Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development

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

Single-cell technologies sharpen up mammalian stem cell research

(2014) Philipp S. Hoppe et al.   NATURE CELL BIOLOGY

Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells

(2014) Huilei Xu et al.   PLoS Computational Biology

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model

(2013) Nicola Bonzanni et al.   BIOINFORMATICS

Engineering of regulated stochastic cell fate determination

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

Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths

(2013) Chunhe Li et al.   PLoS Computational Biology

Lineage-based identification of cellular states and expression programs

(2012) T. Hashimoto et al.   BIOINFORMATICS

Static network structure can be used to model the phenotypic effects of perturbations in regulatory networks

(2012) Ariel Feiglin et al.   BIOINFORMATICS

Cell fate regulation in early mammalian development

(2012) Efrat Oron et al.   PHYSICAL BIOLOGY

TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineages

(2011) A. P. Parikh et al.   BIOINFORMATICS

Stability of building gene regulatory networks with sparse autoregressive models

(2011) Jagath C Rajapakse et al.   BMC BIOINFORMATICS

Cell fate decisions and axis determination in the early mouse embryo

(2011) K. Takaoka et al.   DEVELOPMENT

Primitive Endoderm Differentiates via a Three-Step Mechanism Involving Nanog and RTK Signaling

(2011) Stephen Frankenberg et al.   DEVELOPMENTAL CELL

A General Model for Binary Cell Fate Decision Gene Circuits with Degeneracy: Indeterminacy and Switch Behavior in the Absence of Cooperativity

(2011) Mircea Andrecut et al.   PLoS One

State reduction for network intervention in probabilistic Boolean networks

(2010) Xiaoning Qian et al.   BIOINFORMATICS

BoolNet—an R package for generation, reconstruction and analysis of Boolean networks

(2010) Christoph Müssel et al.   BIOINFORMATICS

FGF signal-dependent segregation of primitive endoderm and epiblast in the mouse blastocyst

(2010) Y. Yamanaka et al.   DEVELOPMENT

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

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Cell Lineage Determination in State Space: A Systems View Brings Flexibility to Dogmatic Canonical Rules

(2010) Sui Huang   PLOS BIOLOGY

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement

(2010) Laurence Calzone et al.   PLoS Computational Biology

Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse

(2009) J. Rossant et al.   DEVELOPMENT

The Hippo Signaling Pathway Components Lats and Yap Pattern Tead4 Activity to Distinguish Mouse Trophectoderm from Inner Cell Mass

(2009) Noriyuki Nishioka et al.   DEVELOPMENTAL CELL

Uncovering operational interactions in genetic networks using asynchronous Boolean dynamics

(2009) L. Tournier et al.   JOURNAL OF THEORETICAL BIOLOGY

Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective

(2009) Sui Huang et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data

(2009) Regina Samaga et al.   PLoS Computational Biology

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS