Sox2 levels regulate the chromatin occupancy of WNT mediators in epiblast progenitors responsible for vertebrate body formation

Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors

(2021) Ryan J. Geusz et al.   Nature Communications

The nf-core framework for community-curated bioinformatics pipelines

(2020) Philip A. Ewels et al.   NATURE BIOTECHNOLOGY

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

(2020) Svetlana O. Dodonova et al.   NATURE

Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites

(2020) Jesse V. Veenvliet et al.   SCIENCE

Complementary Activity of ETV5, RBPJ, and TCF3 Drives Formative Transition from Naive Pluripotency

(2019) Tüzer Kalkan et al.   Cell Stem Cell

Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2

(2019) Vikas Malik et al.   Nature Communications

Evidence for the temporal regulation of insect segmentation by a conserved sequence of transcription factors

(2018) Erik Clark et al.   DEVELOPMENT

Wnt signaling in development and tissue homeostasis

(2018) Zachary Steinhart et al.   DEVELOPMENT

Oct4 regulates the embryonic axis and coordinates exit from pluripotency and germ layer specification in the mouse embryo

(2018) Carla Mulas et al.   DEVELOPMENT

Nervous System Regionalization Entails Axial Allocation before Neural Differentiation

(2018) Vicki Metzis et al.   CELL

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Distinct SoxB1 networks are required for naïve and primed pluripotency

(2017) Andrea Corsinotti et al.   eLife

Singularity: Scientific containers for mobility of compute

(2017) Gregory M. Kurtzer et al.   PLoS One

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Return to quiescence of mouse neural stem cells by degradation of a proactivation protein

(2016) Noelia Urbán et al.   SCIENCE

Cdx and T Brachyury Co-activate Growth Signaling in the Embryonic Axial Progenitor Niche

(2016) Shilu Amin et al.   Cell Reports

Position-dependent plasticity of distinct progenitor types in the primitive streak

(2016) Filip J Wymeersch et al.   eLife

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

Lineage tracing of neuromesodermal progenitors reveals novel Wnt-dependent roles in trunk progenitor cell maintenance and differentiation

(2015) R. J. Garriock et al.   DEVELOPMENT

Neuromesodermal progenitors and the making of the spinal cord

(2015) D. Henrique et al.   DEVELOPMENT

Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis

(2015) Thorsten Boroviak et al.   DEVELOPMENTAL CELL

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

(2015) Alicia N. Schep et al.   GENOME RESEARCH

Functional annotation of native enhancers with a Cas9–histone demethylase fusion

(2015) Nicola A Kearns et al.   NATURE METHODS

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

WNT/β-Catenin Signaling Affects Cell Lineage and Pluripotency-Specific Gene Expression in Bovine Blastocysts: Prospects for Bovine Embryonic Stem Cell Derivation

(2015) Zofia Eliza Madeja et al.   STEM CELLS AND DEVELOPMENT

NANOG and CDX2 Pattern Distinct Subtypes of Human Mesoderm during Exit from Pluripotency

(2014) Sasha Mendjan et al.   Cell Stem Cell

Distinct Wnt-driven primitive streak-like populations reflect in vivo lineage precursors

(2014) A. Tsakiridis et al.   DEVELOPMENT

In Vitro Generation of Neuromesodermal Progenitors Reveals Distinct Roles for Wnt Signalling in the Specification of Spinal Cord and Paraxial Mesoderm Identity

(2014) Mina Gouti et al.   PLOS BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Retinoid Acid Specifies Neuronal Identity through Graded Expression of Ascl1

(2013) John Jacob et al.   CURRENT BIOLOGY

Gene Regulatory Networks Mediating Canonical Wnt Signal-Directed Control of Pluripotency and Differentiation in Embryo Stem Cells

(2013) Xiaoxiao Zhang et al.   STEM CELLS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

Distinct Lineage Specification Roles for NANOG, OCT4, and SOX2 in Human Embryonic Stem Cells

(2012) Zheng Wang et al.   Cell Stem Cell

Transcriptional regulatory networks in epiblast cells and during anterior neural plate development as modeled in epiblast stem cells

(2012) M. Iwafuchi-Doi et al.   DEVELOPMENT

The developmental dismantling of pluripotency is reversed by ectopic Oct4 expression

(2012) R. Osorno et al.   DEVELOPMENT

Canonical Wnt Signaling Dynamically Controls Multiple Stem Cell Fate Decisions during Vertebrate Body Formation

(2012) Benjamin L. Martin et al.   DEVELOPMENTAL CELL

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

TCF/LEFs and Wnt Signaling in the Nucleus

(2012) K. M. Cadigan et al.   Cold Spring Harbor Perspectives in Biology

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

(2011) Matthew Slattery et al.   CELL

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

(2011) Matt Thomson et al.   CELL

Pluripotency factors regulate definitive endoderm specification through eomesodermin

(2011) A. K. K. Teo et al.   GENES & DEVELOPMENT

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

Opposing effects of Tcf3 and Tcf1 control Wnt stimulation of embryonic stem cell self-renewal

(2011) Fei Yi et al.   NATURE CELL BIOLOGY

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

flowCore: a Bioconductor package for high throughput flow cytometry

(2009) Florian Hahne et al.   BMC BIOINFORMATICS

Cross-regulation of the Nanog and Cdx2 promoters

(2009) Lingyi Chen et al.   CELL RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Gradients in the Brain: The Control of the Development of Form and Function in the Cerebral Cortex

(2009) S. N. Sansom et al.   Cold Spring Harbor Perspectives in Biology

Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells

(2008) M. F. Cole et al.   GENES & DEVELOPMENT

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Novel Effectors of Directed and Ngn3-Mediated Differentiation of Mouse Embryonic Stem Cells into Endocrine Pancreas Progenitors

(2007) Ioannis Serafimidis et al.   STEM CELLS