Common genetic variation drives molecular heterogeneity in human iPSCs

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

(2016) Andreas Leha et al.   METHODS

Genetic variants regulating expression levels and isoform diversity during embryogenesis

(2016) Enrico Cannavò et al.   NATURE

A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data

(2016) Petr Danecek et al.   PLoS One

Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level

(2016) Dalila Bensaddek et al.   PROTEOMICS

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

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

(2016) Aija Kyttälä et al.   Stem Cell Reports

Regulation of cell signaling and apoptosis by tumor suppressor WWOX

(2015) Jui-Yen Lo et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The UK10K project identifies rare variants in health and disease

(2015)   NATURE

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

(2015) Jiho Choi et al.   NATURE BIOTECHNOLOGY

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

(2015) Jimmy Z Liu et al.   NATURE GENETICS

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers

(2015) Suna Onengut-Gumuscu et al.   NATURE GENETICS

Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus

(2015) James Bentham et al.   NATURE GENETICS

Efficient set tests for the genetic analysis of correlated traits

(2015) Francesco Paolo Casale et al.   NATURE METHODS

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

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

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

(2015) et al.   SCIENCE

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways

(2015) Heather J. Cordell et al.   Nature Communications

PathCards: multi-source consolidation of human biological pathways

(2015) Frida Belinky et al.   Database-The Journal of Biological Databases and Curation

Cancer-associated TERT promoter mutations abrogate telomerase silencing

(2015) Kunitoshi Chiba et al.   eLife

Constraint and divergence of global gene expression in the mammalian embryo

(2015) Noah Spies et al.   eLife

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

SNPsnap: a Web-based tool for identification and annotation of matched SNPs

(2014) Tune H. Pers et al.   BIOINFORMATICS

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

(2014) Martin J. Aryee et al.   BIOINFORMATICS

Insights into the biological functions of Dock family guanine nucleotide exchange factors

(2014) M. Laurin et al.   GENES & DEVELOPMENT

Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33

(2014) Z. Wang et al.   HUMAN MOLECULAR GENETICS

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Investigating human disease using stem cell models

(2014) Jared L. Sterneckert et al.   NATURE REVIEWS GENETICS

Systematic Genetic Analysis Identifies Cis-eQTL Target Genes Associated with Glioblastoma Patient Survival

(2014) Qing-Rong Chen et al.   PLoS One

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

(2014) Claudia Giambartolomei et al.   PLoS Genetics

Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells

(2014) Foad Rouhani et al.   PLoS Genetics

Genome-wide association study identifies 25 known breast cancer susceptibility loci as risk factors for triple-negative breast cancer

(2013) Kristen S. Purrington et al.   CARCINOGENESIS

Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci

(2013) Qiyuan Li et al.   CELL

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Genome-wide association studies identify four ER negative–specific breast cancer risk loci

(2013) Montserrat Garcia-Closas et al.   NATURE GENETICS

Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis

(2013) Ashley H Beecham et al.   NATURE GENETICS

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer

(2013) Stig E Bojesen et al.   NATURE GENETICS

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

(2013) Jean-Charles Lambert et al.   NATURE GENETICS

ImmunoChip Study Implicates Antigen Presentation to T Cells in Narcolepsy

(2013) Juliette Faraco et al.   PLoS Genetics

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and Their Differentiated Derivatives

(2012) Kristopher L. Nazor et al.   Cell Stem Cell

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells

(2012) Alexej Abyzov et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Mapping cis- and trans-regulatory effects across multiple tissues in twins

(2012) Elin Grundberg et al.   NATURE GENETICS

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

(2012)   NATURE GENETICS

Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity

(2012) Lam C Tsoi et al.   NATURE GENETICS

Donor-dependent variations in hepatic differentiation from human-induced pluripotent stem cells

(2012) M. Kajiwara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ESCs and iPSCs during Reprogramming and Time in Culture

(2011) Louise C. Laurent et al.   Cell Stem Cell

Copy number variation and selection during reprogramming to pluripotency

(2011) Samer M. Hussein et al.   NATURE

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

Karyotypic abnormalities in human induced pluripotent stem cells and embryonic stem cells

(2011) Seth M Taapken et al.   NATURE BIOTECHNOLOGY

Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage

(2011)   NATURE BIOTECHNOLOGY

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

(2011) Kitai Kim et al.   NATURE BIOTECHNOLOGY

Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease

(2011) Gosia Trynka et al.   NATURE GENETICS

A bioinformatic assay for pluripotency in human cells

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

A linear complexity phasing method for thousands of genomes

(2011) Olivier Delaneau et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Identification and Classification of Chromosomal Aberrations in Human Induced Pluripotent Stem Cells

(2010) Yoav Mayshar et al.   Cell Stem Cell

FATS is a transcriptional target of p53 and associated with antitumor activity

(2010) Xifeng Zhang et al.   Molecular Cancer

A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity

(2010) Na-Yu Chia et al.   NATURE

Epigenetic memory in induced pluripotent stem cells

(2010) K. Kim et al.   NATURE

Multiple common variants for celiac disease influencing immune gene expression

(2010) Patrick C A Dubois et al.   NATURE GENETICS

Genetics and Beyond – The Transcriptome of Human Monocytes and Disease Susceptibility

(2010) Tanja Zeller et al.   PLoS One

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Early Cell Fate Decisions of Human Embryonic Stem Cells and Mouse Epiblast Stem Cells Are Controlled by the Same Signalling Pathways

(2009) Ludovic Vallier et al.   PLoS One

Signaling Pathways Controlling Pluripotency and Early Cell Fate Decisions of Human Induced Pluripotent Stem Cells

(2009) Ludovic Vallier et al.   STEM CELLS

Expression Quantitative Trait Loci Are Highly Sensitive to Cellular Differentiation State

(2009) Alice Gerrits et al.   PLoS Genetics

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY