Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

CellNet: Network Biology Applied to Stem Cell Engineering

(2014) Patrick Cahan et al.   CELL

MiR-135b is a direct PAX6 target and specifies human neuroectoderm by inhibiting TGF- /BMP signaling

(2014) A. Bhinge et al.   EMBO JOURNAL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU

(2014) Jessica Severin et al.   NATURE BIOTECHNOLOGY

Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants

(2014) Lorenzo Pasquali et al.   NATURE GENETICS

TFClass: a classification of human transcription factors and their rodent orthologs

(2014) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

Ectopic insulin secreting neuroendocrine tumor of kidney with recurrent hypoglycemia: a diagnostic dilemma

(2014) S Ramkumar et al.   BMC Endocrine Disorders

Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information

(2012) Hatice Osmanbeyoglu et al.   BMC GENOMICS

Combined Transfection of the Three Transcriptional Factors, PDX-1, NeuroD1, and MafA, Causes Differentiation of Bone Marrow Mesenchymal Stem Cells into Insulin-Producing Cells

(2012) Guo Qing-Song et al.   Experimental Diabetes Research

Novel function of transthyretin in pancreatic alpha cells

(2012) Yu Su et al.   FEBS LETTERS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

(2012) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

(2012) Mikhail Pachkov et al.   NUCLEIC ACIDS RESEARCH

Ghrelin Expression in the Mouse Pancreas Defines a Unique Multipotent Progenitor Population

(2012) Luis Arnes et al.   PLoS One

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq

(2011) J. Schodel et al.   BLOOD

Gastrin Treatment Stimulates β-Cell Regeneration and Improves Glucose Tolerance in 95% Pancreatectomized Rats

(2011) Noèlia Téllez et al.   ENDOCRINOLOGY

Unamplified cap analysis of gene expression on a single-molecule sequencer

(2011) M. Kanamori-Katayama et al.   GENOME RESEARCH

ISL1 Promotes Pancreatic Islet Cell Proliferation

(2011) Ting Guo et al.   PLoS One

Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development

(2011) Jason A. Watts et al.   PLoS Genetics

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells

(2010) M. R. Tallack et al.   GENOME RESEARCH

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

Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE

(2010) Morana Vitezic et al.   NUCLEIC ACIDS RESEARCH

Identification of β-catenin binding regions in colon cancer cells using ChIP-Seq

(2010) Daniel Bottomly et al.   NUCLEIC ACIDS RESEARCH

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CEAS: cis-regulatory element annotation system

(2009) Hyunjin Shin et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Detailed transcriptome atlas of the pancreatic beta cell

(2009) Burak Kutlu et al.   BMC Medical Genomics

Distinguishing direct versus indirect transcription factor-DNA interactions

(2009) R. Gordan et al.   GENOME RESEARCH

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis

(2009) Yasuhiro Tomaru et al.   GENOME BIOLOGY

Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation

(2009) Atsutaka Kubosaki et al.   GENOME BIOLOGY

Lack of Nuclear Expression of Hairy and Enhancer of Split-1 (HES1) in Pancreatic Endocrine Tumors

(2008) T. Johansson et al.   HORMONE AND METABOLIC RESEARCH

Pdx1 and BETA2/NeuroD1 Participate in a Transcriptional Complex That Mediates Short-range DNA Looping at the Insulin Gene

(2008) Daniella A. Babu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

GATA4 Is a Direct Transcriptional Activator of Cyclin D2 and Cdk4 and Is Required for Cardiomyocyte Proliferation in Anterior Heart Field-Derived Myocardium

(2008) A. Rojas et al.   MOLECULAR AND CELLULAR BIOLOGY

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

ghrelinis a novel target of Pax4 in endocrine progenitors of the pancreas and duodenum

(2007) Qian Wang et al.   DEVELOPMENTAL DYNAMICS