Inference of Intercellular Communications and Multilayer Gene-Regulations of Epithelial–Mesenchymal Transition From Single-Cell Transcriptomic Data

The Physics of Cellular Decision Making During Epithelial–Mesenchymal Transition

(2020) Shubham Tripathi et al.   Annual Review of Biophysics

Guidelines and definitions for research on epithelial–mesenchymal transition

(2020) Jing Yang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics

(2020) Simon Cabello-Aguilar et al.   NUCLEIC ACIDS RESEARCH

Context specificity of the EMT transcriptional response

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

Inferring spatial and signaling relationships between cells from single cell transcriptomic data

(2020) Zixuan Cang et al.   Nature Communications

A plausible accelerating function of intermediate states in cancer metastasis

(2020) Hanah Goetz et al.   PLoS Computational Biology

Understanding the Principles of Pattern Formation Driven by Notch Signaling by Integrating Experiments and Theoretical Models

(2020) Federico Bocci et al.   Frontiers in Physiology

Toward Modeling Context-Specific EMT Regulatory Networks Using Temporal Single Cell RNA-Seq Data

(2020) Daniel Ramirez et al.   Frontiers in Molecular Biosciences

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

(2020) Yutong Sha et al.   NUCLEIC ACIDS RESEARCH

Cell lineage and communication network inference via optimization for single-cell transcriptomics

(2019) Shuxiong Wang et al.   NUCLEIC ACIDS RESEARCH

TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data

(2019) Shaokun An et al.   BMC GENOMICS

TGF-β-Mediated Epithelial-Mesenchymal Transition and Cancer Metastasis

(2019) Yang Hao et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A gene regulatory network to control EMT programs in development and disease

(2019) Hassan Fazilaty et al.   Nature Communications

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data

(2018) Suoqin Jin et al.   BIOINFORMATICS

A mechanism-based computational model to capture the interconnections among epithelial-mesenchymal transition, cancer stem cells and Notch-Jagged signaling

(2018) Federico Bocci et al.   Oncotarget

Identification of the tumour transition states occurring during EMT

(2018) Ievgenia Pastushenko et al.   NATURE

DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data

(2018) Ziwei Chen et al.   BIOINFORMATICS

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Toward understanding cancer stem cell heterogeneity in the tumor microenvironment

(2018) Federico Bocci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics

(2018) Manu P. Kumar et al.   Cell Reports

Numb prevents a complete epithelial–mesenchymal transition by modulating Notch signalling

(2017) Federico Bocci et al.   Journal of the Royal Society Interface

Multilineage communication regulates human liver bud development from pluripotency

(2017) J. Gray Camp et al.   NATURE

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

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

Notch signalling in context

(2016) Sarah J. Bray   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Quantifying the landscape and kinetic paths for epithelial–mesenchymal transition from a core circuit

(2016) Chunhe Li et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

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

Network biology approach to epithelial–mesenchymal transition in cancer metastasis: three stage theory

(2015) Hiroshi Tanaka et al.   Journal of Molecular Cell Biology

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

Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis

(2015) Mohit Kumar Jolly   Frontiers in Oncology

Regulation of NF-κB by TNF family cytokines

(2014) Matthew S. Hayden et al.   SEMINARS IN IMMUNOLOGY

A Mathematical Model for MicroRNA in Lung Cancer

(2013) Hye-Won Kang et al.   PLoS One

TGF-β-induced epithelial to mesenchymal transition

(2009) Jian Xu et al.   CELL RESEARCH

Mechanisms of the epithelial–mesenchymal transition by TGF-β

(2009) Michael K Wendt et al.   Future Oncology

The basics of epithelial-mesenchymal transition

(2009) Raghu Kalluri et al.   JOURNAL OF CLINICAL INVESTIGATION

Cell Lineages and the Logic of Proliferative Control

(2009) Arthur D Lander et al.   PLOS BIOLOGY