A developmental framework for induced pluripotency

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

(2015) Davide Cacchiarelli et al.   CELL

The differential activation of intracellular signaling pathways confers the permissiveness of embryonic stem cell derivation from different mouse strains

(2015) S. Ohtsuka et al.   DEVELOPMENT

Co-existence of intact stemness and priming of neural differentiation programs in mES cells lacking Trim71

(2015) Sibylle Mitschka et al.   Scientific Reports

KLF4 N-Terminal Variance Modulates Induced Reprogramming to Pluripotency

(2015) Shin-Il Kim et al.   Stem Cell Reports

X Chromosome Reactivation Dynamics Reveal Stages of Reprogramming to Pluripotency

(2014) Vincent Pasque et al.   CELL

Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human

(2014) Yasuhiro Takashima et al.   CELL

Human Somatic Cell Nuclear Transfer Using Adult Cells

(2014) Young Gie Chung et al.   Cell Stem Cell

Two miRNA Clusters Reveal Alternative Paths in Late-Stage Reprogramming

(2014) Ronald J. Parchem et al.   Cell Stem Cell

Comparable Frequencies of Coding Mutations and Loss of Imprinting in Human Pluripotent Cells Derived by Nuclear Transfer and Defined Factors

(2014) Bjarki Johannesson et al.   Cell Stem Cell

Tet and TDG Mediate DNA Demethylation Essential for Mesenchymal-to-Epithelial Transition in Somatic Cell Reprogramming

(2014) Xiao Hu et al.   Cell Stem Cell

In Search of Naivety

(2014) Martin F. Pera   Cell Stem Cell

Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency

(2014) Thorold W. Theunissen et al.   Cell Stem Cell

Loss of Tet Enzymes Compromises Proper Differentiation of Embryonic Stem Cells

(2014) Meelad M. Dawlaty et al.   DEVELOPMENTAL CELL

Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency

(2014) Marc Friedli et al.   GENOME RESEARCH

Telomerase Reverse Transcriptase Has an Extratelomeric Function in Somatic Cell Reprogramming

(2014) Taisuke Kinoshita et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Human oocytes reprogram adult somatic nuclei of a type 1 diabetic to diploid pluripotent stem cells

(2014) Mitsutoshi Yamada et al.   NATURE

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells

(2014) Jichang Wang et al.   NATURE

DNA methylation dynamics of the human preimplantation embryo

(2014) Zachary D. Smith et al.   NATURE

Abnormalities in human pluripotent cells due to reprogramming mechanisms

(2014) Hong Ma et al.   NATURE

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity

(2014) Xinyi Lu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Derivation of naive human embryonic stem cells

(2014) C. B. Ware et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential

(2014) M. Ohnuki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induction of pluripotency in human somatic cells via a transient state resembling primitive streak-like mesendoderm

(2014) Kazutoshi Takahashi et al.   Nature Communications

Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells

(2014) Foad Rouhani et al.   PLoS Genetics

Platform for Induction and Maintenance of Transgene-free hiPSCs Resembling Ground State Pluripotent Stem Cells

(2014) Bahram Valamehr et al.   Stem Cell Reports

Induction of Pluripotency in Mouse Somatic Cells with Lineage Specifiers

(2013) Jian Shu et al.   CELL

Human Embryonic Stem Cells Derived by Somatic Cell Nuclear Transfer

(2013) Masahito Tachibana et al.   CELL

Induction of a Human Pluripotent State with Distinct Regulatory Circuitry that Resembles Preimplantation Epiblast

(2013) Yun-Shen Chan et al.   Cell Stem Cell

Reprogramming of Human Fibroblasts to Pluripotency with Lineage Specifiers

(2013) Nuria Montserrat et al.   Cell Stem Cell

Enhanced Telomere Rejuvenation in Pluripotent Cells Reprogrammed via Nuclear Transfer Relative to Induced Pluripotent Stem Cells

(2013) Rongrong Le et al.   Cell Stem Cell

The let-7/LIN-41 Pathway Regulates Reprogramming to Human Induced Pluripotent Stem Cells by Controlling Expression of Prodifferentiation Genes

(2013) Kathleen A. Worringer et al.   Cell Stem Cell

Combined Deficiency of Tet1 and Tet2 Causes Epigenetic Abnormalities but Is Compatible with Postnatal Development

(2013) Meelad M. Dawlaty et al.   DEVELOPMENTAL CELL

High-resolution analysis with novel cell-surface markers identifies routes to iPS cells

(2013) James O’Malley et al.   NATURE

Derivation of novel human ground state naive pluripotent stem cells

(2013) Ohad Gafni et al.   NATURE

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

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Maturation, not initiation, is the major roadblock during reprogramming toward pluripotency from human fibroblasts

(2013) K. Tanabe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells

(2013) M. Koyanagi-Aoi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pluripotent Stem Cells Induced from Mouse Somatic Cells by Small-Molecule Compounds

(2013) P. Hou et al.   SCIENCE

Oct4 Is Required ∼E7.5 for Proliferation in the Primitive Streak

(2013) Brian DeVeale et al.   PLoS Genetics

Dissecting the Roles of miR-302/367 Cluster in Cellular Reprogramming Using TALE-based Repressor and TALEN

(2013) Zhonghui Zhang et al.   Stem Cell Reports

Generation of Chimeric Rhesus Monkeys

(2012) Masahito Tachibana et al.   CELL

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells

(2012) Jose M. Polo et al.   CELL

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

(2012) Yosef Buganim et al.   CELL

Derivation Conditions Impact X-Inactivation Status in Female Human Induced Pluripotent Stem Cells

(2012) Kiichiro Tomoda et al.   Cell Stem Cell

Distinct Lineage Specification Roles for NANOG, OCT4, and SOX2 in Human Embryonic Stem Cells

(2012) Zheng Wang et al.   Cell Stem Cell

MicroRNAs Are Indispensable for Reprogramming Mouse Embryonic Fibroblasts into Induced Stem Cell-Like Cells

(2012) Byeong-Moo Kim et al.   PLoS One

E-Cadherin Promotes Incorporation of Mouse Epiblast Stem Cells into Normal Development

(2012) Satoshi Ohtsuka et al.   PLoS One

Pluripotency in the Embryo and in Culture

(2012) J. Nichols et al.   Cold Spring Harbor Perspectives in Biology

Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair

(2011) Salvatore Cortellino et al.   CELL

Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines

(2011) Christoph Bock et al.   CELL

The let-7 microRNA target gene, Mlin41/Trim71 is required for mouse embryonic survival and neural tube closure

(2011) Betsy R. Maller Schulman et al.   CELL CYCLE

Tet1 Is Dispensable for Maintaining Pluripotency and Its Loss Is Compatible with Embryonic and Postnatal Development

(2011) Meelad M. Dawlaty et al.   Cell Stem Cell

MicroRNAs and developmental timing

(2011) Victor Ambros   CURRENT OPINION IN GENETICS & DEVELOPMENT

Optimal reprogramming factor stoichiometry increases colony numbers and affects molecular characteristics of murine induced pluripotent stem cells

(2011) Ulf Tiemann et al.   CYTOMETRY PART A

Regulation of lung endoderm progenitor cell behavior by miR302/367

(2011) Ying Tian et al.   DEVELOPMENT

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

Pluripotency factors regulate definitive endoderm specification through eomesodermin

(2011) A. K. K. Teo et al.   GENES & DEVELOPMENT

Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability

(2011) Daniel Cortázar et al.   NATURE

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

Induction of functional hepatocyte-like cells from mouse fibroblasts by defined factors

(2011) Pengyu Huang et al.   NATURE

Direct conversion of mouse fibroblasts to hepatocyte-like cells by defined factors

(2011) Sayaka Sekiya et al.   NATURE

Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells

(2011) Deepa Subramanyam et al.   NATURE BIOTECHNOLOGY

Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells

(2011) Kitai Kim et al.   NATURE BIOTECHNOLOGY

Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells

(2011) Yuki Ohi et al.   NATURE CELL BIOLOGY

Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity

(2011) Johannes M. Freudenberg et al.   NUCLEIC ACIDS RESEARCH

Mir-290-295 deficiency in mice results in partially penetrant embryonic lethality and germ cell defects

(2011) L. A. Medeiros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

EMT and MET as paradigms for cell fate switching

(2011) J. Chen et al.   Journal of Molecular Cell Biology

Reprogramming within hours following nuclear transfer into mouse but not human zygotes

(2011) Dieter Egli et al.   Nature Communications

Lin28: A MicroRNA Regulator with a Macro Role

(2010) Srinivas R. Viswanathan et al.   CELL

Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes by Defined Factors

(2010) Masaki Ieda et al.   CELL

BMPs functionally replace Klf4 and support efficient reprogramming of mouse fibroblasts by Oct4 alone

(2010) Jiekai Chen et al.   CELL RESEARCH

Female Human iPSCs Retain an Inactive X Chromosome

(2010) Jason Tchieu et al.   Cell Stem Cell

Lab-Specific Gene Expression Signatures in Pluripotent Stem Cells

(2010) Aaron M. Newman et al.   Cell Stem Cell

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

Functional Genomics Reveals a BMP-Driven Mesenchymal-to-Epithelial Transition in the Initiation of Somatic Cell Reprogramming

(2010) Payman Samavarchi-Tehrani et al.   Cell Stem Cell

TPP1 Is Required for TERT Recruitment, Telomere Elongation during Nuclear Reprogramming, and Normal Skin Development in Mice

(2010) Agueda M. Tejera et al.   DEVELOPMENTAL CELL

Opposing microRNA families regulate self-renewal in mouse embryonic stem cells

(2010) Collin Melton et al.   NATURE

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification

(2010) Shinsuke Ito et al.   NATURE

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells

(2010) Jose M Polo et al.   NATURE BIOTECHNOLOGY

In Brief

(2010)   NATURE REVIEWS GENETICS

Persistent Donor Cell Gene Expression among Human Induced Pluripotent Stem Cells Contributes to Differences with Human Embryonic Stem Cells

(2010) Zhumur Ghosh et al.   PLoS One

Sox2 expression effects on direct reprogramming efficiency as determined by alternative somatic cell fate

(2010) Shinpei Yamaguchi et al.   Stem Cell Research

TUT4 in Concert with Lin28 Suppresses MicroRNA Biogenesis through Pre-MicroRNA Uridylation

(2009) Inha Heo et al.   CELL

Epithelial-Mesenchymal Transitions in Development and Disease

(2009) Jean Paul Thiery et al.   CELL

Telomeres Acquire Embryonic Stem Cell Characteristics in Induced Pluripotent Stem Cells

(2009) Rosa M. Marion et al.   Cell Stem Cell

iPS Cells Can Support Full-Term Development of Tetraploid Blastocyst-Complemented Embryos

(2009) Lan Kang et al.   Cell Stem Cell

A Small-Molecule Inhibitor of Tgf-β Signaling Replaces Sox2 in Reprogramming by Inducing Nanog

(2009) Justin K. Ichida et al.   Cell Stem Cell

Metastable Pluripotent States in NOD-Mouse-Derived ESCs

(2009) Jacob Hanna et al.   Cell Stem Cell

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

Induced Pluripotent Stem Cells and Embryonic Stem Cells Are Distinguished by Gene Expression Signatures

(2009) Mark H. Chin et al.   Cell Stem Cell

Tgfβ Signal Inhibition Cooperates in the Induction of iPSCs and Replaces Sox2 and cMyc

(2009) Nimet Maherali et al.   CURRENT BIOLOGY

Epigenetic reprogramming and induced pluripotency

(2009) K. Hochedlinger et al.   DEVELOPMENT

Klf4 reverts developmentally programmed restriction of ground state pluripotency

(2009) G. Guo et al.   DEVELOPMENT

Senescence impairs successful reprogramming to pluripotent stem cells

(2009) A. Banito et al.   GENES & DEVELOPMENT

Elite and stochastic models for induced pluripotent stem cell generation

(2009) Shinya Yamanaka   NATURE

Adult mice generated from induced pluripotent stem cells

(2009) Michael J. Boland et al.   NATURE

A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells

(2009) Hitoshi Niwa et al.   NATURE

A role for Lin28 in primordial germ-cell development and germ-cell malignancy

(2009) Jason A. West et al.   NATURE

Linking the p53 tumour suppressor pathway to somatic cell reprogramming

(2009) Teruhisa Kawamura et al.   NATURE

iPS cells produce viable mice through tetraploid complementation

(2009) Xiao-yang Zhao et al.   NATURE

A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity

(2009) Rosa M. Marión et al.   NATURE

Suppression of induced pluripotent stem cell generation by the p53–p21 pathway

(2009) Hyenjong Hong et al.   NATURE

Immortalization eliminates a roadblock during cellular reprogramming into iPS cells

(2009) Jochen Utikal et al.   NATURE

The Ink4/Arf locus is a barrier for iPS cell reprogramming

(2009) Han Li et al.   NATURE

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

(2009) Jie Deng et al.   NATURE BIOTECHNOLOGY

The let-7 target gene mouse lin-41 is a stem cell specific E3 ubiquitin ligase for the miRNA pathway protein Ago2

(2009) Agnieszka Rybak et al.   NATURE CELL BIOLOGY

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

Validated germline-competent embryonic stem cell lines from nonobese diabetic mice

(2009) Jennifer Nichols et al.   NATURE MEDICINE

Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposon

(2009) Kosuke Yusa et al.   NATURE METHODS

Transcriptional Signature and Memory Retention of Human-Induced Pluripotent Stem Cells

(2009) Maria C. N. Marchetto et al.   PLoS One

Stoichiometric and temporal requirements of Oct4, Sox2, Klf4, and c-Myc expression for efficient human iPSC induction and differentiation

(2009) E. P. Papapetrou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Germline Competent Embryonic Stem Cells Derived from Rat Blastocysts

(2008) Ping Li et al.   CELL

Capture of Authentic Embryonic Stem Cells from Rat Blastocysts

(2008) Mia Buehr et al.   CELL

The Growth Factor Environment Defines Distinct Pluripotent Ground States in Novel Blastocyst-Derived Stem Cells

(2008) Yu-Fen Chou et al.   CELL

Lin28 Mediates the Terminal Uridylation of let-7 Precursor MicroRNA

(2008) Inha Heo et al.   MOLECULAR CELL

In vivo reprogramming of adult pancreatic exocrine cells to β-cells

(2008) Qiao Zhou et al.   NATURE

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

A drug-inducible transgenic system for direct reprogramming of multiple somatic cell types

(2008) Marius Wernig et al.   NATURE BIOTECHNOLOGY

A core Klf circuitry regulates self-renewal of embryonic stem cells

(2008) Jianming Jiang et al.   NATURE CELL BIOLOGY

Embryonic stem cell–specific microRNAs regulate the G1-S transition and promote rapid proliferation

(2008) Yangming Wang et al.   NATURE GENETICS

Selective Blockade of MicroRNA Processing by Lin28

(2008) S. R. Viswanathan et al.   SCIENCE