The role of Dichaete in transcriptional regulation during Drosophila embryonic development

Identifying targets of the Sox domain protein Dichaete in the Drosophila CNS via targeted expression of dominant negative proteins

(2013) Shih Pei Shen et al.   BMC DEVELOPMENTAL BIOLOGY

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Disturbed balance between SOX2 and CDX2 in human vitelline duct anomalies and intestinal duplications

(2013) Lalini Raghoebir et al.   VIRCHOWS ARCHIV

Drosophila melanogaster Zelda and Single-minded collaborate to regulate an evolutionarily dynamic CNS midline cell enhancer

(2012) Joseph C. Pearson et al.   DEVELOPMENTAL BIOLOGY

HOT DNAs: a novel class of developmental enhancers

(2012) E. Farley et al.   GENES & DEVELOPMENT

HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature

(2012) E. Z. Kvon et al.   GENES & DEVELOPMENT

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

(2012) Carl Herrmann et al.   NUCLEIC ACIDS RESEARCH

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

A Resource for Manipulating Gene Expression and Analyzing cis-Regulatory Modules in the Drosophila CNS

(2012) Laurina Manning et al.   Cell Reports

A GAL4-Driver Line Resource for Drosophila Neurobiology

(2012) Arnim Jenett et al.   Cell Reports

FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis

(2011) S. Kumar et al.   BIOINFORMATICS

B1 and B2 Sox gene expression during neural plate development in chicken and mouse embryos: Universal versus species-dependent features

(2011) Masanori Uchikawa et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Sequentially acting Sox transcription factors in neural lineage development

(2011) M. Bergsland et al.   GENES & DEVELOPMENT

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

RSAT 2011: regulatory sequence analysis tools

(2011) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Parallel Expansions of Sox Transcription Factor Group B Predating the Diversifications of the Arthropods and Jawed Vertebrates

(2011) Lei Zhong et al.   PLoS One

STAT Is an Essential Activator of the Zygotic Genome in the Early Drosophila Embryo

(2011) Amy Tsurumi et al.   PLoS Genetics

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

(2011) Chung-Yi Nien et al.   PLoS Genetics

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

(2011) Melissa M. Harrison et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence

(2010) David S Huen et al.   BMC BIOINFORMATICS

Replacement of mouse Sox10 by the Drosophila ortholog Sox100B provides evidence for co-option of SoxE proteins into vertebrate-specific gene-regulatory networks through altered expression

(2010) François Cossais et al.   DEVELOPMENTAL BIOLOGY

Interaction of Sox1, Sox2, Sox3 and Oct4 during primary neurogenesis

(2010) Tenley C. Archer et al.   DEVELOPMENTAL BIOLOGY

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

(2010) S. M. Gallo et al.   NUCLEIC ACIDS RESEARCH

Neural stem cell transcriptional networks highlight genes essential for nervous system development

(2009) Tony D Southall et al.   EMBO JOURNAL

Sox2 roles in neural stem cells

(2009) Larysa H. Pevny et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database

(2009) Ulrike Pfreundt et al.   NUCLEIC ACIDS RESEARCH

Impact of normalization on miRNA microarray expression profiling

(2009) S. Pradervand et al.   RNA

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

Evolution of the insect Sox genes

(2008) Megan J Wilson et al.   BMC EVOLUTIONARY BIOLOGY

Temporal Transcription Factors and Their Targets Schedule the End of Neural Proliferation in Drosophila

(2008) Cédric Maurange et al.   CELL

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

(2008) Hsiao-Lan Liang et al.   NATURE

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

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

Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality

(2008) Elena Zotenko et al.   PLoS Computational Biology