(Q42777960)

11 January 2018

title

Using neural networks for reducing the dimensions of single-cell RNA-Seq data (English)

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11 January 2018

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4

Ziv Bar-Joseph

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11 January 2018

author name string

Chieh Lin

series ordinal

1

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11 January 2018

Siddhartha Jain

series ordinal

2

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11 January 2018

Hannah Kim

series ordinal

3

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11 January 2018

language of work or name

English

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publication date

1 September 2017

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11 January 2018

published in

Nucleic Acids Research

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11 January 2018

volume

45

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11 January 2018

issue

17

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11 January 2018

page(s)

e156

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11 January 2018

Creative Commons Attribution-NonCommercial 4.0 International

copyright license

start time

31 July 2017

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

artificial neural network

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based on heuristic

inferred from title

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Disentangling neural cell diversity using single-cell transcriptomics

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Computational genomics tools for dissecting tumour-immune cell interactions

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Brain trauma elicits non-canonical macrophage activation states

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Simultaneous profiling of transcriptome and DNA methylome from a single cell

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

g:Profiler-a web server for functional interpretation of gene lists (2016 update)

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

pcaReduce: hierarchical clustering of single cell transcriptional profiles

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Gene expression inference with deep learning.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Somatosensory neuron types identified by high-coverage single-cell RNA-sequencing and functional heterogeneity

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

A survey of human brain transcriptome diversity at the single cell level

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Transcriptional control of stem cell fate by E2Fs and pocket proteins

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Single-cell gene expression profiles define self-renewing, pluripotent, and lineage primed states of human pluripotent stem cells.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Identifying proteins controlling key disease signaling pathways

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

The role of focal adhesion complexes in fibroblast mechanotransduction during scar formation

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

NCBI GEO: archive for functional genomics data sets--update

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Detecting overlapping protein complexes in protein-protein interaction networks

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Mouse chimeras as a system to investigate development, cell and tissue function, disease mechanisms and organ regeneration

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Human Protein Reference Database--2009 update

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

IRF6 in development and disease: a mediator of quiescence and differentiation

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

The transcriptional coactivator and acetyltransferase p300 in fibroblast biology and fibrosis

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Reducing the dimensionality of data with neural networks

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

BioGRID: a general repository for interaction datasets

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Tight clustering: a resampling-based approach for identifying stable and tight patterns in data

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Missing value estimation methods for DNA microarrays

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737331

Multilayer feedforward networks are universal approximators

27 May 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKX681

A Method for Comparing Two Hierarchical Clusterings

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKX681

21 January 2018

Identifiers

DOI

10.1093/NAR/GKX681

1 reference

11 January 2018

PMC publication ID

5737331

1 reference

11 January 2018

PubMed publication ID

28973464

1 reference

11 January 2018