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Benchmarking principal component analysis for large-scale single-cell RNA-sequencing

Genome Biology, 2020-01, Vol.21 (1), p.9-17, Article 9

2020

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Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

Nature communications, 2018-02, Vol.9 (1), p.619-16, Article 619

2018

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

Bioinformatics (Oxford, England), 2017-08, Vol.33 (15), p.2314-2321

2017

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Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data

BMC bioinformatics, 2023-11, Vol.24 (1), p.420-28, Article 420

2023

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CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing

Genome Biology, 2019-02, Vol.20 (1), p.31-23, Article 31

2019

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Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads

Genome Biology, 2018-03, Vol.19 (1), p.29-29, Article 29

2018

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Tracing the origin of hair follicle stem cells

Nature (London), 2021-06, Vol.594 (7864), p.547-552

2021

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Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids

Molecular psychiatry, 2020-11, Vol.25 (11), p.2695-2711

2020

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Local states of chromatin compaction at transcription start sites control transcription levels

Nucleic acids research, 2021-08, Vol.49 (14), p.8007-8023

2021

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Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers

PLoS genetics, 2022-06, Vol.18 (6), p.e1010235-e1010235

2022

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Author Correction: Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis

Nature communications, 2023-10, Vol.14 (1), p.6540-6540, Article 6540

2023

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Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis

Nature communications, 2023-06, Vol.14 (1), p.3750-3750, Article 3750

2023

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WormTensor: a clustering method for time-series whole-brain activity data from C. elegans

BMC bioinformatics, 2023-06, Vol.24 (1), p.254-21, Article 254

2023

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Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells

Molecular cell, 2013-11, Vol.52 (3), p.380-392

2013

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Single‐oocyte transcriptome analysis reveals aging‐associated effects influenced by life stage and calorie restriction

Aging cell, 2021-08, Vol.20 (8), p.e13428-n/a

2021

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Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets

BMC genomics, 2020-03, Vol.21 (1), p.177-177, Article 177

2020

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MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis

BMC bioinformatics, 2015-02, Vol.16 (1), p.45-45, Article 45

2015

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A common epigenetic mechanism across different cellular origins underlies systemic immune dysregulation in an idiopathic autism mouse model

Molecular psychiatry, 2022-08, Vol.27 (8), p.3343-3354

2022

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Distinctiveness and continuity in transcriptome and connectivity in the anterior-posterior axis of the paraventricular nucleus of the thalamus

Cell reports (Cambridge), 2023-10, Vol.42 (10), p.113309-113309, Article 113309

2023

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Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

Genome biology, 2013-04, Vol.14 (4), p.R31-R31, Article 3097

2013

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Chromatin remodeler CHD7 regulates the stem cell identity of human neural progenitors

Genes & development, 2018-01, Vol.32 (2), p.165-180

2018

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The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression

Cell reports (Cambridge), 2020-06, Vol.31 (9), p.107724-107724, Article 107724

2020

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Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells

Science advances, 2020-06, Vol.6 (25), p.eaaz6699-eaaz6699

2020

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Maternal epigenetic factors in embryonic and postnatal development

Genes to cells : devoted to molecular & cellular mechanisms, 2023-06, Vol.28 (6), p.422-432

2023

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Benchmarking principal component analysis for large-scale single-cell RNA-sequencing

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

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

Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing

Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads

Tracing the origin of hair follicle stem cells

Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids

Local states of chromatin compaction at transcription start sites control transcription levels

Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers

Author Correction: Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis

Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis

WormTensor: a clustering method for time-series whole-brain activity data from C. elegans

Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells

Single‐oocyte transcriptome analysis reveals aging‐associated effects influenced by life stage and calorie restriction

Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis

A common epigenetic mechanism across different cellular origins underlies systemic immune dysregulation in an idiopathic autism mouse model

Distinctiveness and continuity in transcriptome and connectivity in the anterior-posterior axis of the paraventricular nucleus of the thalamus

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

Chromatin remodeler CHD7 regulates the stem cell identity of human neural progenitors

The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression

Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells

Maternal epigenetic factors in embryonic and postnatal development

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