An algebra-based method for inferring gene regulatory networks

Integrating external biological knowledge in the construction of regulatory networks from time-series expression data

(2012) Kenneth Lo et al.   BMC Systems Biology

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

(2012) Anne-Claire Haury et al.   BMC Systems Biology

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Unraveling gene regulatory networks from time-resolved gene expression data -- a measures comparison study

(2011) Sabrina Hempel et al.   BMC BIOINFORMATICS

Identification of genetic network dynamics with unate structure

(2010) Riccardo Porreca et al.   BIOINFORMATICS

Identifying interactions in the time and frequency domains in local and global networks - A Granger Causality Approach

(2010) Cunlu Zou et al.   BMC BIOINFORMATICS

Comparison of evolutionary algorithms in gene regulatory network model inference

(2010) Alina Sîrbu et al.   BMC BIOINFORMATICS

TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach

(2010) Pietro Zoppoli et al.   BMC BIOINFORMATICS

Discretization of Time Series Data

(2010) Elena S. Dimitrova et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2010) Alex Greenfield et al.   PLoS One

A divide-and-conquer approach to analyze underdetermined biochemical models

(2009) Oliver Kotte et al.   BIOINFORMATICS

Optimizing static thermodynamic models of transcriptional regulation

(2009) Denis C. Bauer et al.   BIOINFORMATICS

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

(2009) Irene Cantone et al.   CELL

Synchronous Gene Expression of the Yersinia enterocolitica Ysa Type III Secretion System and Its Effectors

(2009) K. A. Walker et al.   JOURNAL OF BACTERIOLOGY

Synchronous and Stochastic Patterns of Gene Activation in theDrosophilaEmbryo

(2009) Alistair N. Boettiger et al.   SCIENCE

Learning biological networks: from modules to dynamics

(2008) Richard Bonneau   Nature Chemical Biology