Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data

A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells

(2020) Shubham Tripathi et al.   PLoS Computational Biology

Epigenetic feedback and stochastic partitioning during cell division can drive resistance to EMT

(2020) Wen Jia et al.   Oncotarget

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Quantifying Cancer Epithelial-Mesenchymal Plasticity and its Association with Stemness and Immune Response

(2019) Dongya Jia et al.   Journal of Clinical Medicine

Network Topologies That Can Achieve Dual Function of Adaptation and Noise Attenuation

(2019) Lingxia Qiao et al.   Cell Systems

Dynamics of Phenotypic Heterogeneity during EMT and Stemness in Cancer Progression

(2019) Jolly et al.   Journal of Clinical Medicine

Mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution

(2019) Loukia G. Karacosta et al.   Nature Communications

scRCMF: Identification of Cell Subpopulations and Transition States From Single-Cell Transcriptomes

(2019) Xiaoying Zheng et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

(2018) Josip S Herman et al.   NATURE METHODS

Topography of epithelial–mesenchymal plasticity

(2018) Francesc Font-Clos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MFAP2 promotes epithelial–mesenchymal transition in gastric cancer cells by activating TGF-β/SMAD2/3 signaling pathway

(2018) Jian-Kai Wang et al.   OncoTargets and Therapy

Identification of the tumour transition states occurring during EMT

(2018) Ievgenia Pastushenko et al.   NATURE

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Semisoft clustering of single-cell data

(2018) Lingxue Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

EMT Transition States during Tumor Progression and Metastasis

(2018) Ievgenia Pastushenko et al.   TRENDS IN CELL BIOLOGY

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

A sequential EMT-MET mechanism drives the differentiation of human embryonic stem cells towards hepatocytes

(2017) Qiuhong Li et al.   Nature Communications

IGF-1 induces the epithelial-mesenchymal transition via Stat5 in hepatocellular carcinoma

(2017) Chuanzong Zhao et al.   Oncotarget

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures

(2017) Thalia E. Chan et al.   Cell Systems

EMT: 2016

(2016) M. Angela Nieto et al.   CELL

Controlling stochasticity in epithelial-mesenchymal transition through multiple intermediate cellular states

(2016) Catherine Ha Ta et al.   DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS-SERIES B

Notch-Jagged signalling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype

(2016) Marcelo Boareto et al.   Journal of the Royal Society Interface

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Stability of the hybrid epithelial/mesenchymal phenotype

(2016) Mohit Kumar Jolly et al.   Oncotarget

Cell Fate Decision as High-Dimensional Critical State Transition

(2016) Mitra Mojtahedi et al.   PLOS BIOLOGY

Signal Transduction Pathways of EMT Induced by TGF-β, SHH, and WNT and Their Crosstalks

(2016) Jingyu Zhang et al.   Journal of Clinical Medicine

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Epithelial-to-mesenchymal transition induces cell cycle arrest and parenchymal damage in renal fibrosis

(2015) Sara Lovisa et al.   NATURE MEDICINE

OVOL guides the epithelial-hybrid-mesenchymal transition

(2015) Dongya Jia et al.   Oncotarget

An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States

(2015) Tian Hong et al.   PLoS Computational Biology

Network Modeling of TGF  Signaling in Hepatocellular Carcinoma Epithelial-to-Mesenchymal Transition Reveals Joint Sonic Hedgehog and Wnt Pathway Activation

(2014) S. N. Steinway et al.   CANCER RESEARCH

SymNMF: nonnegative low-rank approximation of a similarity matrix for graph clustering

(2014) Da Kuang et al.   JOURNAL OF GLOBAL OPTIMIZATION

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Oncogenic roles of EMT-inducing transcription factors

(2014) Alain Puisieux et al.   NATURE CELL BIOLOGY

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

(2014) J. Zhang et al.   Science Signaling

Coupled Reversible and Irreversible Bistable Switches Underlying TGFβ-induced Epithelial to Mesenchymal Transition

(2013) Xiao-Jun Tian et al.   BIOPHYSICAL JOURNAL

Sequential introduction of reprogramming factors reveals a time-sensitive requirement for individual factors and a sequential EMT–MET mechanism for optimal reprogramming

(2013) Xiaopeng Liu et al.   NATURE CELL BIOLOGY

MicroRNA-based regulation of epithelial-hybrid-mesenchymal fate determination

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

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

Bacterial survival strategies suggest rethinking cancer cooperativity

(2012) Eshel Ben-Jacob et al.   TRENDS IN MICROBIOLOGY

Stochastic State Transitions Give Rise to Phenotypic Equilibrium in Populations of Cancer Cells

(2011) Piyush B. Gupta et al.   CELL

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

SVD based initialization: A head start for nonnegative matrix factorization

(2007) C. Boutsidis et al.   PATTERN RECOGNITION