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spliceJAC: transition genes and state‐specific gene regulation from single‐cell transcriptome data

Molecular systems biology, 2022-11, Vol.18 (11), p.e11176-n/a

2022

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Decoding leader cells in collective cancer invasion

Nature reviews. Cancer, 2021-09, Vol.21 (9), p.592-604

2021

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Toward understanding cancer stem cell heterogeneity in the tumor microenvironment

Proceedings of the National Academy of Sciences - PNAS, 2019-01, Vol.116 (1), p.148-157

2019

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

Frontiers in physiology, 2020-07, Vol.11, p.929-929

2020

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A Biophysical Model Uncovers the Size Distribution of Migrating Cell Clusters across Cancer Types

Cancer research (Chicago, Ill.), 2019-11, Vol.79 (21), p.5527-5535

2019

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Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway

PLoS computational biology, 2022-07, Vol.18 (7), p.e1010306-e1010306

2022

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

Journal of the Royal Society interface, 2017-11, Vol.14 (136), p.20170512

2017

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Spatial–temporal order–disorder transition in angiogenic NOTCH signaling controls cell fate specification

eLife, 2024-02, Vol.12

2024

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

Frontiers in genetics, 2021-01, Vol.11, p.604585-604585

2021

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NRF2 activates a partial epithelial-mesenchymal transition and is maximally present in a hybrid epithelial/mesenchymal phenotype

Integrative biology (Cambridge), 2019-06, Vol.11 (6), p.251-263

2019

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Coupled Feedback Loops Involving PAGE4, EMT and Notch Signaling Can Give Rise to Non-genetic Heterogeneity in Prostate Cancer Cells

Entropy (Basel, Switzerland), 2021-02, Vol.23 (3), p.288

2021

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Editorial: Epithelial to Mesenchymal Plasticity in Colorectal Cancer

Frontiers in cell and developmental biology, 2022-06, Vol.10, p.950980-950980

2022

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Investigating epithelial‐mesenchymal heterogeneity of tumors and circulating tumor cells with transcriptomic analysis and biophysical modeling

Computational and systems oncology, 2021-06, Vol.1 (2), p.n/a

2021

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Nrf2 Modulates the Hybrid Epithelial/Mesenchymal Phenotype and Notch Signaling During Collective Cancer Migration

Frontiers in molecular biosciences, 2022-04, Vol.9, p.807324-807324

2022

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Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data

Biophysical journal, 2024-09, Vol.123 (17), p.2849-2859

2024

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Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level

Biomolecules (Basel, Switzerland), 2019-02, Vol.9 (2), p.77

2019

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Spatial transition tensor of single cells

Nature methods, 2024-06, Vol.21 (6), p.1053

2024

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Single-Cell RNA-Seq Analysis Reveals the Acquisition of Cancer Stem Cell Traits and Increase of Cell-Cell Signaling during EMT Progression

Cancers, 2021-11, Vol.13 (22), p.5726

2021

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Theoretical and computational tools to model multistable gene regulatory networks

Reports on progress in physics, 2023-10, Vol.86 (10), p.106601

2023

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

Oncotarget, 2018-07, Vol.9 (52), p.29906-29920

2018

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Pericytes enable effective angiogenesis in the presence of proinflammatory signals

Proceedings of the National Academy of Sciences - PNAS, 2019-11, Vol.116 (47), p.23551-23561

2019

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Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification

eLife, 2024-02, Vol.12

2024

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Role of metabolic spatiotemporal dynamics in regulating biofilm colony expansion

Proceedings of the National Academy of Sciences - PNAS, 2018-04, Vol.115 (16), p.4288-4293

2018

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Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks

Methods in molecular biology (Clifton, N.J.), 2019, Vol.1912, p.341

2019

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

Journal of clinical medicine, 2019-05, Vol.8 (5), p.725

2019

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spliceJAC: transition genes and state‐specific gene regulation from single‐cell transcriptome data

Decoding leader cells in collective cancer invasion

Toward understanding cancer stem cell heterogeneity in the tumor microenvironment

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

A Biophysical Model Uncovers the Size Distribution of Migrating Cell Clusters across Cancer Types

Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway

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

Spatial–temporal order–disorder transition in angiogenic NOTCH signaling controls cell fate specification

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

NRF2 activates a partial epithelial-mesenchymal transition and is maximally present in a hybrid epithelial/mesenchymal phenotype

Coupled Feedback Loops Involving PAGE4, EMT and Notch Signaling Can Give Rise to Non-genetic Heterogeneity in Prostate Cancer Cells

Editorial: Epithelial to Mesenchymal Plasticity in Colorectal Cancer

Investigating epithelial‐mesenchymal heterogeneity of tumors and circulating tumor cells with transcriptomic analysis and biophysical modeling

Nrf2 Modulates the Hybrid Epithelial/Mesenchymal Phenotype and Notch Signaling During Collective Cancer Migration

Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data

Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level

Spatial transition tensor of single cells

Single-Cell RNA-Seq Analysis Reveals the Acquisition of Cancer Stem Cell Traits and Increase of Cell-Cell Signaling during EMT Progression

Theoretical and computational tools to model multistable gene regulatory networks

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

Pericytes enable effective angiogenesis in the presence of proinflammatory signals

Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification

Role of metabolic spatiotemporal dynamics in regulating biofilm colony expansion

Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks

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

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