An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development

Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types

(2016) Kyle M. Loh et al.   CELL

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily

(2014) Christine B Trame et al.   BMC BIOINFORMATICS

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall 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

How to make a cardiomyocyte

(2014) D. Spater et al.   DEVELOPMENT

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Prospective isolation of human embryonic stem cell-derived cardiovascular progenitors that integrate into human fetal heart tissue

(2013) Reza Ardehali et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Molecular and evolutionary basis of limb field specification and limb initiation

(2012) Mikiko Tanaka   DEVELOPMENT GROWTH & DIFFERENTIATION

Quantum nonlinear optics with single photons enabled by strongly interacting atoms

(2012) Thibault Peyronel et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Measuring reproducibility of high-throughput experiments

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

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Vertebrate Segmentation: From Cyclic Gene Networks to Scoliosis

(2011) Olivier Pourquié   CELL

Optimizing Optical Flow Cytometry for Cell Volume-Based Sorting and Analysis

(2011) Amit Tzur et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Potent agonists of the Hedgehog signaling pathway

(2009) Shirley A. Brunton et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY