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Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE

Nature communications, 2021-03, Vol.12 (1), p.1456-1456, Article 1456

2021

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Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells

Nature communications, 2019-01, Vol.10 (1), p.34-13, Article 34

2019

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Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells

Nucleic acids research, 2021-09, Vol.49 (16), p.9132-9153

2021

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Metabolic and epigenetic dysfunctions underlie the arrest of in vitro fertilized human embryos in a senescent-like state

PLoS biology, 2022-06, Vol.20 (6), p.e3001682-e3001682

2022

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An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis

Nature communications, 2019-04, Vol.10 (1), p.1535-1535, Article 1535

2019

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CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming

Cell reports (Cambridge), 2022-04, Vol.39 (1), p.110626-110626, Article 110626

2022

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Transposable Elements in Pluripotent Stem Cells and Human Disease

Frontiers in genetics, 2022-06, Vol.13, p.902541-902541

2022

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JMJD3 acts in tandem with KLF4 to facilitate reprogramming to pluripotency

Nature communications, 2020-10, Vol.11 (1), p.5061-5061, Article 5061

2020

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Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts

Computational and structural biotechnology journal, 2019-01, Vol.17, p.628-637

2019

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Restricting epigenetic activity promotes the reprogramming of transformed cells to pluripotency in a line-specific manner

Cell death discovery, 2023-07, Vol.9 (1), p.245-245, Article 245

2023

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Unified Analysis of Multiple ChIP-Seq Datasets

Methods in molecular biology (Clifton, N.J.), 2021, Vol.2198, p.451

2021

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DPre: computational identification of differentiation bias and genes underlying cell type conversions

Bioinformatics, 2020-03, Vol.36 (5), p.1637-1639

2020

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A primate-specific endogenous retroviral envelope protein sequesters SFRP2 to regulate human cardiomyocyte development

Cell stem cell, 2024-09, Vol.31 (9), p.1298-1314.e8

2024

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Population structure and evolutionary history of the greater cane rat ( Thryonomys swinderianus ) from the Guinean Forests of West Africa

Frontiers in genetics, 2023-02, Vol.14, p.1041103

2023

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β-Catenin safeguards the ground state of mousepluripotency by strengthening the robustness of the transcriptional apparatus

Science advances, 2020-07, Vol.6 (29), p.eaba1593-eaba1593

2020

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The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome

BMC genomics, 2022-07, Vol.23 (1), p.1-487, Article 487

2022

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Genomic Locations of Conserved Noncoding Sequences and Their Proximal Protein-Coding Genes in Mammalian Expression Dynamics

Molecular biology and evolution, 2016-07, Vol.33 (7), p.1807-1817

2016

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The Dynamics, Causes, and Impacts of Mammalian Evolutionary Rates Revealed by the Analyses of Capybara Draft Genome Sequences

Genome biology and evolution, 2020-08, Vol.12 (8), p.1444-1458

2020

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Diversity and Molecular Phylogeny of Pagurid Hermit Crabs (Anomura: Paguridae: Pagurus)

Diversity (Basel), 2022-02, Vol.14 (2), p.141

2022

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Whole-Genome Sequencing of Six Mauritian Cynomolgus Macaques (Macaca fascicularis) Reveals a Genome-Wide Pattern of Polymorphisms under Extreme Population Bottleneck

Genome biology and evolution, 2015-03, Vol.7 (3), p.821-830

2015

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Whole-genome sequencing of six Mauritian Cynomolgus macaques (Macaca fascicularis) reveals a genome-wide pattern of polymorphisms under extreme population bottleneck

Genome biology and evolution, 2015-03, Vol.7 (3), p.821-830

2015

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Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences

Genome biology and evolution, 2016-07, Vol.8 (7), p.2076-2092

2016

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Single-cell RNA-seq data analysis reveals functionally relevant biomarkers of early brain development and their regulatory footprints in human embryonic stem cells (hESCs)

Briefings in bioinformatics, 2024-03, Vol.25 (3)

2024

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Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders

Genome biology and evolution, 2013-01, Vol.5 (12), p.2330-2343

2013

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3C-07 Rodent phenotypic diversity : insights from conserved noncoding evolution

Genes & Genetic Systems, 2015-12, Vol.90 (6), p.401-401

2015

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Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE

Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells

Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells

Metabolic and epigenetic dysfunctions underlie the arrest of in vitro fertilized human embryos in a senescent-like state

An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis

CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming

Transposable Elements in Pluripotent Stem Cells and Human Disease

JMJD3 acts in tandem with KLF4 to facilitate reprogramming to pluripotency

Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts

Restricting epigenetic activity promotes the reprogramming of transformed cells to pluripotency in a line-specific manner

Unified Analysis of Multiple ChIP-Seq Datasets

DPre: computational identification of differentiation bias and genes underlying cell type conversions

A primate-specific endogenous retroviral envelope protein sequesters SFRP2 to regulate human cardiomyocyte development

Population structure and evolutionary history of the greater cane rat ( Thryonomys swinderianus ) from the Guinean Forests of West Africa

β-Catenin safeguards the ground state of mousepluripotency by strengthening the robustness of the transcriptional apparatus

The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome

Genomic Locations of Conserved Noncoding Sequences and Their Proximal Protein-Coding Genes in Mammalian Expression Dynamics

The Dynamics, Causes, and Impacts of Mammalian Evolutionary Rates Revealed by the Analyses of Capybara Draft Genome Sequences

Diversity and Molecular Phylogeny of Pagurid Hermit Crabs (Anomura: Paguridae: Pagurus)

Whole-Genome Sequencing of Six Mauritian Cynomolgus Macaques (Macaca fascicularis) Reveals a Genome-Wide Pattern of Polymorphisms under Extreme Population Bottleneck

Whole-genome sequencing of six Mauritian Cynomolgus macaques (Macaca fascicularis) reveals a genome-wide pattern of polymorphisms under extreme population bottleneck

Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences

Single-cell RNA-seq data analysis reveals functionally relevant biomarkers of early brain development and their regulatory footprints in human embryonic stem cells (hESCs)

Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders

3C-07 Rodent phenotypic diversity : insights from conserved noncoding evolution

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