Clustering gene expression time series data using an infinite Gaussian process mixture model

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome

(2016) Christopher M. Vockley et al.   CELL

Fast Nonparametric Clustering of Structured Time-Series

(2015) James Hensman et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum

(2015) Christopher L Frank et al.   NATURE NEUROSCIENCE

A Regulatory Hierarchy Controls the Dynamic Transcriptional Response to Extreme Oxidative Stress in Archaea

(2015) Peter D. Tonner et al.   PLoS Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters

(2013) James Hensman et al.   BMC BIOINFORMATICS

Control of cell cycle transcription during G1 and S phases

(2013) Cosetta Bertoli et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Complex dynamics of transcription regulation

(2012) Diana A. Stavreva et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon

(2012) Kriti Sharma et al.   BMC GENOMICS

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements

(2011) Emma J Cooke et al.   BMC BIOINFORMATICS

Activation of the Glucocorticoid Receptor Is Associated with Poor Prognosis in Estrogen Receptor-Negative Breast Cancer

(2011) D. Pan et al.   CANCER RESEARCH

Negative regulation by nuclear receptors: a plethora of mechanisms

(2011) Guilherme M. Santos et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

R/BHC: fast Bayesian hierarchical clustering for microarray data

(2009) Richard S Savage et al.   BMC BIOINFORMATICS

A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection

(2009) Sagi D. Shapira et al.   CELL

Kinetic Complexity of the Global Response to Glucocorticoid Receptor Action

(2009) Sam John et al.   ENDOCRINOLOGY

Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation

(2009) T. E. Reddy et al.   GENOME RESEARCH

Modeling and Visualizing Uncertainty in Gene Expression Clusters Using Dirichlet Process Mixtures

(2009) C.E. Rasmussen et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Bayesian Inference on Changes in Response Densities Over Predictor Clusters

(2009) David B. Dunson et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

Minireview: Latest Perspectives on Antiinflammatory Actions of Glucocorticoids

(2008) Karolien De Bosscher et al.   MOLECULAR ENDOCRINOLOGY

Glucocorticoid receptor dynamics and gene regulation

(2008) Simon C. Biddie et al.   STRESS-THE INTERNATIONAL JOURNAL ON THE BIOLOGY OF STRESS