Addressing variability in iPSC-derived models of human disease: guidelines to promote reproducibility

Pathological priming causes developmental gene network heterochronicity in autistic subject-derived neurons

(2019) Simon T. Schafer et al.   NATURE NEUROSCIENCE

Publisher Correction: Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

(2019) Xuran Wang et al.   Nature Communications

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors

(2019) Alessandra Vigilante et al.   Cell Reports

Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures

(2019) Konstantin Zaitsev et al.   Nature Communications

RNA sequencing reveals MMP2 and TGFB1 downregulation in LRRK2 G2019S Parkinson's iPSC-derived astrocytes

(2019) Heather D.E. Booth et al.   NEUROBIOLOGY OF DISEASE

Large-Scale Single-Cell RNA-Seq Reveals Molecular Signatures of Heterogeneous Populations of Human Induced Pluripotent Stem Cell-Derived Endothelial Cells

(2018) David T Paik et al.   CIRCULATION RESEARCH

Human iPSC-based models highlight defective glial and neuronal differentiation from neural progenitor cells in metachromatic leukodystrophy

(2018) Giacomo Frati et al.   Cell Death & Disease

Combining NGN2 Programming with Developmental Patterning Generates Human Excitatory Neurons with NMDAR-Mediated Synaptic Transmission

(2018) Ralda Nehme et al.   Cell Reports

DNA methylation alterations in iPSC- and hESC-derived neurons: potential implications for neurological disease modeling

(2018) Laura de Boni et al.   Clinical Epigenetics

Representing Diversity in the Dish: Using Patient-Derived in Vitro Models to Recreate the Heterogeneity of Neurological Disease

(2018) Layla T. Ghaffari et al.   Frontiers in Neuroscience

Recent Trends in Research with Human Pluripotent Stem Cells: Impact of Research and Use of Cell Lines in Experimental Research and Clinical Trials

(2018) Anke Guhr et al.   Stem Cell Reports

Sorting cells alters their redox state and cellular metabolome

(2018) Elizabeth M. Llufrio et al.   Redox Biology

Insights into the Mutational Burden of Human Induced Pluripotent Stem Cells from an Integrative Multi-Omics Approach

(2018) Matteo D’Antonio et al.   Cell Reports

Synaptic dysfunction in neurodegenerative and neurodevelopmental diseases: an overview of induced pluripotent stem-cell-based disease models

(2018) Era Taoufik et al.   Open Biology

Reproducibility of Molecular Phenotypes after Long-Term Differentiation to Human iPSC-Derived Neurons: A Multi-Site Omics Study

(2018) Viola Volpato et al.   Stem Cell Reports

Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes

(2018) Charmaine Lang et al.   Cell Stem Cell

Best Practices for Translational Disease Modeling Using Human iPSC-Derived Neurons

(2018) Sandra J. Engle et al.   NEURON

Need for high-resolution Genetic Analysis in iPSC: Results and Lessons from the ForIPS Consortium

(2018) Bernt Popp et al.   Scientific Reports

Impact of regulatory variation across human iPSCs and differentiated cells

(2017) Nicholas E. Banovich et al.   GENOME RESEARCH

APOE ε4/ε4 diminishes neurotrophic function of human iPSC-derived astrocytes

(2017) Jing Zhao et al.   HUMAN MOLECULAR GENETICS

Transcriptomic profiling of purified patient-derived dopamine neurons identifies convergent perturbations and therapeutics for Parkinson’s disease

(2017) Cynthia Sandor et al.   HUMAN MOLECULAR GENETICS

Gene editing and clonal isolation of human induced pluripotent stem cells using CRISPR/Cas9

(2017) Saniye Yumlu et al.   METHODS

Common genetic variation drives molecular heterogeneity in human iPSCs

(2017) Helena Kilpinen et al.   NATURE

Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations

(2017) Florian T. Merkle et al.   NATURE

Molecular and functional variation in iPSC-derived sensory neurons

(2017) Jeremy Schwartzentruber et al.   NATURE GENETICS

Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells

(2017) Steven A. Sloan et al.   NEURON

Gene expression variability and the analysis of large-scale RNA-seq studies with the MDSeq

(2017) Di Ran et al.   NUCLEIC ACIDS RESEARCH

Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse

(2017) Cynthia L Smith et al.   NUCLEIC ACIDS RESEARCH

Rapid establishment of the European Bank for induced Pluripotent Stem Cells (EBiSC) - the Hot Start experience

(2017) Paul A. De Sousa et al.   Stem Cell Research

DNA methylation and transcriptional trajectories during human development and reprogramming of isogenic pluripotent stem cells

(2017) Matthias S. Roost et al.   Nature Communications

How well do you know your mutation? Complex effects of genetic background on expressivity, complementation, and ordering of allelic effects

(2017) Christopher H. Chandler et al.   PLoS Genetics

Taming Human Genetic Variability: Transcriptomic Meta-Analysis Guides the Experimental Design and Interpretation of iPSC-Based Disease Modeling

(2017) Pierre-Luc Germain et al.   Stem Cell Reports

iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types

(2017) Athanasia D. Panopoulos et al.   Stem Cell Reports

Differentiation of Inflammation-Responsive Astrocytes from Glial Progenitors Generated from Human Induced Pluripotent Stem Cells

(2017) Renata Santos et al.   Stem Cell Reports

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells

(2016) Gioele La Manno et al.   CELL

Transcriptome Profiling of Patient-Specific Human iPSC-Cardiomyocytes Predicts Individual Drug Safety and Efficacy Responses In Vitro

(2016) Elena Matsa et al.   Cell Stem Cell

Organoid-on-a-chip and body-on-a-chip systems for drug screening and disease modeling

(2016) Aleksander Skardal et al.   DRUG DISCOVERY TODAY

Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics

(2016) Adam E. Handel et al.   HUMAN MOLECULAR GENETICS

A high-content platform to characterise human induced pluripotent stem cell lines

(2016) Andreas Leha et al.   METHODS

Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology

(2016) C Bardy et al.   MOLECULAR PSYCHIATRY

Pharmacological reversal of a pain phenotype in iPSC-derived sensory neurons and patients with inherited erythromelalgia

(2016) Lishuang Cao et al.   Science Translational Medicine

Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs

(2016) Courtney K. Burrows et al.   PLoS Genetics

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

(2016) Nathan Salomonis et al.   Stem Cell Reports

Genetic Variability Overrides the Impact of Parental Cell Type and Determines iPSC Differentiation Potential

(2016) Aija Kyttälä et al.   Stem Cell Reports

Differential responses to lithium in hyperexcitable neurons from patients with bipolar disorder

(2015) Jerome Mertens et al.   NATURE

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Automated, high-throughput derivation, characterization and differentiation of induced pluripotent stem cells

(2015) Daniel Paull et al.   NATURE METHODS

Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature

(2015) Samantha M. Thomas et al.   PLoS Genetics

Long-term electrophysiological activity and pharmacological response of a human induced pluripotent stem cell-derived neuron and astrocyte co-culture

(2014) A. Odawara et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Assessing Kinetics from Fixed Cells Reveals Activation of the Mitotic Entry Network at the S/G2 Transition

(2014) Karen Akopyan et al.   MOLECULAR CELL

A three-dimensional human neural cell culture model of Alzheimer’s disease

(2014) Se Hoon Choi et al.   NATURE

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Intrinsic Membrane Hyperexcitability of Amyotrophic Lateral Sclerosis Patient-Derived Motor Neurons

(2014) Brian J. Wainger et al.   Cell Reports

Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells

(2014) Foad Rouhani et al.   PLoS Genetics

Dynamic changes in DNA methylation and hydroxymethylation when hES cells undergo differentiation toward a neuronal lineage

(2013) Mirang Kim et al.   HUMAN MOLECULAR GENETICS

Glia co-culture with neurons in microfluidic platforms promotes the formation and stabilization of synaptic contacts

(2013) Mingjian Shi et al.   LAB ON A CHIP

Gain of 20q11.21 in human embryonic stem cells improves cell survival by increased expression of Bcl-xL

(2013) H.T. Nguyen et al.   MOLECULAR HUMAN REPRODUCTION

Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle

(2013) Ran Kafri et al.   NATURE

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Erosion of Dosage Compensation Impacts Human iPSC Disease Modeling

(2012) Shila Mekhoubad et al.   Cell Stem Cell

Pharmacological Rescue of Mitochondrial Deficits in iPSC-Derived Neural Cells from Patients with Familial Parkinson's Disease

(2012) O. Cooper et al.   Science Translational Medicine

Recapitulation of premature ageing with iPSCs from Hutchinson–Gilford progeria syndrome

(2011) Guang-Hui Liu et al.   NATURE

Concise Review: Induced Pluripotent Stem Cells Versus Embryonic Stem Cells: Close Enough or Yet Too Far Apart?

(2011) Josipa Bilic et al.   STEM CELLS

Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency

(2010) B.-Y. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neuronal Nuclei Isolation from Human Postmortem Brain Tissue

(2008) Anouch Matevossian et al.   Jove-Journal of Visualized Experiments