Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development

Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours

(2017) J. Justin Milner et al.   NATURE

Dysfunction of IKZF1/MYC/MDIG axis contributes to liver cancer progression through regulating H3K9me3/p21 activity

(2017) Qi Huo et al.   Cell Death & Disease

OBOX Proteins Are Recruited During Oocyte Maturation and Are Essential for Early Development in Mouse.

(2017) Paula Stein et al.   BIOLOGY OF REPRODUCTION

MITF and BRN2 contribute to metastatic growth after dissemination of melanoma

(2017) Jacinta L. Simmons et al.   Scientific Reports

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

Constructing 3D interaction maps from 1D epigenomes

(2016) Yun Zhu et al.   Nature Communications

Identification of candidate genes for congenital heart defects on proximal chromosome 8p

(2016) Tingting Li et al.   Scientific Reports

Creating reference gene annotation for the mouse C57BL6/J genome assembly

(2015) Jonathan M. Mudge et al.   MAMMALIAN GENOME

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

(2015) M. L. Arrieta-Ortiz et al.   Molecular Systems Biology

The ETS Factor, ETV2: a Master Regulator for Vascular Endothelial Cell Development

(2015)   MOLECULES AND CELLS

Estimating the activity of transcription factors by the effect on their target genes

(2014) Theresa Schacht et al.   BIOINFORMATICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Lung development: orchestrating the generation and regeneration of a complex organ

(2014) M. Herriges et al.   DEVELOPMENT

Growth Factor Independence 1b (Gfi1b) Is Important for the Maturation of Erythroid Cells and the Regulation of Embryonic Globin Expression

(2014) Lothar Vassen et al.   PLoS One

Regulation of transcription factor activity by interconnected post-translational modifications

(2014) Theresa M. Filtz et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Gata5 Deficiency Causes Airway Constrictor Hyperresponsiveness in Mice

(2013) Bohao Chen et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Overlapping cortical malformations and mutations in TUBB2B and TUBA1A

(2013) Thomas D. Cushion et al.   BRAIN

Tbx20 acts upstream of Wnt signaling to regulate endocardial cushion formation and valve remodeling during mouse cardiogenesis

(2013) X. Cai et al.   DEVELOPMENT

odd-skipped related 2is required for fin chondrogenesis in zebrafish

(2013) Pui-Ying Lam et al.   DEVELOPMENTAL DYNAMICS

Estrogen-related receptor gamma induces cardiac hypertrophy by activating GATA4

(2013) Duk-Hwa Kwon et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Hippo-Foxa2 signaling pathway plays a role in peripheral lung maturation and surfactant homeostasis

(2013) C. Chung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coordination of organ growth: principles and outstanding questions from the world of insects

(2013) D.S. Andersen et al.   TRENDS IN CELL BIOLOGY

Sim2 prevents entry into the myogenic program by repressing MyoD transcription during limb embryonic myogenesis

(2012) E. Havis et al.   DEVELOPMENT

EKLF/KLF1, a Tissue-Restricted Integrator of Transcriptional Control, Chromatin Remodeling, and Lineage Determination

(2012) Y. Y. Yien et al.   MOLECULAR AND CELLULAR BIOLOGY

NF-E2-Related Factor 1 (Nrf1) Serves as a Novel Regulator of Hepatic Lipid Metabolism through Regulation of the Lipin1 and PGC-1  Genes

(2012) Y. Hirotsu et al.   MOLECULAR AND CELLULAR BIOLOGY

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Transcriptional Programs Controlling Perinatal Lung Maturation

(2012) Yan Xu et al.   PLoS One

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

(2012) Ripla Arora et al.   PLoS Genetics

A role for transcription factor E2F2 in hepatocyte proliferation and timely liver regeneration

(2011) Igotz Delgado et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods

(2011) Thomas Schaffter et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Microarrays and RNA-Seq identify molecular mechanisms driving the end of nephron production

(2011) Eric W Brunskill et al.   BMC DEVELOPMENTAL BIOLOGY

HNF4A is essential for specification of hepatic progenitors from human pluripotent stem cells

(2011) A. DeLaForest et al.   DEVELOPMENT

Msx1 and Msx2 in limb mesenchyme modulate digit number and identity

(2011) Vardina Bensoussan-Trigano et al.   DEVELOPMENTAL DYNAMICS

Requirement for the paired-like homeodomain transcription factor VSX1 in type 3a mouse retinal bipolar cell terminal differentiation

(2011) Zhiwei Shi et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Hox genes and kidney development

(2011) Deneen M. Wellik   PEDIATRIC NEPHROLOGY

cAMP Response Element Binding Protein Is Required for Differentiation of Respiratory Epithelium during Murine Development

(2011) A. Daniel Bird et al.   PLoS One

Pax6 Is a Human Neuroectoderm Cell Fate Determinant

(2010) Xiaoqing Zhang et al.   Cell Stem Cell

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Foxa2 regulates polarity and epithelialization in the endoderm germ layer of the mouse embryo

(2009) I. Burtscher et al.   DEVELOPMENT

Analysis of hoxa11 and hoxa13 expression during patternless limb regeneration in Xenopus

(2009) Shiro Ohgo et al.   DEVELOPMENTAL BIOLOGY

The Role of Sonic Hedgehog of Neural Origin in Thalamic Differentiation in the Mouse

(2009) N.-E. Szabo et al.   JOURNAL OF NEUROSCIENCE

HNF1B Mutations Associate with Hypomagnesemia and Renal Magnesium Wasting

(2009) S. Adalat et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Misexpression of ELF5 disrupts lung branching and inhibits epithelial differentiation

(2008) David E. Metzger et al.   DEVELOPMENTAL BIOLOGY

Myogenin regulates a distinct genetic program in adult muscle stem cells

(2008) Eric Meadows et al.   DEVELOPMENTAL BIOLOGY

Role for Spi-C in the development of red pulp macrophages and splenic iron homeostasis

(2008) Masako Kohyama et al.   NATURE

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY