE BIOTECHNOLOGY
- Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
- (2020) Qiao Rui Xing et al. GENOME RESEARCH
- 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing
- (2020) Huy Q. Nguyen et al. NATURE METHODS
- Single-molecule regulatory architectures captured by chromatin fiber sequencing
- (2020) Andrew B. Stergachis et al. SCIENCE
- Uncovering an Organ’s Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics
- (2020) Jie Liao et al. TRENDS IN BIOTECHNOLOGY
- Multiplexed imaging of nucleome architectures in single cells of mammalian tissue
- (2020) Miao Liu et al. Nature Communications
- Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin
- (2020) Sai Ma et al. CELL
- Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin
- (2020) Jun-Han Su et al. CELL
- A Highly Scalable Method for Joint Whole-Genome Sequencing and Gene-Expression Profiling of Single Cells
- (2020) Vasilios Zachariadis et al. MOLECULAR CELL
- Jointly defining cell types from multiple single-cell datasets using LIGER
- (2020) Jialin Liu et al. Nature Protocols
- Somatic mutations in neurodegeneration: An update
- (2020) Christos Proukakis NEUROBIOLOGY OF DISEASE
- High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue
- (2020) Yang Liu et al. CELL
- A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens
- (2019) Molly Gasperini et al. CELL
- Spatial proteomics: a powerful discovery tool for cell biology
- (2019) Emma Lundberg et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells
- (2019) Jan. P. Gerlach et al. Scientific Reports
- Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity
- (2019) Longqi Liu et al. Nature Communications
- Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution
- (2019) Samuel G. Rodriques et al. SCIENCE
- Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution
- (2019) Yibin Liu et al. NATURE BIOTECHNOLOGY
- Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+
- (2019) Chee-Huat Linus Eng et al. NATURE
- Visualizing DNA folding and RNA in embryos at single-cell resolution
- (2019) Leslie J. Mateo et al. NATURE
- Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing
- (2019) Alba Rodriguez-Meira et al. MOLECULAR CELL
- Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms
- (2019) Andrés M. Cardozo Gizzi et al. MOLECULAR CELL
- A guide to visualizing the spatial epigenome with super‐resolution microscopy
- (2019) Jianquan Xu et al. FEBS Journal
- Genome–lamina interactions are established de novo in the early mouse embryo
- (2019) Máté Borsos et al. NATURE
- Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells
- (2019) Eleni P. Mimitou et al. NATURE METHODS
- Comprehensive Integration of Single-Cell Data
- (2019) Tim Stuart et al. CELL
- Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity
- (2019) Joshua D. Welch et al. CELL
- Simultaneous quantification of protein–DNA contacts and transcriptomes in single cells
- (2019) Koos Rooijers et al. NATURE BIOTECHNOLOGY
- High-Throughput Single-Cell Sequencing with Linear Amplification
- (2019) Yi Yin et al. MOLECULAR CELL
- Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues
- (2019) Sinem K. Saka et al. NATURE BIOTECHNOLOGY
- Simultaneous profiling of 3D genome structure and DNA methylation in single human cells
- (2019) Dong-Sung Lee et al. NATURE METHODS
- High-definition spatial transcriptomics for in situ tissue profiling
- (2019) Sanja Vickovic et al. NATURE METHODS
- Joint profiling of DNA methylation and chromatin architecture in single cells
- (2019) Guoqiang Li et al. NATURE METHODS
- Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression
- (2019) Chenglong Xia et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Exploring genetic interaction manifolds constructed from rich single-cell phenotypes
- (2019) Thomas M. Norman et al. SCIENCE
- High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell
- (2019) Song Chen et al. NATURE BIOTECHNOLOGY
- An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome
- (2019) Chenxu Zhu et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Multi-omics profiling of mouse gastrulation at single-cell resolution
- (2019) Ricard Argelaguet et al. NATURE
- Toward Minimal Residual Disease-Directed Therapy in Melanoma
- (2018) Florian Rambow et al. CELL
- Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH
- (2018) Sheel Shah et al. CELL
- Single-cell multi-omics sequencing of human early embryos
- (2018) Lin Li et al. NATURE CELL BIOLOGY
- Exponential scaling of single-cell RNA-seq in the past decade
- (2018) Valentine Svensson et al. Nature Protocols
- Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation
- (2018) Jonathan Packer et al. TRENDS IN GENETICS
- scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells
- (2018) Stephen J. Clark et al. Nature Communications
- Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy
- (2018) Guiping Wang et al. Scientific Reports
- CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
- (2018) Gabriel N Aughey et al. eLife
- DNA-based memory devices for recording cellular events
- (2018) Ravi U. Sheth et al. NATURE REVIEWS GENETICS
- Joint profiling of chromatin accessibility and gene expression in thousands of single cells
- (2018) Junyue Cao et al. SCIENCE
- Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks
- (2018) Adam J. Rubin et al. CELL
- Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
- (2018) Chan Gu et al. CELL RESEARCH
- A test metric for assessing single-cell RNA-seq batch correction
- (2018) Maren Büttner et al. NATURE METHODS
- Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections
- (2018) Fredrik Salmén et al. Nature Protocols
- Single-cell multiomics sequencing and analyses of human colorectal cancer
- (2018) Shuhui Bian et al. SCIENCE
- SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells
- (2017) Kyung Yeon Han et al. GENOME RESEARCH
- Genome editing reveals a role for OCT4 in human embryogenesis
- (2017) Norah M. E. Fogarty et al. NATURE
- Multiplexed quantification of proteins and transcripts in single cells
- (2017) Vanessa M Peterson et al. NATURE BIOTECHNOLOGY
- SCENIC: single-cell regulatory network inference and clustering
- (2017) Sara Aibar et al. NATURE METHODS
- Simultaneous epitope and transcriptome measurement in single cells
- (2017) Marlon Stoeckius et al. NATURE METHODS
- Pooled CRISPR screening with single-cell transcriptome readout
- (2017) Paul Datlinger et al. NATURE METHODS
- seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus
- (2017) Sheel Shah et al. NEURON
- Complete sequence-based pathway analysis by differential on-chip DNA and RNA extraction from a single cell
- (2017) D. van Strijp et al. Scientific Reports
- The Human Cell Atlas
- (2017) Aviv Regev et al. eLife
- Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells
- (2017) Sebastian Pott eLife
- Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq
- (2016) Diego Adhemar Jaitin et al. CELL
- Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens
- (2016) Atray Dixit et al. CELL
- Single-cell triple omics sequencing reveals genetic, epigenetic and transcriptomic heterogeneity in hepatocellular carcinomas
- (2016) Yu Hou et al. CELL RESEARCH
- Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity
- (2016) Christof Angermueller et al. NATURE METHODS
- Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq
- (2016) Iain C Macaulay et al. Nature Protocols
- Single-cell genome sequencing: current state of the science
- (2016) Charles Gawad et al. NATURE REVIEWS GENETICS
- Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
- (2016) P. L. Stahl et al. SCIENCE
- Design and Analysis of Single-Cell Sequencing Experiments
- (2015) Dominic Grün et al. CELL
- The Technology and Biology of Single-Cell RNA Sequencing
- (2015) Aleksandra A. Kolodziejczyk et al. MOLECULAR CELL
- Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles
- (2015) Wenge Li et al. MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS
- Integrated genome and transcriptome sequencing of the same cell
- (2015) Siddharth S Dey et al. NATURE BIOTECHNOLOGY
- G&T-seq: parallel sequencing of single-cell genomes and transcriptomes
- (2015) Iain C Macaulay et al. NATURE METHODS
- Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues
- (2015) Je Hyuk Lee et al. Nature Protocols
- Spatially resolved, highly multiplexed RNA profiling in single cells
- (2015) K. H. Chen et al. SCIENCE
- BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
- (2015) Catalina A. Vallejos et al. PLoS Computational Biology
- Full-length RNA-seq from single cells using Smart-seq2
- (2014) Simone Picelli et al. Nature Protocols
- Highly Multiplexed Subcellular RNA Sequencing in Situ
- (2014) J. H. Lee et al. SCIENCE
- Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform
- (2014) Lin Han et al. Scientific Reports
- Single Cell Genomics: Advances and Future Perspectives
- (2014) Iain C. Macaulay et al. PLoS Genetics
- In situ sequencing for RNA analysis in preserved tissue and cells
- (2013) Rongqin Ke et al. NATURE METHODS
- RNAscope
- (2011) Fay Wang et al. JOURNAL OF MOLECULAR DIAGNOSTICS
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreFind the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
Search