Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells

(2017) Rhishikesh Bargaje et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells

(2017) Stefan Semrau et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

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

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

Sall4 controls differentiation of pluripotent cells independently of the Nucleosome Remodelling and Deacetylation (NuRD) complex

(2016) Anzy Miller et al.   DEVELOPMENT

A Structural Investigation into Oct4 Regulation by Orphan Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and Liver Receptor Homolog-1 (LRH-1)

(2016) Emily R. Weikum et al.   JOURNAL OF MOLECULAR BIOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

The human-induced pluripotent stem cell initiative—data resources for cellular genetics

(2016) Ian Streeter et al.   NUCLEIC ACIDS RESEARCH

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

(2015) Nicola K. Wilson et al.   Cell Stem Cell

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

A qPCR ScoreCard quantifies the differentiation potential of human pluripotent stem cells

(2015) Alexander M Tsankov et al.   NATURE BIOTECHNOLOGY

Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

(2015) Ning Leng et al.   NATURE METHODS

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA-dependent Oct4–Sox2 interaction and diffusion properties characteristic of the pluripotent cell state revealed by fluorescence spectroscopy

(2012) Chen Sok Lam et al.   BIOCHEMICAL JOURNAL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH

Strong rules for discarding predictors in lasso-type problems

(2011) Robert Tibshirani et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Transcriptional control of embryonic and induced pluripotent stem cells

(2011) Matthew G Guenther   Epigenomics

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

A Novel SALL4/OCT4 Transcriptional Feedback Network for Pluripotency of Embryonic Stem Cells

(2010) Jianchang Yang et al.   PLoS One

A human functional protein interaction network and its application to cancer data analysis

(2010) Guanming Wu et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Direct cell reprogramming is a stochastic process amenable to acceleration

(2009) Jacob Hanna et al.   NATURE

A Continuum of Cell States Spans Pluripotency and Lineage Commitment in Human Embryonic Stem Cells

(2009) Shelley R. Hough et al.   PLoS One

Hypoxia inducible factors regulate pluripotency and proliferation in human embryonic stem cells cultured at reduced oxygen tensions

(2009) Catherine E Forristal et al.   REPRODUCTION