Genome-scale screens identify JNK–JUN signaling as a barrier for pluripotency exit and endoderm differentiation

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Predicting enhancer activity and variant impact using gkm-SVM

(2017) Michael A. Beer   HUMAN MUTATION

Predicting gene expression in massively parallel reporter assays: A comparative study

(2017) Anat Kreimer et al.   HUMAN MUTATION

AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection

(2017) Thomas Vierbuchen et al.   MOLECULAR CELL

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

(2017) Douglas H. Phanstiel et al.   MOLECULAR CELL

GATA6 is essential for endoderm formation from human pluripotent stem cells

(2017) J. B. Fisher et al.   Biology Open

GATA6 Plays an Important Role in the Induction of Human Definitive Endoderm, Development of the Pancreas, and Functionality of Pancreatic β Cells

(2017) Amita Tiyaboonchai et al.   Stem Cell Reports

Genome Editing of Lineage Determinants in Human Pluripotent Stem Cells Reveals Mechanisms of Pancreatic Development and Diabetes

(2016) Zengrong Zhu et al.   Cell Stem Cell

CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs

(2016) Mohammad A. Mandegar et al.   Cell Stem Cell

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Transition states and cell fate decisions in epigenetic landscapes

(2016) Naomi Moris et al.   NATURE REVIEWS GENETICS

Epigenomic landscapes of retinal rods and cones

(2016) Alisa Mo et al.   eLife

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

(2015) Oren Parnas et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

SMADs and YAP Compete to Control Elongation of β-Catenin:LEF-1-Recruited RNAPII during hESC Differentiation

(2015) Conchi Estarás et al.   MOLECULAR CELL

Transcription factor binding dynamics during human ES cell differentiation

(2015) Alexander M. Tsankov et al.   NATURE

The oncogene c-Jun impedes somatic cell reprogramming

(2015) Jing Liu et al.   NATURE CELL BIOLOGY

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

Efficient Generation of NKX6-1+ Pancreatic Progenitors from Multiple Human Pluripotent Stem Cell Lines

(2015) M. Cristina Nostro et al.   Stem Cell Reports

A CRISPR/Cas-Mediated Selection-free Knockin Strategy in Human Embryonic Stem Cells

(2015) Zengrong Zhu et al.   Stem Cell Reports

Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space

(2015) Rahul Karnik et al.   PLoS One

Generation of Functional Human Pancreatic β Cells In Vitro

(2014) Felicia W. Pagliuca et al.   CELL

Efficient Endoderm Induction from Human Pluripotent Stem Cells by Logically Directing Signals Controlling Lineage Bifurcations

(2014) Kyle M. Loh et al.   Cell Stem Cell

An iCRISPR Platform for Rapid, Multiplexable, and Inducible Genome Editing in Human Pluripotent Stem Cells

(2014) Federico González et al.   Cell Stem Cell

Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells

(2014) Alireza Rezania et al.   NATURE BIOTECHNOLOGY

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Dose-dependent Nodal/Smad signals pattern the early mouse embryo

(2014) Elizabeth J. Robertson   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Generation of Alveolar Epithelial Spheroids via Isolated Progenitor Cells from Human Pluripotent Stem Cells

(2014) Shimpei Gotoh et al.   Stem Cell Reports

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

(2013) Y. Liao et al.   BIOINFORMATICS

Human pluripotent stem cells: an emerging model in developmental biology

(2013) Z. Zhu et al.   DEVELOPMENT

Effect of natural genetic variation on enhancer selection and function

(2013) S. Heinz et al.   NATURE

Efficient generation of lung and airway epithelial cells from human pluripotent stem cells

(2013) Sarah X L Huang et al.   NATURE BIOTECHNOLOGY

Switch Enhancers Interpret TGF-β and Hippo Signaling to Control Cell Fate in Human Embryonic Stem Cells

(2013) Tobias A. Beyer et al.   Cell Reports

Discovery of Potent and Selective Covalent Inhibitors of JNK

(2012) Tinghu Zhang et al.   CHEMISTRY & BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling

(2011) Alan C. Mullen et al.   CELL

Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines

(2011) Christoph Bock et al.   CELL

Pluripotency factors regulate definitive endoderm specification through eomesodermin

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

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

(2011) Simon C. Biddie et al.   MOLECULAR CELL

Generation of anterior foregut endoderm from human embryonic and induced pluripotent stem cells

(2011) Michael D Green et al.   NATURE BIOTECHNOLOGY

Activin/Nodal Signaling Controls Divergent Transcriptional Networks in Human Embryonic Stem Cells and in Endoderm Progenitors

(2011) Stephanie Brown et al.   STEM CELLS

BigWig and BigBed: enabling browsing of large distributed datasets

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

c-Jun NH2-Terminal Kinase Is Required for Lineage-Specific Differentiation but Not Stem Cell Self-Renewal

(2010) P. Xu et al.   MOLECULAR AND CELLULAR BIOLOGY

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

Vertebrate Endoderm Development and Organ Formation

(2009) Aaron M. Zorn et al.   Annual Review of Cell and Developmental Biology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling

(2009) Stuart M Chambers et al.   NATURE BIOTECHNOLOGY

Pivotal roles for eomesodermin during axis formation, epithelium-to-mesenchyme transition and endoderm specification in the mouse

(2008) S. J. Arnold et al.   DEVELOPMENT

Marked differences in differentiation propensity among human embryonic stem cell lines

(2008) Kenji Osafune et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY