Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

(2014) Cosmas D Arnold et al.   NATURE GENETICS

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

SoxNeuro orchestrates central nervous system specification and differentiation in Drosophila and is only partially redundant with Dichaete

(2014) Enrico Ferrero et al.   GENOME BIOLOGY

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

The role of Dichaete in transcriptional regulation during Drosophila embryonic development

(2013) Jelena Aleksic et al.   BMC GENOMICS

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

(2013) Klara Stefflova et al.   CELL

Characterization of Enhancers Active in the Mouse Embryonic Cerebral Cortex Suggests Sox/Pou cis-Regulatory Logics and Heterogeneity of Cortical Progenitors

(2013) A. Bery et al.   CEREBRAL CORTEX

The transcription factor sry-related HMG box-4 (SOX4) is required for normal renal developmentin vivo

(2013) Jez Huang et al.   DEVELOPMENTAL DYNAMICS

Widespread Misinterpretable ChIP-seq Bias in Yeast

(2013) Daechan Park et al.   PLoS One

Large-Scale Quality Analysis of Published ChIP-seq Data

(2013) Georgi K. Marinov et al.   G3-Genes Genomes Genetics

Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression

(2013) Mathilde Paris et al.   PLoS Genetics

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Systematic evaluation of factors influencing ChIP-seq fidelity

(2012) Yiwen Chen et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

(2012) W. W. Fisher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Laurina Manning et al.   Cell Reports

Tempo and Mode in Evolution of Transcriptional Regulation

(2012) Kacy L. Gordon et al.   PLoS Genetics

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant 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

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

SOX after SOX: SOXession regulates neurogenesis

(2011) M. Wegner   GENES & DEVELOPMENT

Sequentially acting Sox transcription factors in neural lineage development

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

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

(2011) Qiye He et al.   NATURE GENETICS

A computational pipeline for comparative ChIP-seq analyses

(2011) Anaïs F Bardet et al.   Nature Protocols

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

Genome-Wide Tissue-Specific Occupancy of the Hox Protein Ultrabithorax and Hox Cofactor Homothorax in Drosophila

(2011) Matthew Slattery et al.   PLoS One

Consequences of Eukaryotic Enhancer Architecture for Gene Expression Dynamics, Development, and Fitness

(2011) Michael Z. Ludwig et al.   PLoS Genetics

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

(2011) Tommy Kaplan et al.   PLoS Genetics

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

(2011) Xiao-Yong Li et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

(2010) Michael W. Perry et al.   CURRENT BIOLOGY

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

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

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

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

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

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Organogenesis relies on SoxC transcription factors for the survival of neural and mesenchymal progenitors

(2010) Pallavi Bhattaram et al.   Nature Communications

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

(2010) Robert K. Bradley et al.   PLOS BIOLOGY

B1 SOX Coordinate Cell Specification with Patterning and Morphogenesis in the Early Zebrafish Embryo

(2010) Yuichi Okuda et al.   PLoS Genetics

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

No backbone but lots of Sox: Invertebrate Sox genes

(2009) Nichanun Phochanukul et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

ChIPing away at the genome: the new frontier travel guide

(2009) Jelena Aleksic et al.   Molecular BioSystems

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Evolution of Regulatory Sequences in 12 Drosophila Species

(2009) Jaebum Kim et al.   PLoS Genetics

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

Shaping segments:Hoxgene function in the genomic age

(2008) Stefanie D. Hueber et al.   BIOESSAYS

Gene duplications, robustness and evolutionary innovations

(2008) Andreas Wagner   BIOESSAYS

Evolution of the insect Sox genes

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

Having it both ways: Sox protein function between conservation and innovation

(2008) S. I. E. Guth et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Insights into the early evolution ofSOXgenes from expression analyses in a ctenophore

(2008) Muriel Jager et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

The Trichoplax genome and the nature of placozoans

(2008) Mansi Srivastava et al.   NATURE

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

(2008) Jean-Valery Turatsinze et al.   Nature Protocols

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution

(2008) Tanya Vavouri et al.   TRENDS IN GENETICS

Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation

(2008) Emily E. Hare et al.   PLoS Genetics