Functional association networks as priors for gene regulatory network inference

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

(2013) Alex Greenfield et al.   BIOINFORMATICS

Optimal Sparsity Criteria for Network Inference

(2013) Andreas Tjärnberg et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

FunCoup 3.0: database of genome-wide functional coupling networks

(2013) Thomas Schmitt et al.   NUCLEIC ACIDS RESEARCH

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation inSaccharomyces cerevisiae

(2013) Miguel Cacho Teixeira et al.   NUCLEIC ACIDS RESEARCH

A single source k-shortest paths algorithm to infer regulatory pathways in a gene network

(2012) Yu-Keng Shih et al.   BIOINFORMATICS

Boolean network inference from time series data incorporating prior biological knowledge

(2012) Saad Haider et al.   BMC GENOMICS

Biological network inference for drug discovery

(2012) Paola Lecca et al.   DRUG DISCOVERY TODAY

Reconstruction of Biological Networks by Incorporating Prior Knowledge into Bayesian Network Models

(2012) Baikang Pei et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Process-Driven Inference of Biological Network Structure: Feasibility, Minimality, and Multiplicity

(2012) Guanyu Wang et al.   PLoS One

Inferring stable genetic networks from steady-state data

(2011) Michael M. Zavlanos et al.   AUTOMATICA

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods

(2011) Thomas Schaffter et al.   BIOINFORMATICS

How to infer gene networks from expression profiles, revisited

(2011) C. A. Penfold et al.   Interface Focus

Inferring the conservative causal core of gene regulatory networks

(2010) Gökmen Altay et al.   BMC Systems Biology

From biological pathways to regulatory networks

(2010) Ritwik K. Layek et al.   Molecular BioSystems

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk 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

Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data

(2010) Kevin Y. Yip et al.   PLoS One

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

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

Lessons from the DREAM2 Challenges

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

Genetic network identification using convex programming

(2009) A. Julius et al.   IET Systems Biology

Incorporating Existing Network Information into Gene Network Inference

(2009) Scott Christley et al.   PLoS One

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

(2008) Michael Hecker et al.   BIOSYSTEMS

Seeded Bayesian Networks: Constructing genetic networks from microarray data

(2008) Amira Djebbari et al.   BMC Systems Biology