Impact of regulatory variation across human iPSCs and differentiated cells

Common genetic variation drives molecular heterogeneity in human iPSCs

(2017) Helena Kilpinen et al.   NATURE

Convolutional neural network architectures for predicting DNA–protein binding

(2016) Haoyang Zeng et al.   BIOINFORMATICS

A synergistic DNA logic predicts genome-wide chromatin accessibility

(2016) Tatsunori Hashimoto et al.   GENOME RESEARCH

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

Human induced pluripotent stem cell–derived cardiomyocytes recapitulate the predilection of breast cancer patients to doxorubicin-induced cardiotoxicity

(2016) Paul W Burridge et al.   NATURE MEDICINE

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

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

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

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs

(2015) Jiho Choi et al.   NATURE BIOTECHNOLOGY

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

WASP: allele-specific software for robust molecular quantitative trait locus discovery

(2015) Bryce van de Geijn et al.   NATURE METHODS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

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

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

Large-scale generation of human iPSC-derived neural stem cells/early neural progenitor cells and their neuronal differentiation

(2015) Leonardo D’Aiuto et al.   Organogenesis

Generation of Functional Human Pancreatic β Cells In Vitro

(2014) Felicia W. Pagliuca et al.   CELL

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Chemically defined generation of human cardiomyocytes

(2014) Paul W Burridge et al.   NATURE METHODS

Macrophage Models of Gaucher Disease for Evaluating Disease Pathogenesis and Candidate Drugs

(2014) E. Aflaki et al.   Science Translational Medicine

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

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Human iPSC-Based Modeling of Late-Onset Disease via Progerin-Induced Aging

(2013) Justine D. Miller et al.   Cell Stem Cell

Drug Screening Using a Library of Human Induced Pluripotent Stem Cell–Derived Cardiomyocytes Reveals Disease-Specific Patterns of Cardiotoxicity

(2013) Ping Liang et al.   CIRCULATION

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

Efficient drug screening and gene correction for treating liver disease using patient-specific stem cells

(2013) Su Mi Choi et al.   HEPATOLOGY

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Switched on with magnets

(2013) Sanjay Kumar   Nature Nanotechnology

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

(2013) H. Kilpinen et al.   SCIENCE

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

(2013) Maria Gutierrez-Arcelus et al.   eLife

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes

(2012) Darren A. Cusanovich et al.   HUMAN MOLECULAR GENETICS

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Modeling familial Alzheimer's disease with induced pluripotent stem cells

(2011) Takuya Yagi et al.   HUMAN MOLECULAR GENETICS

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

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

(2010) Galih Kunarso et al.   NATURE GENETICS

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

(2010) J. Raphael Gibbs et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY