Windowed Granger causal inference strategy improves discovery of gene regulatory networks

An acetylatable lysine controls CRP function in E. coli

(2017) Robert Davis et al.   MOLECULAR MICROBIOLOGY

Inferring causal molecular networks: empirical assessment through a community-based effort

(2016) Steven M Hill et al.   NATURE METHODS

Discovering governing equations from data by sparse identification of nonlinear dynamical systems

(2016) Steven L. Brunton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative random forest for gene regulatory network inference

(2015) Francesca Petralia et al.   BIOINFORMATICS

Combining tree-based and dynamical systems for the inference of gene regulatory networks

(2015) Vân Anh Huynh-Thu et al.   BIOINFORMATICS

The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets

(2015) Mark F. Ciaccio et al.   Integrative Biology

Identifying causal gateways and mediators in complex spatio-temporal systems

(2015) Jakob Runge et al.   Nature Communications

Functional association networks as priors for gene regulatory network inference

(2014) Matthew E. Studham et al.   BIOINFORMATICS

A Systems Approach to Integrative Biology: An Overview of Statistical Methods to Elucidate Association and Architecture

(2014) M. F. Ciaccio et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Sorad: a systems biology approach to predict and modulate dynamic signaling pathway response from phosphoproteome time-course measurements

(2013) Tarmo Äijö et al.   BIOINFORMATICS

Delayed Protein Synthesis Reduces the Correlation between mRNA and Protein Fluctuations

(2012) Tomáš Gedeon et al.   BIOPHYSICAL JOURNAL

Simultaneous learning of instantaneous and time-delayed genetic interactions using novel information theoretic scoring technique

(2012) Nizamul Morshed 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

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

(2011) Thomas Schaffter et al.   BIOINFORMATICS

Identifiability and observability analysis for experimental design in nonlinear dynamical models

(2011) A. Raue et al.   CHAOS

Novel Roles of cAMP Receptor Protein (CRP) in Regulation of Transport and Metabolism of Carbon Sources

(2011) Tomohiro Shimada et al.   PLoS One

Discovering graphical Granger causality using the truncating lasso penalty

(2010) A. Shojaie et al.   BIOINFORMATICS

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

(2010) Pietro Zoppoli et al.   BMC BIOINFORMATICS

Estimating the directed information to infer causal relationships in ensemble neural spike train recordings

(2010) Christopher J. Quinn et al.   JOURNAL OF COMPUTATIONAL NEUROSCIENCE

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Grouped graphical Granger modeling for gene expression regulatory networks discovery

(2009) A. C. Lozano et al.   BIOINFORMATICS