An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome

Construction of human activity-based phosphorylation networks

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On the origins of hierarchy in complex networks

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Understanding transcriptional regulation by integrative analysis of transcription factor binding data

(2012) C. Cheng et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

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Hierarchy Measure for Complex Networks

(2012) Enys Mones et al.   PLoS One

TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles

(2011) Chao Cheng et al.   BIOINFORMATICS

Dissecting phosphorylation networks: lessons learned from yeast

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Phosphorylation network rewiring by gene duplication

(2011) L. Freschi et al.   Molecular Systems Biology

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data

(2011) Chao Cheng et al.   PLoS Computational Biology

HiNO: An Approach for Inferring Hierarchical Organization from Regulatory Networks

(2010) Mara L. Hartsperger et al.   PLoS One

Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks

(2010) K.-K. Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Rewiring of Transcriptional Regulatory Networks: Hierarchy, Rather Than Connectivity, Better Reflects the Importance of Regulators

(2010) N. Bhardwaj et al.   Science Signaling

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture

(2009) Raja Jothi et al.   Molecular Systems Biology

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Systematic Mapping of Genetic Interaction Networks

(2008) Scott J. Dixon et al.   Annual Review of Genetics

Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks

(2008) Iaroslav Ispolatov et al.   BMC BIOINFORMATICS