Defining Cell Identity with Single-Cell Omics

Comprehensive chromosomal and mitochondrial copy number profiling in human IVF embryos

(2018) Wei Shang et al.   REPRODUCTIVE BIOMEDICINE ONLINE

Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer

(2017) Marco L. Leung et al.   GENOME RESEARCH

Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types

(2017) Santiago J. Carmona et al.   GENOME RESEARCH

InDrops and Drop-seq technologies for single-cell sequencing

(2017) Allon M. Klein et al.   LAB ON A CHIP

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

The Human Cell Atlas: from vision to reality

(2017) Orit Rozenblatt-Rosen et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding

(2017) Freeman Lan et al.   NATURE BIOTECHNOLOGY

Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia

(2017) Alice Giustacchini et al.   NATURE MEDICINE

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Sequencing thousands of single-cell genomes with combinatorial indexing

(2017) Sarah A Vitak et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

The trajectory of microbial single-cell sequencing

(2017) Tanja Woyke et al.   NATURE METHODS

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs

(2017) Ashley D Sanders et al.   Nature Protocols

Genome-wide mapping of DNase I hypersensitive sites in rare cell populations using single-cell DNase sequencing

(2017) James Cooper et al.   Nature Protocols

Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices

(2017) Sanjay M. Prakadan et al.   NATURE REVIEWS GENETICS

Comparison of whole genome amplification techniques for human single cell exome sequencing

(2017) Erik Borgström et al.   PLoS One

Ultraaccurate genome sequencing and haplotyping of single human cells

(2017) Wai Keung Chu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Single-cell epigenomics: Recording the past and predicting the future

(2017) Gavin Kelsey et al.   SCIENCE

Single-Cell Multiomics: Multiple Measurements from Single Cells

(2017) Iain C. Macaulay et al.   TRENDS IN GENETICS

Plant Systems Biology at the Single-Cell Level

(2017) Marc Libault et al.   TRENDS IN PLANT SCIENCE

Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer

(2017) Ruli Gao et al.   Nature Communications

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles

(2017) Ramunas Stepanauskas et al.   Nature Communications

Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment

(2017) Kristina Kirschner et al.   Cell Reports

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

(2017) Hisham Mohammed et al.   Cell Reports

Dissecting the human microbiome with single-cell genomics

(2017) Andrew C. Tolonen et al.   Genome Medicine

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

Heterogeneity in Pure Microbial Systems: Experimental Measurements and Modeling

(2017) Rebeca González-Cabaleiro et al.   Frontiers in Microbiology

Sequencing of Single Pollen Nuclei Reveals Meiotic Recombination Events at Megabase Resolution and Circumvents Segregation Distortion Caused by Postmeiotic Processes

(2017) Steven Dreissig et al.   Frontiers in Plant Science

Single-cell multiplexed cytokine profiling of CD19 CAR-T cells reveals a diverse landscape of polyfunctional antigen-specific response

(2017) Qiong Xue et al.   Journal for ImmunoTherapy of Cancer

Subcellular western blotting of single cells

(2017) Kevin A. Yamauchi et al.   Microsystems & Nanoengineering

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

(2017) Payam Shahi et al.   Scientific Reports

STRT-seq-2i: dual-index 5ʹ single cell and nucleus RNA-seq on an addressable microwell array

(2017) Hannah Hochgerner et al.   Scientific Reports

Single-Cell, Multiplexed Protein Detection of Rare Tumor Cells Based on a Beads-on-Barcode Antibody Microarray

(2016) Liu Yang et al.   ANALYTICAL CHEMISTRY

Single Cell Proteomics Using Frog (Xenopus laevis) Blastomeres Isolated from Early Stage Embryos, Which Form a Geometric Progression in Protein Content

(2016) Liangliang Sun et al.   ANALYTICAL CHEMISTRY

Single-Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16-Cell Frog (Xenopus ) Embryo

(2016) Camille Lombard-Banek et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos

(2016) Mubeen Goolam et al.   CELL

Single-cell triple omics sequencing reveals genetic, epigenetic and transcriptomic heterogeneity in hepatocellular carcinomas

(2016) Yu Hou et al.   CELL RESEARCH

Supramolecular Probes for Assessing Glutamine Uptake Enable Semi-Quantitative Metabolic Models in Single Cells

(2016) Min Xue et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction

(2016) Dylan Mooijman et al.   NATURE BIOTECHNOLOGY

Plants: a tool box of cell-based assays

(2016) Vivien Marx   NATURE METHODS

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

Highly multiplexed targeted DNA sequencing from single nuclei

(2016) Marco L Leung et al.   Nature Protocols

Single cell–resolution western blotting

(2016) Chi-Chih Kang et al.   Nature Protocols

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

(2016) Naomi Habib et al.   SCIENCE

Clinical Applications of Circulating Tumor Cells and Circulating Tumor DNA as Liquid Biopsy

(2016) C. Alix-Panabieres et al.   Cancer Discovery

Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells

(2016) Spyros Darmanis et al.   Cell Reports

Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells

(2016) Iain C. Macaulay et al.   Cell Reports

Revised Estimates for the Number of Human and Bacteria Cells in the Body

(2016) Ron Sender et al.   PLOS BIOLOGY

Hydrogel Pore-Size Modulation for Enhanced Single-Cell Western Blotting

(2015) Todd A. Duncombe et al.   ADVANCED MATERIALS

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

(2015) Jop Kind et al.   CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury

(2015) Enric Llorens-Bobadilla et al.   Cell Stem Cell

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

(2015) Nicola K. Wilson et al.   Cell Stem Cell

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

Unraveling cell populations in tumors by single-cell mass cytometry

(2015) Serena Di Palma et al.   CURRENT OPINION IN BIOTECHNOLOGY

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

Chemical Methods for the Simultaneous Quantitation of Metabolites and Proteins from Single Cells

(2015) Min Xue et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

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

Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing

(2015) Hongshan Guo et al.   Nature Protocols

Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification

(2015) Yusi Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands

(2015) Yao Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Quantitative assessment of single-cell whole genome amplification methods for detecting copy number variation using hippocampal neurons

(2015) Luwen Ning et al.   Scientific Reports

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

(2015) Matthias Farlik et al.   Cell Reports

Quantification of cell identity from single-cell gene expression profiles

(2015) Idan Efroni et al.   GENOME BIOLOGY

Single-Cell Western Blotting after Whole-Cell Imaging to Assess Cancer Chemotherapeutic Response

(2014) Chi-Chih Kang et al.   ANALYTICAL CHEMISTRY

Two different microarray technologies for preimplantation genetic diagnosis and screening, due to reciprocal translocation imbalances, demonstrate equivalent euploidy and clinical pregnancy rates

(2014) Kyle J. Tobler et al.   JOURNAL OF ASSISTED REPRODUCTION AND GENETICS

Ultrasensitive proteome analysis using paramagnetic bead technology

(2014) C. S. Hughes et al.   Molecular Systems Biology

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

Deconstructing transcriptional heterogeneity in pluripotent stem cells

(2014) Roshan M. Kumar et al.   NATURE

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

Single-cell western blotting

(2014) Alex J Hughes et al.   NATURE METHODS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Use of array comparative genomic hybridization (array-CGH) for embryo assessment: clinical results

(2013) Carmen Rubio et al.   FERTILITY AND STERILITY

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Platelet-biased stem cells reside at the apex of the haematopoietic stem-cell hierarchy

(2013) Alejandra Sanjuan-Pla et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells

(2013) Jeff Gole et al.   NATURE BIOTECHNOLOGY

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Qualitative and quantitative metabolomic investigation of single neurons by capillary electrophoresis electrospray ionization mass spectrometry

(2013) Peter Nemes et al.   Nature Protocols

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA-sequencing from single nuclei

(2013) R. V. Grindberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients

(2013) X. Ni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mass spectrometry-based metabolomics of single yeast cells

(2013) A. J. Ibanez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Metabolomics: Analytical and Biological Perspectives

(2013) R. Zenobi   SCIENCE

Small is fast: astrocytic glucose and lactate metabolism at cellular resolution

(2013) L. F. Barros et al.   Frontiers in Cellular Neuroscience

Multifunctional T-cell Analyses to Study Response and Progression in Adoptive Cell Transfer Immunotherapy

(2013) Chao Ma et al.   Cancer Discovery

Microchip platforms for multiplex single-cell functional proteomics with applications to immunology and cancer research

(2013) Wei Wei et al.   Genome Medicine

Development and validation of an accurate quantitative real-time polymerase chain reaction–based assay for human blastocyst comprehensive chromosomal aneuploidy screening

(2012) Nathan R. Treff et al.   FERTILITY AND STERILITY

Transcriptome sequencing of single cells with Smart-Seq

(2012) Jillian J Goetz et al.   NATURE BIOTECHNOLOGY

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing

(2012) S. Lu et al.   SCIENCE

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells

(2011) Q. Shi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct Hematopoietic Stem Cell Subtypes Are Differentially Regulated by TGF-β1

(2010) Grant A. Challen et al.   Cell Stem Cell

Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

(2010) Fuchou Tang et al.   Cell Stem Cell

Heterogeneity and hierarchy within the most primitive hematopoietic stem cell compartment

(2010) Yohei Morita et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Functionally distinct hematopoietic stem cells modulate hematopoietic lineage potential during aging by a mechanism of clonal expansion

(2010) I. Beerman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic DNA amplification by the multiple displacement amplification (MDA) method: Figure 1

(2009) Roger S. Lasken   BIOCHEMICAL SOCIETY TRANSACTIONS

Prospective isolation and molecular characterization of hematopoietic stem cells with durable self-renewal potential

(2009) D. G. Kent et al.   BLOOD

Modelling and measuring single cell RNA expression levels find considerable transcriptional differences among phenotypically identical cells

(2008) Tatiana Subkhankulova et al.   BMC GENOMICS

High-throughput Procedure for Single Pollen Grain Collection and Polymerase Chain Reaction in Plants

(2008) Ping-Hua Chen et al.   Journal of Integrative Plant Biology