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

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

(2011) Chao Cheng et al.   GENOME BIOLOGY

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

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

Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels

(2010) N. Bhardwaj et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Landscape of C. elegans 3'UTRs

(2010) M. Mangone et al.   SCIENCE

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

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

Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets

(2010) Nitin Bhardwaj et al.   PLoS Computational Biology

Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response

(2010) Mei Zhong et al.   PLoS Genetics

Massively parallel sequencing of the polyadenylated transcriptome of C. elegans

(2009) L. W. Hillier et al.   GENOME RESEARCH

Chromatin poises miRNA- and protein-coding genes for expression

(2009) A. Barski et al.   GENOME RESEARCH

Genome-wide survey of microRNA–transcription factor feed-forward regulatory circuits in human

(2009) Angela Re et al.   Molecular BioSystems

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

WormBase: a comprehensive resource for nematode research

(2009) Todd W. Harris et al.   NUCLEIC ACIDS RESEARCH

Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development

(2009) Masaomi Kato et al.   GENOME BIOLOGY

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity

(2008) N. J. Martinez et al.   GENES & DEVELOPMENT

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Analysis of regulatory network topology reveals functionally distinct classes of microRNAs

(2008) Xueping Yu et al.   NUCLEIC ACIDS RESEARCH

Signatures of combinatorial regulation in intrinsic biological noise

(2008) A. Warmflash et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA