The Cumulative Formation of R-loop Interacts with Histone Modifications to Shape Cell Reprogramming

mRNALocater: Enhance the prediction accuracy of eukaryotic mRNA subcellular localization by using model fusion strategy

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HelPredictor models single-cell transcriptome to predict human embryo lineage allocation

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Nuclear Transfer Arrest Embryos Show Massive Dysregulation of Genes Involved in Transcription Pathways

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Regulatory R-loops as facilitators of gene expression and genome stability

(2020) Christof Niehrs et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A Comparative Analysis of Single-Cell Transcriptome Identifies Reprogramming Driver Factors for Efficiency Improvement

(2020) Hanshuang Li et al.   Molecular Therapy-Nucleic Acids

Genome-wide R-loop Landscapes during Cell Differentiation and Reprogramming

(2020) Pengze Yan et al.   Cell Reports

R-loops coordinate with SOX2 in regulating reprogramming to pluripotency

(2020) Yaoyi Li et al.   Science Advances

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Dppa2/4 as a trigger of signaling pathways to promote zygote genome activation by binding to CG-rich region

(2020) Hanshuang Li et al.   BRIEFINGS IN BIOINFORMATICS

DPPA2 and DPPA4 are necessary to establish a 2C‐like state in mouse embryonic stem cells

(2019) Alberto De Iaco et al.   EMBO REPORTS

The spatial binding model of the pioneer factor Oct4 with its target genes during cell reprogramming

(2019) Hanshuang Li et al.   Computational and Structural Biotechnology Journal

R Loops: From Physiological to Pathological Roles

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Epigenetic modifications in the embryonic and induced pluripotent stem cells

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Unique molecular events during reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) at naïve state

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Short-Term Mitochondrial Permeability Transition Pore Opening Modulates Histone Lysine Methylation at the Early Phase of Somatic Cell Reprogramming

(2018) Zhongfu Ying et al.   Cell Metabolism

R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters

(2017) Liang Chen et al.   MOLECULAR CELL

Histone Mutants Separate R Loop Formation from Genome Instability Induction

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Induced pluripotent stem cells reprogramming: Epigenetics and applications in the regenerative medicine

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RNA-Seq differential expression analysis: An extended review and a software tool

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Transcription as a Threat to Genome Integrity

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Statistical tests, P values, confidence intervals, and power: a guide to misinterpretations

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Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals

(2016) Lionel A. Sanz et al.   MOLECULAR CELL

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(2016) Xiaoyu Liu et al.   NATURE

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

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Hierarchical Oct4 Binding in Concert with Primed Epigenetic Rearrangements during Somatic Cell Reprogramming

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Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing

(2016) Wenqiang Liu et al.   Cell Discovery

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(2015) Guangchuang Yu et al.   BIOINFORMATICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

R loops: new modulators of genome dynamics and function

(2015) José M. Santos-Pereira et al.   NATURE REVIEWS GENETICS

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

(2015) Julie Nadel et al.   Epigenetics & Chromatin

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(2014) S. Anders et al.   BIOINFORMATICS

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A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression

(2014) K. Skourti-Stathaki et al.   GENES & DEVELOPMENT

A Survey and Comparative Study of Statistical Tests for Identifying Differential Expression from Microarray Data

(2014) Sanghamitra Bandyopadhyay et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

R-loops induce repressive chromatin marks over mammalian gene terminators

(2014) Konstantina Skourti-Stathaki et al.   NATURE

Genome-wide characterization of the routes to pluripotency

(2014) Samer M. I. Hussein et al.   NATURE

GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination

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The homologous recombination machinery modulates the formation of RNA–DNA hybrids and associated chromosome instability

(2013) Lamia Wahba et al.   eLife

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

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(2012) Ben Langmead et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

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Molecular Analyses of Human Induced Pluripotent Stem Cells and Embryonic Stem Cells

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