SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis (Q35850720)

10 August 2017

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

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10 August 2017

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Minzhe Guo

1

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10 August 2017

Hui Wang

2

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10 August 2017

S Steven Potter

3

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10 August 2017

Jeffrey A Whitsett

4

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10 August 2017

Yan Xu

5

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10 August 2017

24 November 2015

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PLOS Computational Biology

10 August 2017

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10 August 2017

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10 August 2017

e1004575

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10 August 2017

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Creative Commons Attribution 4.0 International

10 August 2017

start time

24 November 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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11 July 2018

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

11 July 2018

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

11 July 2018

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

11 July 2018

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Lineage-negative progenitors mobilize to regenerate lung epithelium after major injury

11 July 2018

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

11 July 2018

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

11 July 2018

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Identifying cell types from spatially referenced single-cell expression datasets

11 July 2018

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Single-cell RNA-seq: advances and future challenges

11 July 2018

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Bayesian approach to single-cell differential expression analysis

11 July 2018

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

11 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

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

11 July 2018

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The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse

11 July 2018

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

11 July 2018

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

11 July 2018

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

11 July 2018

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

11 July 2018

1 reference

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

11 July 2018

1 reference

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

11 July 2018

1 reference

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Kras(G12D) and Nkx2-1 haploinsufficiency induce mucinous adenocarcinoma of the lung

11 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Single-neuron RNA-Seq: technical feasibility and reproducibility

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Transcriptional programs controlling perinatal lung maturation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Integrating external biological knowledge in the construction of regulatory networks from time-series expression data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Wisdom of crowds for robust gene network inference

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Regulated noise in the epigenetic landscape of development and disease

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Investigating meta-approaches for reconstructing gene networks in a mammalian cellular context.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Robust rank aggregation for gene list integration and meta-analysis

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Microfluidics for single cell analysis

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells

11 July 2018

1 reference

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Stochastic mechanisms of cell fate specification that yield random or robust outcomes.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

The Generalization of `Student's' Problem when Several Different Population Variances are Involved

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Coexistence of quiescent and active adult stem cells in mammals

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Fast and accurate short read alignment with Burrows-Wheeler transform

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

mRNA-Seq whole-transcriptome analysis of a single cell

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

TopHat: discovering splice junctions with RNA-Seq

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Inferring dynamic genetic networks with low order independencies

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Network analysis in the social sciences

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Nature, nurture, or chance: stochastic gene expression and its consequences

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Survival of the sparsest: robust gene networks are parsimonious

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Epigenetic gene expression noise and phenotypic diversification of clonal cell populations

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Physical and functional interactions between homeodomain NKX2.1 and winged helix/forkhead FOXA1 in lung epithelial cells

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Hop functions downstream of Nkx2.1 and GATA6 to mediate HDAC-dependent negative regulation of pulmonary gene expression

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

ROCR: visualizing classifier performance in R

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Bioconductor: open software development for computational biology and bioinformatics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Identification of genes differentially expressed in rat alveolar type I cells

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

TTF-1 phosphorylation is required for peripheral lung morphogenesis, perinatal survival, and tissue-specific gene expression

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Transforming growth factor-beta inhibits pulmonary surfactant protein B gene transcription through SMAD3 interactions with NKX2.1 and HNF-3 transcription factors

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

claudin-18, a novel downstream target gene for the T/EBP/NKX2.1 homeodomain transcription factor, encodes lung- and stomach-specific isoforms through alternative splicing

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Protein-protein interaction of retinoic acid receptor alpha and thyroid transcription factor-1 in respiratory epithelial cells

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

BR22, a novel protein, interacts with thyroid transcription factor-1 and activates the human surfactant protein B promoter

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Functional analysis of surfactant protein B (SP-B) promoter. Sp1, Sp3, TTF-1, and HNF-3alpha transcription factors are necessary for lung cell-specific activation of SP-B gene transcription

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Transcription of the lung-specific surfactant protein C gene is mediated by thyroid transcription factor 1

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

The T/ebp null mouse: thyroid-specific enhancer-binding protein is essential for the organogenesis of the thyroid, lung, ventral forebrain, and pituitary

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

The lung-specific surfactant protein B gene promoter is a target for thyroid transcription factor 1 and hepatocyte nuclear factor 3, indicating common factors for organ-specific gene expression along the foregut axis

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Probability plotting methods for the analysis of data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Fallacies inherent in the proband method of analysis of human pedigrees for inheritance of recessive traits; two methods of correction of the formula.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Microarray analysis of blood microvessels from PDGF-B and PDGF-Rbeta mutant mice identifies novel markers for brain pericytes.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Low-order conditional independence graphs for inferring genetic networks.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

The TTF-1/TAP26 complex differentially modulates surfactant protein-B (SP-B) and -C (SP-C) promoters in lung cells.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Increased expression of thyroid transcription factor-1 (TTF-1) in respiratory epithelial cells inhibits alveolarization and causes pulmonary inflammation.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4658017

Topological keystone species: measures of positional importance in food webs

24 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004575

Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26600239

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1004575

1 reference

journals/ploscb/GuoWPWX15

10 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

10 August 2017

1 reference