LiPLike: towards gene regulatory network predictions of high certainty

A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors

(2018) Mariano J. Alvarez et al.   NATURE GENETICS

Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection

(2018) Heeju Noh et al.   NUCLEIC ACIDS RESEARCH

Predicting perturbation patterns from the topology of biological networks

(2018) Marc Santolini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network-based approach to prediction and population-based validation of in silico drug repurposing

(2018) Feixiong Cheng et al.   Nature Communications

GeneSPIDER – gene regulatory network inference benchmarking with controlled network and data properties

(2017) Andreas Tjärnberg et al.   Molecular BioSystems

Can we predict protein from mRNA levels?

(2017) Nikolaus Fortelny et al.   NATURE

LASSIM—A network inference toolbox for genome-wide mechanistic modeling

(2017) Rasmus Magnusson et al.   PLoS Computational Biology

Network-based in silico drug efficacy screening

(2016) Emre Guney et al.   Nature Communications

Avoiding pitfalls in L1-regularised inference of gene networks

(2015) Andreas Tjärnberg et al.   Molecular BioSystems

CN: a consensus algorithm for inferring gene regulatory networks using the SORDER algorithm and conditional mutual information test

(2015) Rosa Aghdam et al.   Molecular BioSystems

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

(2015) M. L. Arrieta-Ortiz et al.   Molecular Systems Biology

A validated gene regulatory network and GWAS identifies early regulators of T cell–associated diseases

(2015) Mika Gustafsson et al.   Science Translational Medicine

Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks

(2014) Xiujun Zhang et al.   NUCLEIC ACIDS RESEARCH

Maximum Likelihood, Profile Likelihood, and Penalized Likelihood: A Primer

(2013) S. R. Cole et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Profile likelihood in systems biology

(2013) Clemens Kreutz et al.   FEBS Journal

Network link prediction by global silencing of indirect correlations

(2013) Baruch Barzel et al.   NATURE BIOTECHNOLOGY

Network deconvolution as a general method to distinguish direct dependencies in networks

(2013) Soheil Feizi et al.   NATURE BIOTECHNOLOGY

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Gene Regulatory Network Inference from Multifactorial Perturbation Data Using both Regression and Correlation Analyses

(2012) Jie Xiong et al.   PLoS One

A Measure of the Signal-to-Noise Ratio of Microarray Samples and Studies Using Gene Correlations

(2012) David Venet et al.   PLoS One

Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets

(2012) Piyush B Madhamshettiwar et al.   Genome Medicine

Random lasso

(2011) Sijian Wang et al.   Annals of Applied Statistics

Sparse Algorithms Are Not Stable: A No-Free-Lunch Theorem

(2011) Huan Xu et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

(2010) Celine Lefebvre et al.   Molecular Systems Biology

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