Single-cell transcriptome sequencing: recent advances and remaining challenges (Q26767451)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26949524%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

volume

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26949524%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

1 June 2020

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17 February 2016

1 reference

April 2022 Public Data File from Crossref

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Single-cell RNA-seq: advances and future challenges

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MicroRNAs: small RNAs with a big role in gene regulation

7 April 2017

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Application of single-cell genomics in cancer: promise and challenges

7 April 2017

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Image-based transcriptomics in thousands of single human cells at single-molecule resolution

7 April 2017

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mRNA-Seq whole-transcriptome analysis of a single cell

7 April 2017

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Tumour evolution inferred by single-cell sequencing

7 April 2017

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Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

7 April 2017

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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

7 April 2017

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Circular RNAs are a large class of animal RNAs with regulatory potency

7 April 2017

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RNA sequencing: advances, challenges and opportunities

7 April 2017

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Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons

7 April 2017

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ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis

28 September 2017

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Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

28 September 2017

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Identification of Distinct Tumor Subpopulations in Lung Adenocarcinoma via Single-Cell RNA-seq

28 September 2017

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Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

28 September 2017

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Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

28 September 2017

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Single-cell messenger RNA sequencing reveals rare intestinal cell types

28 September 2017

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

28 September 2017

1 reference

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Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos.

28 September 2017

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Single-cell chromatin accessibility reveals principles of regulatory variation

28 September 2017

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The technology and biology of single-cell RNA sequencing

28 September 2017

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

28 September 2017

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Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

28 September 2017

1 reference

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Single-cell transcriptome analyses reveal signals to activate dormant neural stem cells

28 September 2017

1 reference

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Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing

28 September 2017

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G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

28 September 2017

1 reference

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Single-cell, locus-specific bisulfite sequencing (SLBS) for direct detection of epimutations in DNA methylation patterns

28 September 2017

1 reference

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Spatial reconstruction of single-cell gene expression data

28 September 2017

1 reference

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High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

28 September 2017

1 reference

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RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells

28 September 2017

1 reference

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A stochastic transcriptional switch model for single cell imaging data

28 September 2017

1 reference

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Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Decoding the regulatory network of early blood development from single-cell gene expression measurements.

28 September 2017

1 reference

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Expression profiling. Combinatorial labeling of single cells for gene expression cytometry

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Computational and analytical challenges in single-cell transcriptomics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Integrated genome and transcriptome sequencing of the same cell

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Single-cell mass cytometry reveals intracellular survival/proliferative signaling in FLT3-ITD-mutated AML stem/progenitor cells

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Inferring single-cell gene expression mechanisms using stochastic simulation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

In the right place at the right time: visualizing and understanding mRNA localization.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Computational and experimental single cell biology techniques for the definition of cell type heterogeneity, interplay and intracellular dynamics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Bayesian approach to single-cell differential expression analysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Detecting and characterizing circular RNAs

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Validation of noise models for single-cell transcriptomics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Review on statistical methods for gene network reconstruction using expression data.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Digital encoding of cellular mRNAs enabling precise and absolute gene expression measurement by single-molecule counting

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Highly multiplexed subcellular RNA sequencing in situ

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Quantitative single-cell RNA-seq with unique molecular identifiers

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

RNA-sequencing from single nuclei

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Mosaic copy number variation in human neurons

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Quantitative transcriptomics using designed primer-based amplification

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Single-cell systems biology by super-resolution imaging and combinatorial labeling

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Counting absolute numbers of molecules using unique molecular identifiers

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Synthetic spike-in standards for RNA-seq experiments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Counting individual DNA molecules by the stochastic attachment of diverse labels

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Transcript amplification from single bacterium for transcriptome analysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

A method for counting PCR template molecules with application to next-generation sequencing

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Mammalian genes are transcribed with widely different bursting kinetics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Genomewide characterization of non-polyadenylated RNAs

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

A brief review on the mechanisms of miRNA regulation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Normalization and noise reduction for single cell RNA-seq experiments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Deconstructing transcriptional heterogeneity in pluripotent stem cells

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Accounting for technical noise in single-cell RNA-seq experiments.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

How to infer gene networks from expression profiles

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Single-cell transcriptomics and functional target validation of brown adipocytes show their complex roles in metabolic homeostasis

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

In situ sequencing for RNA analysis in preserved tissue and cells.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Highly multiplexed and strand-specific single-cell RNA 5' end sequencing

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Reconstructing gene networks: what are the limits?

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

Measurement of the Number of Molecules of a Single mRNA Species in a Complex mRNA Preparation

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4758375

10.12688/F1000RESEARCH.7223.1

28 November 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26949524%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26949524%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

PubMed publication ID

26949524

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26949524%20AND%20SRC:MED&resulttype=core&format=json