Interrogating the topological robustness of gene regulatory circuits by randomization

Relative stability of network states in Boolean network models of gene regulation in development

(2016) Joseph Xu Zhou et al.   BIOSYSTEMS

EMT: 2016

(2016) M. Angela Nieto et al.   CELL

Molecular stripping, targets and decoys as modulators of oscillations in the NF-κB/IκBα/DNA genetic network

(2016) Zhipeng Wang et al.   Journal of the Royal Society Interface

What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast

(2016) Artémis Llamosi et al.   PLoS Computational Biology

The relationship between stochastic and deterministic quasi-steady state approximations

(2015) Jae Kyoung Kim et al.   BMC Systems Biology

Chromosomal Arrangement of Phosphorelay Genes Couples Sporulation and DNA Replication

(2015) Jatin Narula et al.   CELL

Metabolic co-dependence gives rise to collective oscillations within biofilms

(2015) Jintao Liu et al.   NATURE

Stochastic Phenotype Transition of a Single Cell in an Intermediate Region of Gene State Switching

(2015) Hao Ge et al.   PHYSICAL REVIEW LETTERS

Mutation-induced protein interaction kinetics changes affect apoptotic network dynamic properties and facilitate oncogenesis

(2015) Linjie Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determination of in vivo target search kinetics of regulatory noncoding RNA

(2015) J. Fei et al.   SCIENCE

Endogenous molecular network reveals two mechanisms of heterogeneity within gastric cancer

(2015) Site Li et al.   Oncotarget

Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis

(2015) Mohit Kumar Jolly   Frontiers in Oncology

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

(2014) Pablo Meyer et al.   BMC Systems 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

Landscape and flux reveal a new global view and physical quantification of mammalian cell cycle

(2014) Chunhe Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A circadian gene expression atlas in mammals: Implications for biology and medicine

(2014) Ray Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) J. Zhang et al.   Science Signaling

Tristability in Cancer-Associated MicroRNA-TF Chimera Toggle Switch

(2013) Mingyang Lu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

(2013) Victoria Moignard 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

Hybrid T-Helper Cells: Stabilizing the Moderate Center in a Polarized System

(2013) Sui Huang   PLOS BIOLOGY

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Quantifying the Waddington landscape and biological paths for development and differentiation

(2011) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput DNA sequencing - concepts and limitations

(2010) Martin Kircher et al.   BIOESSAYS

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

Epithelial-Mesenchymal Transitions in Development and Disease

(2009) Jean Paul Thiery et al.   CELL

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm

(2008) Jun Yan et al.   PLoS Computational Biology