Semi-supervised prediction of gene regulatory networks using machine learning algorithms

NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks

(2014) Daniel G. Hurley et al.   BIOINFORMATICS

CompareSVM: supervised, Support Vector Machine (SVM) inference of gene regularity networks

(2014) Zeeshan Gillani et al.   BMC BIOINFORMATICS

Gene network inference using continuous time Bayesian networks: a comparative study and application to Th17 cell differentiation

(2014) Enzo Acerbi et al.   BMC BIOINFORMATICS

Exact reconstruction of gene regulatory networks using compressive sensing

(2014) Young Hwan Chang et al.   BMC BIOINFORMATICS

Supervised, semi-supervised and unsupervised inference of gene regulatory networks

(2013) S. R. Maetschke et al.   BRIEFINGS IN BIOINFORMATICS

Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators

(2012) Shwe L. Chin et al.   FEBS Journal

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Chromosomal duplication is a transient evolutionary solution to stress

(2012) A. H. Yona et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

Principles and Strategies for Developing Network Models in Cancer

(2011) Dana Pe'er et al.   CELL

Overexpression of Cloned RhsA Sequences Perturbs the Cellular Translational Machinery in Escherichia coli

(2011) K. Aggarwal et al.   JOURNAL OF BACTERIOLOGY

Evolutionary genome engineering using a restriction–modification system

(2011) Yoko Asakura et al.   NUCLEIC ACIDS RESEARCH

Gene Regulatory Network Reconstruction Using Bayesian Networks, the Dantzig Selector, the Lasso and Their Meta-Analysis

(2011) Matthieu Vignes et al.   PLoS One

Learning gene regulatory networks from only positive and unlabeled data

(2010) Luigi Cerulo et al.   BMC BIOINFORMATICS

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface

(2010) D. Abdulrehman et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Robert J. Prill 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

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

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

SIRENE: supervised inference of regulatory networks

(2008) F. Mordelet et al.   BIOINFORMATICS

The Rcs Phosphorelay Is a Cell Envelope Stress Response Activated by Peptidoglycan Stress and Contributes to Intrinsic Antibiotic Resistance

(2008) M. E. Laubacher et al.   JOURNAL OF BACTERIOLOGY

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation

(2008) Ophir Shalem et al.   Molecular Systems Biology

Global control of cell-cycle transcription by coupled CDK and network oscillators

(2008) David A. Orlando et al.   NATURE