SOX2 regulates common and specific stem cell features in the CNS and endoderm derived organs

Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells

(2016) Daniel W. Hagey et al.   GENOME RESEARCH

Sox2 Suppresses Gastric Tumorigenesis in Mice

(2016) Abby Sarkar et al.   Cell Reports

A direct fate exclusion mechanism by Sonic hedgehog-regulated transcriptional repressors

(2015) Yuichi Nishi et al.   DEVELOPMENT

The cell of origin and subtype of K-Ras-induced lung tumors are modified by Notch and Sox2

(2014) Xia Xu et al.   GENES & DEVELOPMENT

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

Sox2 Acts in a Dose-Dependent Fashion to Regulate Proliferation of Cortical Progenitors

(2014) Daniel W. Hagey et al.   Cell Reports

The Sox Family of Transcription Factors: Versatile Regulators of Stem and Progenitor Cell Fate

(2013) Abby Sarkar et al.   Cell Stem Cell

Sox proteins: regulators of cell fate specification and differentiation

(2013) Y. Kamachi et al.   DEVELOPMENT

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

The SOX2-Interactome in Brain Cancer Cells Identifies the Requirement of MSI2 and USP9X for the Growth of Brain Tumor Cells

(2013) Jesse L. Cox et al.   PLoS One

SOX2 Co-Occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State

(2013) Michael A. Lodato et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Stem cells and lineages of the intestine: a developmental and evolutionary perspective

(2012) Shigeo Takashima et al.   DEVELOPMENT GENES AND EVOLUTION

Mechanistic Differences in the Transcriptional Interpretation of Local and Long-Range Shh Morphogen Signaling

(2012) Tony Oosterveen et al.   DEVELOPMENTAL CELL

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Multiple Roles and Interactions of Tbx4 and Tbx5 in Development of the Respiratory System

(2012) Ripla Arora et al.   PLoS Genetics

SOX2 expression levels distinguish between neural progenitor populations of the developing dorsal telencephalon

(2011) Scott R. Hutton et al.   DEVELOPMENTAL BIOLOGY

Sequentially acting Sox transcription factors in neural lineage development

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

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Sox2 cooperates with Chd7 to regulate genes that are mutated in human syndromes

(2011) Erik Engelen et al.   NATURE GENETICS

SoxB1 transcription factors restrict organizer gene expression by repressing multiple events downstream of Wnt signalling

(2010) Y.-H. Shih et al.   DEVELOPMENT

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

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems

(2010) V. Kaimal et al.   NUCLEIC ACIDS RESEARCH

In vivo targeting of subventricular zone astrocytes

(2010) Carlyn Mamber et al.   PROGRESS IN NEUROBIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Groucho binds two conserved regions of LEF-1 for HDAC-dependent repression

(2009) Laura Arce et al.   BMC CANCER

SOX–partner code for cell specification: Regulatory target selection and underlying molecular mechanisms

(2009) Hisato Kondoh et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Hippocampal development and neural stem cell maintenance require Sox2-dependent regulation of Shh

(2009) Rebecca Favaro et al.   NATURE NEUROSCIENCE

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) Xi Chen et al.   CELL

Sox2 is important for two crucial processes in lung development: Branching morphogenesis and epithelial cell differentiation

(2008) Cristina Gontan et al.   DEVELOPMENTAL BIOLOGY

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH