Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo

High-intensity UV laser ChIP-seq for the study of protein-DNA interactions in living cells

(2017) Arndt Steube et al.   Nature Communications

Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression

(2016) Belinda Phipson et al.   Annals of Applied Statistics

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

(2016) Philip Ewels et al.   BIOINFORMATICS

Oct4 Is a Key Regulator of Vertebrate Trunk Length Diversity

(2016) Rita Aires et al.   DEVELOPMENTAL CELL

Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo

(2016) Guangdun Peng et al.   DEVELOPMENTAL CELL

OCT4 Acts as an Integrator of Pluripotency and Signal-Induced Differentiation

(2016) Zoltan Simandi et al.   MOLECULAR CELL

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Inducible DamID systems for genomic mapping of chromatin proteins inDrosophila

(2016) Alexey V. Pindyurin et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Abdenour Soufi et al.   CELL

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

(2015) Jop Kind et al.   CELL

ChIP bias as a function of cross-linking time

(2015) Laura Baranello et al.   CHROMOSOME RESEARCH

Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells

(2015) T. K. Mistri et al.   EMBO REPORTS

The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing

(2015) Filipe V. Jacinto et al.   GENES & DEVELOPMENT

CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins

(2015) Daniel Savic et al.   GENOME RESEARCH

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

(2015) Christian Schmidl et al.   NATURE METHODS

Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments

(2015) Dhawal Jain et al.   NUCLEIC ACIDS RESEARCH

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

(2015) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets

(2015) Romaric Bouveret et al.   eLife

quantro: a data-driven approach to guide the choice of an appropriate normalization method

(2015) Stephanie Hicks et al.   GENOME BIOLOGY

Dam it's good! DamID profiling of protein-DNA interactions

(2015) Gabriel N. Aughey et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal

(2014) Juan L. Mateo et al.   GENOME RESEARCH

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses

(2014) Luana Micallef et al.   PLoS One

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis

(2013) D. R. Zerbino et al.   BIOINFORMATICS

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

The Transcriptional and Functional Properties of Mouse Epiblast Stem Cells Resemble the Anterior Primitive Streak

(2013) Yoji Kojima et al.   Cell Stem Cell

Cell-Type-Specific Profiling of Gene Expression and Chromatin Binding without Cell Isolation: Assaying RNA Pol II Occupancy in Neural Stem Cells

(2013) Tony D. Southall et al.   DEVELOPMENTAL CELL

A Network Model of the Molecular Organization of Chromatin in Drosophila

(2013) Joke G. van Bemmel et al.   MOLECULAR CELL

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Widespread Misinterpretable ChIP-seq Bias in Yeast

(2013) Daechan Park et al.   PLoS One

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

(2013) L. Teytelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oct4 Is Required ∼E7.5 for Proliferation in the Primitive Streak

(2013) Brian DeVeale et al.   PLoS Genetics

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

The developmental dismantling of pluripotency is reversed by ectopic Oct4 expression

(2012) R. Osorno et al.   DEVELOPMENT

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

BigWig and BigBed: enabling browsing of large distributed datasets

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

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

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

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

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Redefining the Progression of Lineage Segregations during Mammalian Embryogenesis by Clonal Analysis

(2009) Elena Tzouanacou et al.   DEVELOPMENTAL CELL

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE