Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data

Decoding the regulatory network of early blood development from single-cell gene expression measurements

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

Causal network inference using biochemical kinetics

(2014) Chris J. Oates et al.   BIOINFORMATICS

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data

(2014) Fernando Amat et al.   NATURE METHODS

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation

(2014) Juliane Liepe et al.   Nature Protocols

Model Selection in Systems Biology Depends on Experimental Design

(2014) Daniel Silk et al.   PLoS Computational Biology

Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics

(2013) Andrea Ocone et al.   BIOINFORMATICS

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

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

Markov chain Monte Carlo inference for Markov jump processes via the linear noise approximation

(2013) V. Stathopoulos et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Reprogramming Cellular Identity for Regenerative Medicine

(2012) Anne B.C. Cherry et al.   CELL

Reconstructing transcription factor activities in hierarchical transcription network motifs

(2011) Andrea Ocone et al.   BIOINFORMATICS

The Use of Induced Pluripotent Stem Cells in Drug Development

(2011) H Inoue et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Heritable GATA2 mutations associated with familial myelodysplastic syndrome and acute myeloid leukemia

(2011) Christopher N Hahn et al.   NATURE GENETICS

Comprehensive qPCR profiling of gene expression in single neuronal cells

(2011) Ami Citri et al.   Nature Protocols

Signal-dependent dynamics of transcription factor translocation controls gene expression

(2011) Nan Hao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

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

Model-based method for transcription factor target identification with limited data

(2010) Antti Honkela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Switching regulatory models of cellular stress response

(2009) Guido Sanguinetti et al.   BIOINFORMATICS

Estimating Bayes factors via thermodynamic integration and population MCMC

(2009) Ben Calderhead et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Stochastic modelling for quantitative description of heterogeneous biological systems

(2009) Darren J. Wilkinson   NATURE REVIEWS GENETICS

Bistable switches control memory and plasticity in cellular differentiation

(2009) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hematopoiesis: An Evolving Paradigm for Stem Cell Biology

(2008) Stuart H. Orkin et al.   CELL