Robust Target Gene Discovery through Transcriptome Perturbations and Genome-Wide Enhancer Predictions in Drosophila Uncovers a Regulatory Basis for Sensory Specification

Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances

(2010) Jaebum Kim et al.   PLoS Computational Biology

A MicroRNA Imparts Robustness against Environmental Fluctuation during Development

(2009) Xin Li et al.   CELL

Fasciclin 2, the Drosophila orthologue of neural cell-adhesion molecule, inhibits EGF receptor signalling

(2009) Y. Mao et al.   DEVELOPMENT

A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo

(2009) Yi-Hsien Su et al.   DEVELOPMENTAL BIOLOGY

Distinguishing direct versus indirect transcription factor-DNA interactions

(2009) R. Gordan et al.   GENOME RESEARCH

The evolution of hierarchical gene regulatory networks

(2009) Douglas H. Erwin et al.   NATURE REVIEWS GENETICS

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes

(2009) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2010

(2009) B. Rhead et al.   NUCLEIC ACIDS RESEARCH

Deletion of Atoh1 Disrupts Sonic Hedgehog Signaling in the Developing Cerebellum and Prevents Medulloblastoma

(2009) A. Flora et al.   SCIENCE

The Atonal Proneural Transcription Factor Links Differentiation and Tumor Formation in Drosophila

(2009) Wouter Bossuyt et al.   PLOS BIOLOGY

Atonal homolog 1 Is a Tumor Suppressor Gene

(2009) Wouter Bossuyt et al.   PLOS BIOLOGY

PASTAA: identifying transcription factors associated with sets of co-regulated genes

(2008) Helge G. Roider et al.   BIOINFORMATICS

Two-step selection of a single R8 photoreceptor: a bistable loop between senseless and rough locks in R8 fate

(2008) K. L. Pepple et al.   DEVELOPMENT

Gene regulatory networks underlying the compartmentalization of the Ciona central nervous system

(2008) K. S. Imai et al.   DEVELOPMENT

Gene induction following wounding of wild-type versus macrophage-deficient Drosophila embryos

(2008) Brian Stramer et al.   EMBO REPORTS

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

(2008) Marcus B. Noyes et al.   NUCLEIC ACIDS RESEARCH

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

A gene regulatory network armature for T lymphocyte specification

(2008) C. Georgescu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY

ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

(2008) Peter Van Loo et al.   GENOME BIOLOGY