The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

Metabolomics and transcriptomics identify pathway differences between visceral and subcutaneous adipose tissue in colorectal cancer patients: the ColoCare study

(2015) David B Liesenfeld et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

An alternative pluripotent state confers interspecies chimaeric competency

(2015) Jun Wu et al.   NATURE

Alternative Routes to Induce Naïve Pluripotency in Human Embryonic Stem Cells

(2015) Galbha Duggal et al.   STEM CELLS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Yasuhiro Takashima et al.   CELL

Methionine Metabolism Regulates Maintenance and Differentiation of Human Pluripotent Stem Cells

(2014) Nobuaki Shiraki et al.   Cell Metabolism

Hypoxia-Inducible Factors Have Distinct and Stage-Specific Roles during Reprogramming of Human Cells to Pluripotency

(2014) Julie Mathieu et al.   Cell Stem Cell

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

Epigenomic Comparison Reveals Activation of “Seed” Enhancers during Transition from Naive to Primed Pluripotency

(2014) Daniel C. Factor et al.   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

An iCRISPR Platform for Rapid, Multiplexable, and Inducible Genome Editing in Human Pluripotent Stem Cells

(2014) Federico González et al.   Cell Stem Cell

miR-155 Activates Cytokine Gene Expression in Th17 Cells by Regulating the DNA-Binding Protein Jarid2 to Relieve Polycomb-Mediated Repression

(2014) Thelma M. Escobar et al.   IMMUNITY

Nicotinamide N-methyltransferase knockdown protects against diet-induced obesity

(2014) Daniel Kraus et al.   NATURE

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

miRNA sensitivity to Drosha levels correlates with pre-miRNA secondary structure

(2014) H. Sperber et al.   RNA

An integral program for tissue renewal and regeneration: Wnt signaling and stem cell control

(2014) H. Clevers et al.   SCIENCE

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

(2014) Bahram Valamehr et al.   Stem Cell Reports

Targeted enrichment and high-resolution digital profiling of mitochondrial DNA deletions in human brain

(2013) Sean D. Taylor et al.   AGING CELL

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

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

Molecular mechanism of sphingosine-1-phosphate action in Duchenne muscular dystrophy

(2013) D.-H. Nguyen-Tran et al.   Disease Models & Mechanisms

Energy metabolism and energy-sensing pathways in mammalian embryonic and adult stem cell fate

(2013) V. A. Rafalski et al.   JOURNAL OF CELL SCIENCE

Derivation of novel human ground state naive pluripotent stem cells

(2013) Ohad Gafni et al.   NATURE

NNMT promotes epigenetic remodeling in cancer by creating a metabolic methylation sink

(2013) Olesya A Ulanovskaya et al.   Nature Chemical Biology

LipidBlast in silico tandem mass spectrometry database for lipid identification

(2013) Tobias Kind et al.   NATURE METHODS

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

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

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

Hypoxia induces re-entry of committed cells into pluripotency

(2013) Julie Mathieu et al.   STEM CELLS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The updated biology of hypoxia-inducible factor

(2012) Samantha N Greer et al.   EMBO JOURNAL

HIF1α induced switch from bivalent to exclusively glycolytic metabolism during ESC-to-EpiSC/hESC transition

(2012) Wenyu Zhou et al.   EMBO JOURNAL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Induced Pluripotent Stem Cells Show Metabolomic Differences to Embryonic Stem Cells in Polyunsaturated Phosphatidylcholines and Primary Metabolism

(2012) John K. Meissen et al.   PLoS One

Wnt/ -catenin signaling promotes differentiation, not self-renewal, of human embryonic stem cells and is repressed by Oct4

(2012) K. C. Davidson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Influence of Threonine Metabolism on S-Adenosylmethionine and Histone Methylation

(2012) N. Shyh-Chang et al.   SCIENCE

Endogenous Wnt signalling in human embryonic stem cells generates an equilibrium of distinct lineage-specified progenitors

(2012) Timothy A. Blauwkamp et al.   Nature Communications

Somatic Oxidative Bioenergetics Transitions into Pluripotency-Dependent Glycolysis to Facilitate Nuclear Reprogramming

(2011) Clifford D.L. Folmes et al.   Cell Metabolism

The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming

(2011) Athanasia D Panopoulos et al.   CELL RESEARCH

UCP2 regulates energy metabolism and differentiation potential of human pluripotent stem cells

(2011) Jin Zhang et al.   EMBO JOURNAL

Modulation of mitochondrial biogenesis and bioenergetic metabolism upon in vitro and in vivo differentiation of human ES and iPS cells

(2011) Alessandro Prigione et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

An endogenous tumour-promoting ligand of the human aryl hydrocarbon receptor

(2011) Christiane A. Opitz et al.   NATURE

Embryonic stem cells require Wnt proteins to prevent differentiation to epiblast stem cells

(2011) Derk ten Berge et al.   NATURE CELL BIOLOGY

Energy Metabolism in Human Pluripotent Stem Cells and Their Differentiated Counterparts

(2011) Sandra Varum et al.   PLoS One

Assessment of Hypoxia Inducible Factor Levels in Cancer Cell Lines upon Hypoxic Induction Using a Novel Reporter Construct

(2011) Wenyu Zhou et al.   PLoS One

The Role of the Leukemia Inhibitory Factor (LIF) — Pathway in Derivation and Maintenance of Murine Pluripotent Stem Cells

(2011) Urs Graf et al.   Genes

A framework for oligonucleotide microarray preprocessing

(2010) Benilton S. Carvalho et al.   BIOINFORMATICS

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

O2 regulates stem cells through Wnt/β-catenin signalling

(2010) Jolly Mazumdar et al.   NATURE CELL BIOLOGY

Metabolic oxidation regulates embryonic stem cell differentiation

(2010) Oscar Yanes et al.   Nature Chemical Biology

Carbon metabolism–mediated myogenic differentiation

(2010) Abigail L Bracha et al.   Nature Chemical Biology

Genetic Evidence for High-Altitude Adaptation in Tibet

(2010) T. S. Simonson et al.   SCIENCE

Inactive yet indispensable: the tale of Jarid2

(2010) David Landeira et al.   TRENDS IN CELL BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

FiehnLib: Mass Spectral and Retention Index Libraries for Metabolomics Based on Quadrupole and Time-of-Flight Gas Chromatography/Mass Spectrometry

(2009) Tobias Kind et al.   ANALYTICAL CHEMISTRY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY