Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics

SQSTM1/p62-Directed Metabolic Reprogramming Is Essential for Normal Neurodifferentiation

(2019) Javier Calvo-Garrido et al.   Stem Cell Reports

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

(2019) Alex A. Pollen et al.   CELL

Species-specific maturation profiles of human, chimpanzee and bonobo neural cells

(2019) Maria C Marchetto et al.   eLife

Alignment of single-cell trajectories to compare cellular expression dynamics

(2018) Ayelet Alpert et al.   NATURE METHODS

Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments

(2018) Rhonda Bacher et al.   BMC BIOINFORMATICS

Prolonged human neural stem cell maturation supports recovery in injured rodent CNS

(2017) Paul Lu et al.   JOURNAL OF CLINICAL INVESTIGATION

High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci

(2017) Brian S. Gloss et al.   Scientific Reports

2D and 3D Stem Cell Models of Primate Cortical Development Identify Species-Specific Differences in Progenitor Behavior Contributing to Brain Size

(2016) Tomoki Otani et al.   Cell Stem Cell

Stem Cell Models of Human Brain Development

(2016) Iva Kelava et al.   Cell Stem Cell

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development

(2016) Felipe Mora-Bermúdez et al.   eLife

LIF signaling in stem cells and development

(2015) K. Onishi et al.   DEVELOPMENT

Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation

(2015) Dimos Gaidatzis et al.   NATURE BIOTECHNOLOGY

Ubiquitin homeostasis: from neural stem cell differentiation to neuronal development

(2015) Kwon-Yul Ryu et al.   Neural Regeneration Research

Differences in the Early Development of Human and Mouse Embryonic Stem Cells

(2015) R. Gabdoulline et al.   PLoS One

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

A cost-effective RNA sequencing protocol for large-scale gene expression studies

(2015) Zhonggang Hou et al.   Scientific Reports

Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response

(2015) Stuart Aitken et al.   PLoS Computational Biology

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Mouse and human blastocyst-derived stem cells: vive les differences

(2014) J. Rossant   DEVELOPMENT

CORTECON: A Temporal Transcriptome Analysis of In Vitro Human Cerebral Cortex Development from Human Embryonic Stem Cells

(2014) Joyce van de Leemput et al.   NEURON

Drosophila Embryogenesis Scales Uniformly across Temperature in Developmentally Diverse Species

(2014) Steven G. Kuntz et al.   PLoS Genetics

Modeling physiological and pathological human neurogenesis in the dish

(2014) Vania Broccoli et al.   Frontiers in Neuroscience

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Global expression profiling reveals genetic programs underlying the developmental divergence between mouse and human embryogenesis

(2013) Lu Xue et al.   BMC GENOMICS

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

Pyramidal Neurons Derived from Human Pluripotent Stem Cells Integrate Efficiently into Mouse Brain Circuits In Vivo

(2013) Ira Espuny-Camacho et al.   NEURON

Analysis of human embryos from zygote to blastocyst reveals distinct gene expression patterns relative to the mouse

(2012) Kathy K. Niakan et al.   DEVELOPMENTAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Human cerebral cortex development from pluripotent stem cells to functional excitatory synapses

(2012) Yichen Shi et al.   NATURE NEUROSCIENCE

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Dopamine neurons derived from human ES cells efficiently engraft in animal models of Parkinson’s disease

(2011) Sonja Kriks et al.   NATURE

Specification of transplantable astroglial subtypes from human pluripotent stem cells

(2011) Robert Krencik et al.   NATURE BIOTECHNOLOGY

Lack of adrenomedullin affects growth and differentiation of adult neural stem/progenitor cells

(2010) Eva Vergaño-Vera et al.   CELL AND TISSUE RESEARCH

Conserved and Divergent Roles of FGF Signaling in Mouse Epiblast Stem Cells and Human Embryonic Stem Cells

(2010) Boris Greber et al.   Cell Stem Cell

Pax6 Is a Human Neuroectoderm Cell Fate Determinant

(2010) Xiaoqing Zhang et al.   Cell Stem Cell

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Technical Challenges in Using Human Induced Pluripotent Stem Cells to Model Disease

(2009) Krishanu Saha et al.   Cell Stem Cell

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

(2009) Stuart M Chambers et al.   NATURE BIOTECHNOLOGY

Transcriptional neoteny in the human brain

(2009) M. Somel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

An intrinsic mechanism of corticogenesis from embryonic stem cells

(2008) Nicolas Gaspard et al.   NATURE

In vivo quantification of embryonic and placental growth during gestation in mice using micro-ultrasound

(2008) Junwu Mu et al.   Reproductive Biology and Endocrinology