Synergetic effects of DNA methylation and histone modification during mouse induced pluripotent stem cell generation

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells

(2015) Jing Liao et al.   NATURE GENETICS

The miR-29b–Sirt1 axis regulates self-renewal of mouse embryonic stem cells in response to reactive oxygen species

(2014) Zengguang Xu et al.   CELLULAR SIGNALLING

Cytoscape App Store

(2013) S. Lotia et al.   BIOINFORMATICS

High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells

(2013) Gang Chang et al.   CELL RESEARCH

MiRNA-29: A microRNA Family with Tumor-Suppressing and Immune-Modulating Properties

(2013) M.J. Schmitt et al.   CURRENT MOLECULAR MEDICINE

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse

(2013) Qixuan Wang et al.   NUCLEIC ACIDS RESEARCH

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells

(2012) Jose M. Polo et al.   CELL

microRNA-29b is a novel mediator of Sox2 function in the regulation of somatic cell reprogramming

(2012) Xudong Guo et al.   CELL RESEARCH

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

iPS cells generated without c-Myc have active Dlk1-Dio3 region and are capable of producing full-term mice through tetraploid complementation

(2011) Wei Li et al.   CELL RESEARCH

De novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells to a pluripotent state

(2011) M. Pawlak et al.   GENES & DEVELOPMENT

Global epigenetic changes during somatic cell reprogramming to iPS cells

(2011) Anna Mattout et al.   Journal of Molecular Cell Biology

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells

(2010) Matthew G. Guenther et al.   Cell Stem Cell

A Mesenchymal-to-Epithelial Transition Initiates and Is Required for the Nuclear Reprogramming of Mouse Fibroblasts

(2010) Ronghui Li et al.   Cell Stem Cell

The miR-290-295 cluster promotes pluripotency maintenance by regulating cell cycle phase distribution in mouse embryonic stem cells

(2010) Zsuzsanna Lichner et al.   DIFFERENTIATION

Activation of the ImprintedDlk1-Dio3Region Correlates with Pluripotency Levels of Mouse Stem Cells

(2010) Lei Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Epigenetic memory in induced pluripotent stem cells

(2010) K. Kim et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Defining Hypo-Methylated Regions of Stem Cell-Specific Promoters in Human iPS Cells Derived from Extra-Embryonic Amnions and Lung Fibroblasts

(2010) Koichiro Nishino et al.   PLoS One

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

(2009) Akiko Doi et al.   NATURE GENETICS

Linking DNA methylation and histone modification: patterns and paradigms

(2009) Howard Cedar et al.   NATURE REVIEWS GENETICS

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Induction of Pluripotent Stem Cells from Mouse Embryonic Fibroblasts by Oct4 and Klf4 with Small-Molecule Compounds

(2008) Yan Shi et al.   Cell Stem Cell

Dissecting direct reprogramming through integrative genomic analysis

(2008) Tarjei S. Mikkelsen et al.   NATURE

Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds

(2008) Danwei Huangfu et al.   NATURE BIOTECHNOLOGY