Inferring Regulatory Networks by Combining Perturbation Screens and Steady State Gene Expression Profiles

Causal Inference Using Graphical Models with theRPackagepcalg

(2015) Markus Kalisch et al.   Journal of Statistical Software

Autoregressive models for gene regulatory network inference: Sparsity, stability and causality issues

(2013) George Michailidis et al.   MATHEMATICAL BIOSCIENCES

Joint estimation of multiple graphical models

(2011) J. Guo et al.   BIOMETRIKA

TRANSWESD: inferring cellular networks with transitive reduction

(2010) Steffen Klamt et al.   BIOINFORMATICS

Discovering graphical Granger causality using the truncating lasso penalty

(2010) A. Shojaie et al.   BIOINFORMATICS

Penalized likelihood methods for estimation of sparse high-dimensional directed acyclic graphs

(2010) A. Shojaie et al.   BIOMETRIKA

Functional Overlap and Regulatory Links Shape Genetic Interactions between Signaling Pathways

(2010) Sake van Wageningen et al.   CELL

Predicting causal effects in large-scale systems from observational data

(2010) Marloes H Maathuis et al.   NATURE METHODS

Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets

(2010) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

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

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

From Knockouts to Networks: Establishing Direct Cause-Effect Relationships through Graph Analysis

(2010) Andrea Pinna 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

Network Enrichment Analysis in Complex Experiments

(2010) Ali Shojaie et al.   Statistical Applications in Genetics and Molecular Biology

KELLER: estimating time-varying interactions between genes

(2009) L. Song et al.   BIOINFORMATICS

Analysis of Gene Sets Based on the Underlying Regulatory Network

(2009) Ali Shojaie et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods

(2009) Daniel Marbach et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Complex Systems: From Chemistry to Systems Biology Special Feature: Modeling the temporal interplay of molecular signaling and gene expression by using dynamic nested effects models

(2009) B. Anchang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure Learning in Nested Effects Models

(2008) Achim Tresch et al.   Statistical Applications in Genetics and Molecular Biology