Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

(2012) Marcel H Schulz et al.   BMC Systems Biology

A Validated Regulatory Network for Th17 Cell Specification

(2012) Maria Ciofani et al.   CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

(2012) P. Nicolas et al.   SCIENCE

Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities

(2011) Yao Fu et al.   BMC BIOINFORMATICS

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

(2010) S. M. Gallo et al.   NUCLEIC ACIDS RESEARCH

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

(2010) S. Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Gene Expression Prediction by Soft Integration and the Elastic Net—Best Performance of the DREAM3 Gene Expression Challenge

(2010) Mika Gustafsson et al.   PLoS One

DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator

(2010) Aviv Madar et al.   PLoS One

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

(2010) Robert J. Prill et al.   PLoS One

DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models

(2010) Alex Greenfield et al.   PLoS One

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the adaptive elastic-net with a diverging number of parameters

(2009) Hui Zou et al.   ANNALS OF STATISTICS

Lessons from the DREAM2 Challenges

(2009) Gustavo Stolovitzky et al.   Annals of the New York Academy of Sciences

A dynamic network of transcription in LPS-treated human subjects

(2009) Junhee Seok et al.   BMC Systems Biology

Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis

(2009) C. R. Lammers et al.   MICROBIOLOGY-SGM

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki

(2009) L. A. Florez et al.   Database-The Journal of Biological Databases and Curation

Network-constrained regularization and variable selection for analysis of genomic data

(2008) C. Li et al.   BIOINFORMATICS

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

(2008) Michael Hecker et al.   BIOSYSTEMS

A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli

(2008) Jason Ernst et al.   PLoS Computational Biology