Evaluation of variability in human kidney organoids

Patient-iPSC-Derived Kidney Organoids Show Functional Validation of a Ciliopathic Renal Phenotype and Reveal Underlying Pathogenetic Mechanisms

(2018) Thomas A. Forbes et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Simultaneous reprogramming and gene editing of human fibroblasts

(2018) Sara E Howden et al.   Nature Protocols

Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease

(2018) Jihwan Park et al.   SCIENCE

Human induced pluripotent stem cells for modelling neurodevelopmental disorders

(2017) Karthikeyan Ardhanareeswaran et al.   Nature Reviews Neurology

Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression

(2016) Belinda Phipson et al.   Annals of Applied Statistics

ALPK3-deficient cardiomyocytes generated from patient-derived induced pluripotent stem cells and mutant human embryonic stem cells display abnormal calcium handling and establish that ALPK3 deficiency underlies familial cardiomyopathy

(2016) Dean G. Phelan et al.   EUROPEAN HEART JOURNAL

Gene correction in patient-specific iPSCs for therapy development and disease modeling

(2016) Yoon-Young Jang et al.   HUMAN GENETICS

Personalized genome sequencing coupled with iPSC technology identifies GTDC1 as a gene involved in neurodevelopmental disorders

(2016) Irene Aksoy et al.   HUMAN MOLECULAR GENETICS

Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9

(2016) Dominik Paquet et al.   NATURE

Generation of kidney organoids from human pluripotent stem cells

(2016) Minoru Takasato et al.   Nature Protocols

Modeling mouse and human development using organoid cultures

(2015) M. Huch et al.   DEVELOPMENT

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis

(2015) Minoru Takasato et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Modeling human development in 3D culture

(2014) Marius Ader et al.   CURRENT OPINION IN CELL BIOLOGY

Modelling human development and disease in pluripotent stem-cell-derived gastric organoids

(2014) Kyle W. McCracken et al.   NATURE

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

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

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

(2013) Y. Liao et al.   BIOINFORMATICS

Isogenic human pluripotent stem cell pairs reveal the role of a KCNH2 mutation in long-QT syndrome

(2013) Milena Bellin et al.   EMBO JOURNAL

Studying arrhythmogenic right ventricular dysplasia with patient-specific iPSCs

(2013) Changsung Kim et al.   NATURE

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell-derived neocortex

(2013) T. Kadoshima 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

Self-Formation of Optic Cups and Storable Stratified Neural Retina from Human ESCs

(2012) Tokushige Nakano et al.   Cell Stem Cell

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Integration-Free Induced Pluripotent Stem Cells Model Genetic and Neural Developmental Features of Down Syndrome Etiology

(2012) James A. Briggs et al.   STEM CELLS

Self-formation of functional adenohypophysis in three-dimensional culture

(2011) Hidetaka Suga et al.   NATURE

Self-organizing optic-cup morphogenesis in three-dimensional culture

(2011) Mototsugu Eiraku et al.   NATURE

Defining the Molecular Character of the Developing and Adult Kidney Podocyte

(2011) Eric W. Brunskill et al.   PLoS One

Whole-exome sequencing for finding de novo mutations in sporadic mental retardation

(2011) Peter N Robinson   GENOME BIOLOGY

ROAST: rotation gene set tests for complex microarray experiments

(2010) Di Wu et al.   BIOINFORMATICS

Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro

(2010) Jason R. Spence et al.   NATURE

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Testing significance relative to a fold-change threshold is a TREAT

(2009) D. J. McCarthy et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Human Induced Pluripotent Stem Cells Free of Vector and Transgene Sequences

(2009) J. Yu et al.   SCIENCE