Polycomb repressive complex 2 shields naïve human pluripotent cells from trophectoderm differentiation

ShinyCell: simple and sharable visualization of single-cell gene expression data

(2021) John F Ouyang et al.   BIOINFORMATICS

Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification

(2021) Dimitri Meistermann et al.   Cell Stem Cell

CellProfiler 4: improvements in speed, utility and usability

(2021) David R. Stirling et al.   BMC BIOINFORMATICS

MSX2 safeguards syncytiotrophoblast fate of human trophoblast stem cells

(2021) Ruth Hornbachner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BMP-treated human embryonic stem cells transcriptionally resemble amnion cells in the monkey embryo

(2021) Sapna Chhabra et al.   Biology Open

Single-cell transcriptomic characterization of a gastrulating human embryo

(2021) Richard C. V. Tyser et al.   NATURE

The nf-core framework for community-curated bioinformatics pipelines

(2020) Philip A. Ewels et al.   NATURE BIOTECHNOLOGY

GATA3 Mediates a Fast, Irreversible Commitment to BMP4-Driven Differentiation in Human Embryonic Stem Cells

(2020) Alexandra Gunne-Braden et al.   Cell Stem Cell

Cell-Surface Proteomics Identifies Differences in Signaling and Adhesion Protein Expression between Naive and Primed Human Pluripotent Stem Cells

(2020) Katarzyna Wojdyla et al.   Stem Cell Reports

Naive Human Embryonic Stem Cells Can Give Rise to Cells with a Trophoblast-like Transcriptome and Methylome

(2020) Jessica K. Cinkornpumin et al.   Stem Cell Reports

Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution

(2019) Tobias Messmer et al.   Cell Reports

Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression

(2019) Nadezda A. Fursova et al.   MOLECULAR CELL

Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States

(2019) Stephanie L. Battle et al.   Stem Cell Reports

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Controlled modelling of human epiblast and amnion development using stem cells

(2019) Yi Zheng et al.   NATURE

Quantitative Multiplexed ChIP Reveals Global Alterations that Shape Promoter Bivalency in Ground State Embryonic Stem Cells

(2019) Banushree Kumar et al.   Cell Reports

Untargeted histone profiling during naive conversion uncovers conserved modification markers between mouse and human

(2019) Laura De Clerck et al.   Scientific Reports

Histone H2AK119 Mono-Ubiquitination Is Essential for Polycomb-Mediated Transcriptional Repression

(2019) Simone Tamburri et al.   MOLECULAR CELL

PRC1 Catalytic Activity Is Central to Polycomb System Function

(2019) Neil P. Blackledge et al.   MOLECULAR CELL

A developmental landscape of 3D-cultured human pre-gastrulation embryos

(2019) Lifeng Xiang et al.   NATURE

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

TFAP2C regulates transcription in human naive pluripotency by opening enhancers

(2018) William A. Pastor et al.   NATURE CELL BIOLOGY

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency

(2018) Guido van Mierlo et al.   Cell Stem Cell

An allosteric PRC2 inhibitor targeting the H3K27me3 binding pocket of EED

(2017) Wei Qi et al.   Nature Chemical Biology

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency

(2017) Christian Krendl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor

(2017) James D. Moody et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PRC2 specifies ectoderm lineages and maintains pluripotency in primed but not naïve ESCs

(2017) Yongli Shan et al.   Nature Communications

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

(2016) Charles Girardot et al.   BMC BIOINFORMATICS

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

Molecular Criteria for Defining the Naive Human Pluripotent State

(2016) Thorold W. Theunissen et al.   Cell Stem Cell

A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes

(2016) Peter van Galen et al.   MOLECULAR CELL

Dynamic stem cell states: naive to primed pluripotency in rodents and humans

(2016) Leehee Weinberger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Concise Review: Lessons from Naïve Human Pluripotent Cells

(2016) Carol B. Ware   STEM CELLS

An annotated list of bivalent chromatin regions in human ES cells: a new tool for cancer epigenetic research

(2016) Franck Court et al.   Oncotarget

A High-Density Map for Navigating the Human Polycomb Complexome

(2016) Simon Hauri et al.   Cell Reports

Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells

(2016) Adam Collinson et al.   Cell Reports

Defining the three cell lineages of the human blastocyst by single-cell RNA-seq

(2015) Paul Blakeley et al.   DEVELOPMENT

Efficient solar-to-fuels production from a hybrid microbial–water-splitting catalyst system

(2015) Joseph P. Torella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CD24 tracks divergent pluripotent states in mouse and human cells

(2015) Nika Shakiba et al.   Nature Communications

Variant PRC1 Complex-Dependent H2A Ubiquitylation Drives PRC2 Recruitment and Polycomb Domain Formation

(2014) Neil P. Blackledge et al.   CELL

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

(2014) Yasuhiro Takashima et al.   CELL

The Naive State of Human Pluripotent Stem Cells: A Synthesis of Stem Cell and Preimplantation Embryo Transcriptome Analyses

(2014) Kevin Huang 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

Selective Inhibition of EZH2 by EPZ-6438 Leads to Potent Antitumor Activity in EZH2-Mutant Non-Hodgkin Lymphoma

(2014) S. K. Knutson et al.   MOLECULAR CANCER THERAPEUTICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

Clonal culturing of human embryonic stem cells on laminin-521/E-cadherin matrix in defined and xeno-free environment

(2014) Sergey Rodin et al.   Nature Communications

Genome-wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblasts

(2014) Helen Pemberton et al.   GENOME BIOLOGY

Nonredundant and locus-specific gene repression functions of PRC1 paralog family members in human hematopoietic stem/progenitor cells

(2013) V. van den Boom et al.   BLOOD

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

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

BMP4-directed trophoblast differentiation of human embryonic stem cells is mediated through a ΔNp63 + cytotrophoblast stem cell state

(2013) Yingchun Li et al.   DEVELOPMENT

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

Durable tumor regression in genetically altered malignant rhabdoid tumors by inhibition of methyltransferase EZH2

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

Complete and unidirectional conversion of human embryonic stem cells to trophoblast by BMP4

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

RYBP-PRC1 Complexes Mediate H2A Ubiquitylation at Polycomb Target Sites Independently of PRC2 and H3K27me3

(2012) Lígia Tavares et al.   CELL

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Isolation of primitive endoderm, mesoderm, vascular endothelial and trophoblast progenitors from human pluripotent stem cells

(2012) Micha Drukker et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcriptomic Signature of Trophoblast Differentiation in a Human Embryonic Stem Cell Model1

(2011) Melanie Marchand et al.   BIOLOGY OF REPRODUCTION

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells

(2011) Oren Ram et al.   CELL

Dissecting the First Transcriptional Divergence During Human Embryonic Development

(2011) Qiang Bai et al.   Stem Cell Reviews and Reports

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2

(2010) A. Ralston et al.   DEVELOPMENT

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

Polycomb group proteins Ring1A/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity

(2008) M. Endoh et al.   DEVELOPMENT

BCRP/ABCG2 in the Placenta: Expression, Function and Regulation

(2008) Qingcheng Mao   PHARMACEUTICAL RESEARCH

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

(2008) Manching Ku et al.   PLoS Genetics