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

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

(2014) Martin J. Aryee et al.   BIOINFORMATICS

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

(2014) Nicholas E. Banovich et al.   PLoS Genetics

Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells

(2014) Foad Rouhani et al.   PLoS Genetics

X Chromosome of Female Cells Shows Dynamic Changes in Status during Human Somatic Cell Reprogramming

(2014) Kun-Yong Kim et al.   Stem Cell Reports

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Origins and implications of pluripotent stem cell variability and heterogeneity

(2013) Patrick Cahan et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Low Incidence of DNA Sequence Variation in Human Induced Pluripotent Stem Cells Generated by Nonintegrating Plasmid Expression

(2012) Linzhao Cheng et al.   Cell Stem Cell

Deciphering the complexities of human diseases and disorders by coupling induced-pluripotent stem cells and systems genetics

(2012) Wing Y. Chang et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

(2012) Jovana Maksimovic et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Epigenetic Memory and Preferential Lineage-Specific Differentiation in Induced Pluripotent Stem Cells Derived from Human Pancreatic Islet Beta Cells

(2011) Ori Bar-Nur et al.   Cell Stem Cell

Derivation of Human Induced Pluripotent Stem Cells for Cardiovascular Disease Modeling

(2011) Kamileh Narsinh et al.   CIRCULATION RESEARCH

Induced pluripotent stem cell-derived cardiomyocytes as models for genetic cardiovascular disorders

(2011) Rebecca Josowitz et al.   CURRENT OPINION IN CARDIOLOGY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells

(2011) Kitai Kim et al.   NATURE BIOTECHNOLOGY

Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells

(2011) Yuki Ohi et al.   NATURE CELL BIOLOGY

Chemically defined conditions for human iPSC derivation and culture

(2011) Guokai Chen et al.   NATURE METHODS

A bioinformatic assay for pluripotency in human cells

(2011) Franz-Josef Müller et al.   NATURE METHODS

A more efficient method to generate integration-free human iPS cells

(2011) Keisuke Okita et al.   NATURE METHODS

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells

(2010) Matthew G. Guenther et al.   Cell Stem Cell

Epigenetic memory in induced pluripotent stem cells

(2010) K. Kim et al.   NATURE

Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells

(2010) Jose M Polo et al.   NATURE BIOTECHNOLOGY

Persistent Donor Cell Gene Expression among Human Induced Pluripotent Stem Cells Contributes to Differences with Human Embryonic Stem Cells

(2010) Zhumur Ghosh et al.   PLoS One

Induced Pluripotent Stem Cells and Embryonic Stem Cells Are Distinguished by Gene Expression Signatures

(2009) Mark H. Chin et al.   Cell Stem Cell

lumi: a pipeline for processing Illumina microarray

(2008) P. Du et al.   BIOINFORMATICS

Disease-Specific Induced Pluripotent Stem Cells

(2008) In-Hyun Park et al.   CELL