The Human Cell Atlas: Technical approaches and challenges (Q48563763)

12 February 2018

http://europepmc.org/abstract/MED/29092000

3 references

19 September 2019

28 January 2021

7 April 2021

The Human Cell Atlas: Technical approaches and challenges (English)

1 reference

12 February 2018

http://europepmc.org/abstract/MED/29092000

main subject

biomedical investigative technique

1 reference

19 September 2019

0 references

0 references

1 reference

28 January 2021

gene expression profiling

1 reference

7 April 2021

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29092000 AND SRC:MED&resulttype=core&format=json

6 June 2020

Piero Carninci

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29092000 AND SRC:MED&resulttype=core&format=json

6 June 2020

Michael J T Stubbington

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29092000 AND SRC:MED&resulttype=core&format=json

6 June 2020

2

Jay W Shin

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29092000 AND SRC:MED&resulttype=core&format=json

6 June 2020

publication date

28 October 2017

1 reference

12 February 2018

http://europepmc.org/abstract/MED/29092000

1 July 2018

3 references

19 September 2019

28 January 2021

7 April 2021

Briefings in functional genomics

4 references

19 September 2019

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29092000 AND SRC:MED&resulttype=core&format=json

6 June 2020

28 January 2021

7 April 2021

17

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29092000 AND SRC:MED&resulttype=core&format=json

6 June 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29092000 AND SRC:MED&resulttype=core&format=json

6 June 2020

page(s)

283-294

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29092000 AND SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

6 June 2020

copyright license

3 references

19 September 2019

28 January 2021

Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans

7 April 2021

0 references

1 reference

A promoter-level mammalian expression atlas

21 January 2018

1 reference

RNA-seq: impact of RNA degradation on transcript quantification

21 January 2018

1 reference

Tracing the dynamics of gene transcripts after organismal death.

21 January 2018

1 reference

Principles of low temperature cell preservation

21 January 2018

1 reference

Low temperature cell pausing: an alternative short-term preservation method for use in cell therapies including stem cell applications.

21 January 2018

1 reference

Distribution and compartmentalization of human circulating and tissue-resident memory T cell subsets

21 January 2018

1 reference

Augmentation of Recipient Adaptive Alloimmunity by Donor Passenger Lymphocytes within the Transplant

21 January 2018

1 reference

Cholangiocytes derived from human induced pluripotent stem cells for disease modeling and drug validation

21 January 2018

1 reference

Single-cell transcriptome analysis of endometrial tissue.

21 January 2018

1 reference

Massively parallel digital transcriptional profiling of single cells

21 January 2018

1 reference

Single-cell transcriptome conservation in cryopreserved cells and tissues

21 January 2018

1 reference

Cell fixation and preservation for droplet-based single-cell transcriptomics

21 January 2018

1 reference

RNA-sequencing from single nuclei

21 January 2018

1 reference

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

T cell fate and clonality inference from single-cell transcriptomes

21 January 2018

1 reference

A cost effective 5΄ selective single cell transcriptome profiling approach with improved UMI design.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Single-cell mRNA isoform diversity in the mouse brain

21 January 2018

1 reference

Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision

21 January 2018

1 reference

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells.

21 January 2018

1 reference

Single-cell genome sequencing: current state of the science

21 January 2018

1 reference

Single-cell chromatin accessibility reveals principles of regulatory variation

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Massively multiplex single-cell Hi-C.

21 January 2018

1 reference

Single-cell DNA-methylation analysis reveals epigenetic chimerism in preimplantation embryos

21 January 2018

1 reference

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

21 January 2018

1 reference

Simultaneous profiling of transcriptome and DNA methylome from a single cell

21 January 2018

1 reference

Imaging individual mRNA molecules using multiple singly labeled probes

21 January 2018

1 reference

Visualization of Single RNA Transcripts in Situ

21 January 2018

1 reference

Single-cell in situ RNA profiling by sequential hybridization

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Highly multiplexed subcellular RNA sequencing in situ

21 January 2018

1 reference

Spatial reconstruction of single-cell gene expression data

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Multiplexed ion beam imaging of human breast tumors

21 January 2018

1 reference

Comparative Analysis of Single-Cell RNA Sequencing Methods.

21 January 2018

1 reference

Single-cell sequencing in stem cell biology

21 January 2018

1 reference

An atlas of human long non-coding RNAs with accurate 5' ends.

21 January 2018

1 reference

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

21 January 2018

1 reference

Deconstructing transcriptional heterogeneity in pluripotent stem cells

21 January 2018

1 reference

Quality control of single-cell RNA-seq by SinQC.

21 January 2018

1 reference

Classification of low quality cells from single-cell RNA-seq data

21 January 2018

1 reference

SCell: integrated analysis of single-cell RNA-seq data

21 January 2018

1 reference

Normalizing single-cell RNA sequencing data: challenges and opportunities

21 January 2018

1 reference

SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization

21 January 2018

1 reference

Normalization and noise reduction for single cell RNA-seq experiments

21 January 2018

1 reference

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

21 January 2018

1 reference

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.

21 January 2018

1 reference

SCnorm: robust normalization of single-cell RNA-seq data

21 January 2018

1 reference

Single-cell mRNA quantification and differential analysis with Census

21 January 2018

1 reference

Normalization of RNA-seq data using factor analysis of control genes or samples

21 January 2018

1 reference

Batch effects and the effective design of single-cell gene expression studies

21 January 2018

1 reference

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

21 January 2018

1 reference

Exploiting single-cell expression to characterize co-expression replicability

21 January 2018

1 reference

Removal of batch effects using distribution-matching residual networks.

21 January 2018

1 reference

Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data.

21 January 2018

1 reference

Power analysis of single-cell RNA-sequencing experiments

21 January 2018

1 reference

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

21 January 2018

1 reference

Adjusting batch effects in microarray expression data using empirical Bayes methods

21 January 2018

1 reference

Revealing the vectors of cellular identity with single-cell genomics

21 January 2018

1 reference

Dimension reduction techniques for the integrative analysis of multi-omics data

21 January 2018

1 reference

Robust classification of single-cell transcriptome data by nonnegative matrix factorization

21 January 2018

1 reference

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

21 January 2018

1 reference

destiny: diffusion maps for large-scale single-cell data in R.

21 January 2018

1 reference

Diffusion maps for high-dimensional single-cell analysis of differentiation data.

21 January 2018

1 reference

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

21 January 2018

1 reference

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data

21 January 2018

1 reference

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

21 January 2018

1 reference

Identification of cell types from single-cell transcriptomes using a novel clustering method.

21 January 2018

1 reference

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

21 January 2018

1 reference

pcaReduce: hierarchical clustering of single cell transcriptional profiles

21 January 2018

1 reference

SC3: consensus clustering of single-cell RNA-seq data

21 January 2018

1 reference

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice.

21 January 2018

1 reference

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

21 January 2018

1 reference

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

21 January 2018

1 reference

Visualizing the structure of RNA-seq expression data using grade of membership models.

21 January 2018

1 reference

Single-cell messenger RNA sequencing reveals rare intestinal cell types

21 January 2018

1 reference

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index

21 January 2018

1 reference

Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria

21 January 2018

1 reference

Defining cell types and states with single-cell genomics

21 January 2018

1 reference

Computational methods for trajectory inference from single-cell transcriptomics

21 January 2018

1 reference

Pseudotime estimation: deconfounding single cell time series

21 January 2018

1 reference

Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference

21 January 2018

1 reference

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

21 January 2018

1 reference

Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm

21 January 2018

1 reference

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data

21 January 2018

1 reference

Diffusion pseudotime robustly reconstructs lineage branching

21 January 2018

1 reference

Robust lineage reconstruction from high-dimensional single-cell data.

21 January 2018

1 reference

Probabilistic modeling of bifurcations in single-cell gene expression data using a Bayesian mixture of factor analyzers.

21 January 2018

1 reference

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

21 January 2018

1 reference

Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development

21 January 2018

1 reference

SCOUP: a probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation

21 January 2018

1 reference

Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development

21 January 2018

1 reference

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

21 January 2018

1 reference

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

21 January 2018

1 reference

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

21 January 2018

1 reference

TASIC: Determining branching models from time series single cell data

21 January 2018

1 reference

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

21 January 2018

1 reference

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

21 January 2018

1 reference

Wishbone identifies bifurcating developmental trajectories from single-cell data

21 January 2018

1 reference

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

21 January 2018

1 reference

Beta-Poisson model for single-cell RNA-seq data analyses

21 January 2018

1 reference

Bayesian approach to single-cell differential expression analysis

21 January 2018

1 reference

Discrete distributional differential expression (D3E)--a tool for gene expression analysis of single-cell RNA-seq data

21 January 2018

1 reference

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments

21 January 2018

1 reference

Coupling and coordination in gene expression processes: a systems biology view

21 January 2018

1 reference

Wisdom of crowds for robust gene network inference

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis

21 January 2018

1 reference

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

21 January 2018

1 reference

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

21 January 2018

1 reference

Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data

21 January 2018

1 reference

Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development

21 January 2018

1 reference

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

21 January 2018

1 reference

BTR: training asynchronous Boolean models using single-cell expression data

21 January 2018

1 reference

Studying and modelling dynamic biological processes using time-series gene expression data

21 January 2018

1 reference

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation.

21 January 2018

1 reference

A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data

21 January 2018

1 reference

WGCNA: an R package for weighted correlation network analysis

21 January 2018

1 reference

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells

21 January 2018

1 reference

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

21 January 2018

1 reference

Automatic single cell segmentation on highly multiplexed tissue images.

21 January 2018

1 reference

An ontology for cell types

21 January 2018

1 reference

Uberon, an integrative multi-species anatomy ontology

21 January 2018

1 reference

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

21 January 2018

1 reference

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

21 January 2018

1 reference

Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE).

21 January 2018

1 reference

Visualization and cellular hierarchy inference of single-cell data using SPADE.

21 January 2018

1 reference

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

BEARscc determines robustness of single-cell clusters using simulated technical replicates.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

A general and flexible method for signal extraction from single-cell RNA-seq data.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

SPRING: a kinetic interface for visualizing high dimensional single-cell expression data

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

Controlling for Confounding Effects in Single Cell RNA Sequencing Studies Using both Control and Target Genes

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

powsimR: power analysis for bulk and single cell RNA-seq experiments.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

Splatter: simulation of single-cell RNA sequencing data

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

Model-based branching point detection in single-cell data by K-Branches clustering

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

switchde: inference of switch-like differential expression along single-cell trajectories

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

SLICE: determining cell differentiation and lineage based on single cell entropy

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

TRACING CO-REGULATORY NETWORK DYNAMICS IN NOISY, SINGLE-CELL TRANSCRIPTOME TRAJECTORIES.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

Single-cell sequencing of the small-RNA transcriptome

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

INTRODUCTION: Harmonizing Privacy Laws to Enable International Biobank Research

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

Fixed single-cell transcriptomic characterization of human radial glial diversity.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

Quantitative single-cell RNA-seq with unique molecular identifiers

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

Principles of solid-organ preservation by cold storage

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

SpatialDE: identification of spatially variable genes

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6063304

1 December 2018

Identifiers

DOI

10.1093/BFGP/ELX029

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29092000 AND SRC:MED&resulttype=core&format=json

6 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29092000 AND SRC:MED&resulttype=core&format=json

6 June 2020

1 reference