CTCF Expression and Dynamic Motif Accessibility Modulates Epithelial–Mesenchymal Gene Expression

Functional hierarchy and cooperation of EMT master transcription factors in breast cancer metastasis

(2021) Joseph B Addison et al.   MOLECULAR CANCER RESEARCH

A Computational Systems Biology Approach Identifies SLUG as a Mediator of Partial Epithelial-Mesenchymal Transition (EMT)

(2021) Ayalur R. Subbalakshmi et al.   CELLS TISSUES ORGANS

Identification of EMT signaling cross-talk and gene regulatory networks by single-cell RNA sequencing

(2021) Abhijeet P. Deshmukh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tximeta: Reference sequence checksums for provenance identification in RNA-seq

(2020) Michael I. Love et al.   PLoS Computational Biology

Context specificity of the EMT transcriptional response

(2020) David P. Cook et al.   Nature Communications

Comparative Study of Transcriptomics-Based Scoring Metrics for the Epithelial-Hybrid-Mesenchymal Spectrum

(2020) Priyanka Chakraborty et al.   Frontiers in Bioengineering and Biotechnology

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

CD44 splice isoform switching determines breast cancer stem cell state

(2019) Honghong Zhang et al.   GENES & DEVELOPMENT

A Hierarchical Regulatory Landscape during the Multiple Stages of EMT

(2019) Nathalie Meyer-Schaller et al.   DEVELOPMENTAL CELL

CTCF: a Swiss-army knife for genome organization and transcription regulation

(2019) Luca Braccioli et al.   Essays in Biochemistry

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

Dysregulation of EMT Drives the Progression to Clinically Aggressive Sarcomatoid Bladder Cancer

(2019) Charles C. Guo et al.   Cell Reports

An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis

(2019) Jiao Li et al.   Nature Communications

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells

(2019) David N. Debruyne et al.   NATURE

E-cadherin is required for metastasis in multiple models of breast cancer

(2019) Veena Padmanaban et al.   NATURE

A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition

(2019) José L. McFaline-Figueroa et al.   NATURE GENETICS

Author Correction: Competitive endogenous RNA is an intrinsic component of EMT regulatory circuits and modulates EMT

(2019) Yuwei Liu et al.   Nature Communications

Context Dependency of Epithelial-to-Mesenchymal Transition for Metastasis

(2019) Tatiana Revenco et al.   Cell Reports

Gene signatures of tumor inflammation and epithelial-to-mesenchymal transition (EMT) predict responses to immune checkpoint blockade in lung cancer with high accuracy

(2019) Jeffrey C. Thompson et al.   LUNG CANCER

Developing in 3D: the role of CTCF in cell differentiation

(2018) Rodrigo G. Arzate-Mejía et al.   DEVELOPMENT

EMT Subtype Influences Epithelial Plasticity and Mode of Cell Migration

(2018) Nicole M. Aiello et al.   DEVELOPMENTAL CELL

GIGGLE: a search engine for large-scale integrated genome analysis

(2018) Ryan M Layer et al.   NATURE METHODS

Epigenetic and Transcriptomic Profiling of Mammary Gland Development and Tumor Models Disclose Regulators of Cell State Plasticity

(2018) Christopher Dravis et al.   CANCER CELL

Identification of the tumour transition states occurring during EMT

(2018) Ievgenia Pastushenko et al.   NATURE

Hybrid epithelial/mesenchymal phenotypes promote metastasis and therapy resistance across carcinomas

(2018) Mohit Kumar Jolly et al.   PHARMACOLOGY & THERAPEUTICS

Non-redundant functions of EMT transcription factors

(2018) Marc P. Stemmler et al.   NATURE CELL BIOLOGY

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

(2018) Rongbin Zheng et al.   NUCLEIC ACIDS RESEARCH

Intranuclear and higher-order chromatin organization of the major histone gene cluster in breast cancer

(2017) Andrew J. Fritz et al.   JOURNAL OF CELLULAR PHYSIOLOGY

The CCCTC-binding factor (CTCF)-forkhead box protein M1 axis regulates tumour growth and metastasis in hepatocellular carcinoma

(2017) Bin Zhang et al.   JOURNAL OF PATHOLOGY

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Breast tumor cell-specific knockout ofTwist1inhibits cancer cell plasticity, dissemination, and lung metastasis in mice

(2017) Yixiang Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrin-β4 identifies cancer stem cell-enriched populations of partially mesenchymal carcinoma cells

(2017) Brian Bierie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predictive value of epithelial-mesenchymal-transition (EMT) signature and PARP-1 in prostate cancer radioresistance

(2017) Timothy W. Stark et al.   PROSTATE

Epithelial-to-Mesenchymal Transition: Epigenetic Reprogramming Driving Cellular Plasticity

(2017) Nicolas Skrypek et al.   TRENDS IN GENETICS

CTCF promotes epithelial ovarian cancer metastasis by broadly controlling the expression of metastasis-associated genes

(2017) Lintao Zhao et al.   Oncotarget

The H3K27me3-demethylase KDM6A is suppressed in breast cancer stem-like cells, and enables the resolution of bivalency during the mesenchymal-epithelial transition

(2017) Joseph H. Taube et al.   Oncotarget

Dynamics of chromatin accessibility during TGF-β-induced EMT of Ras-transformed mammary gland epithelial cells

(2017) Mayu Arase et al.   Scientific Reports

The Z-cad dual fluorescent sensor detects dynamic changes between the epithelial and mesenchymal cellular states

(2016) M. J. Toneff et al.   BMC BIOLOGY

EMT: 2016

(2016) M. Angela Nieto et al.   CELL

CTCF: making the right connections

(2016) Rodolfo Ghirlando et al.   GENES & DEVELOPMENT

Grainyhead-like 2 downstream targets act to suppress epithelial-to-mesenchymal transition during neural tube closure

(2016) Heather J. Ray et al.   JOURNAL OF CELL SCIENCE

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

CELF1 is a central node in post-transcriptional regulatory programmes underlying EMT

(2016) Arindam Chaudhury et al.   Nature Communications

The histone variant H2A.X is a regulator of the epithelial–mesenchymal transition

(2016) Urbain Weyemi et al.   Nature Communications

Mutational Biases Drive Elevated Rates of Substitution at Regulatory Sites across Cancer Types

(2016) Vera B. Kaiser et al.   PLoS Genetics

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Distinct EMT programs control normal mammary stem cells and tumour-initiating cells

(2015) Xin Ye et al.   NATURE

Stemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival

(2015) Anne Grosse-Wilde et al.   PLoS One

Epithelial to mesenchymal transition is associated with rapamycin resistance

(2015) Ashley M. Holder et al.   Oncotarget

Sox10 Regulates Stem/Progenitor and Mesenchymal Cell States in Mammary Epithelial Cells

(2015) Christopher Dravis et al.   Cell Reports

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

P-Cadherin Linking Breast Cancer Stem Cells and Invasion: A Promising Marker to Identify an “Intermediate/Metastable” EMT State

(2015) Ana Sofia Ribeiro et al.   Frontiers in Oncology

Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis

(2015) Mohit Kumar Jolly   Frontiers in Oncology

Transient SNAIL1 Expression Is Necessary for Metastatic Competence in Breast Cancer

(2014) H. D. Tran et al.   CANCER RESEARCH

TGF- -induced epithelial-to-mesenchymal transition proceeds through stepwise activation of multiple feedback loops

(2014) J. Zhang et al.   Science Signaling

FOXC2 Expression Links Epithelial-Mesenchymal Transition and Stem Cell Properties in Breast Cancer

(2013) B. G. Hollier et al.   CANCER RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Investigating the Link between Molecular Subtypes of Glioblastoma, Epithelial-Mesenchymal Transition, and CD133 Cell Surface Protein

(2013) Hadi Zarkoob et al.   PLoS One

Transcription Factors OVOL1 and OVOL2 Induce the Mesenchymal to Epithelial Transition in Human Cancer

(2013) Hernan Roca et al.   PLoS One

An EMT spectrum defines an anoikis-resistant and spheroidogenic intermediate mesenchymal state that is sensitive to e-cadherin restoration by a src-kinase inhibitor, saracatinib (AZD0530)

(2013) R Y-J Huang et al.   Cell Death & Disease

Epigenetic silencing of microRNA-203 is required for EMT and cancer stem cell properties

(2013) Joseph H. Taube et al.   Scientific Reports

Architecture of epigenetic reprogramming following Twist1-mediated epithelial-mesenchymal transition

(2013) Gabriel G Malouf et al.   GENOME BIOLOGY

Spatiotemporal Regulation of Epithelial-Mesenchymal Transition Is Essential for Squamous Cell Carcinoma Metastasis

(2012) Jeff H. Tsai et al.   CANCER CELL

An Epithelial-Mesenchymal Transition Gene Signature Predicts Resistance to EGFR and PI3K Inhibitors and Identifies Axl as a Therapeutic Target for Overcoming EGFR Inhibitor Resistance

(2012) L. A. Byers et al.   CLINICAL CANCER RESEARCH

Matrix rigidity regulates a switch between TGF-β1–induced apoptosis and epithelial–mesenchymal transition

(2012) Jennifer L. Leight et al.   MOLECULAR BIOLOGY OF THE CELL

Elf5 inhibits the epithelial–mesenchymal transition in mammary gland development and breast cancer metastasis by transcriptionally repressing Snail2

(2012) Rumela Chakrabarti et al.   NATURE CELL BIOLOGY

MicroRNAs as regulators of epithelial-mesenchymal transition

(2011) Philip A. Gregory et al.   CELL CYCLE

CD44 splice isoform switching in human and mouse epithelium is essential for epithelial-mesenchymal transition and breast cancer progression

(2011) Rhonda L. Brown et al.   JOURNAL OF CLINICAL INVESTIGATION

Identification of an mRNP Complex Regulating Tumorigenesis at the Translational Elongation Step

(2011) George S. Hussey et al.   MOLECULAR CELL

Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition

(2011) Oliver G McDonald et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

miR-9, a MYC/MYCN-activated microRNA, regulates E-cadherin and cancer metastasis

(2010) Li Ma et al.   NATURE CELL BIOLOGY

Role for DNA Methylation in the Regulation of miR-200c and miR-141 Expression in Normal and Cancer Cells

(2010) Lukas Vrba et al.   PLoS One

Core epithelial-to-mesenchymal transition interactome gene-expression signature is associated with claudin-low and metaplastic breast cancer subtypes

(2010) J. H. Taube et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

TGF-β-induced epithelial to mesenchymal transition

(2009) Jian Xu et al.   CELL RESEARCH

The EMT-activator ZEB1 promotes tumorigenicity by repressing stemness-inhibiting microRNAs

(2009) Ulrich Wellner et al.   NATURE CELL BIOLOGY

A Double-Negative Feedback Loop between ZEB1-SIP1 and the microRNA-200 Family Regulates Epithelial-Mesenchymal Transition

(2008) C. P. Bracken et al.   CANCER RESEARCH

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

Direct regulation of TWIST by HIF-1α promotes metastasis

(2008) Muh-Hwa Yang et al.   NATURE CELL BIOLOGY