Identification of context-specific gene regulatory networks with GEMULA—gene expression modeling using LAsso

LLM3D: a log-linear modeling-based method to predict functional gene regulatory interactions from genome-wide expression data

(2011) Geert Geeven et al.   NUCLEIC ACIDS RESEARCH

Support union recovery in high-dimensional multivariate regression

(2010) Guillaume Obozinski et al.   ANNALS OF STATISTICS

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites

(2010) Stephen A. Ramsey et al.   BIOINFORMATICS

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Genome-wide gene expression and promoter binding analysis identifies NFIL3 as a repressor of C/EBP target genes in neuronal outgrowth

(2010) Harold D. MacGillavry et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

Gene Regulatory Networks from Multifactorial Perturbations Using Graphical Lasso: Application to the DREAM4 Challenge

(2010) Patricia Menéndez et al.   PLoS One

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells

(2010) Florian Markowetz et al.   PLoS Computational Biology

Regularized estimation of large-scale gene association networks using graphical Gaussian models

(2009) Nicole Krämer et al.   BMC BIOINFORMATICS

NFIL3 and cAMP Response Element-Binding Protein Form a Transcriptional Feedforward Loop that Controls Neuronal Regeneration-Associated Gene Expression

(2009) H. D. MacGillavry et al.   JOURNAL OF NEUROSCIENCE

BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments

(2008) Claudia Angelini et al.   BMC BIOINFORMATICS

Identifying gene regulatory modules of heat shock response in yeast

(2008) Wei-Sheng Wu et al.   BMC GENOMICS