Population- and individual-specific regulatory variation in Sardinia

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A Burden of Rare Variants Associated with Extremes of Gene Expression in Human Peripheral Blood

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Analysis of protein-coding genetic variation in 60,706 humans

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Health and population effects of rare gene knockouts in adult humans with related parents

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Individualized Iterative Phenotyping for Genome-wide Analysis of Loss-of-Function Mutations

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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 method for calculating probabilities of fitness consequences for point mutations across the human genome

(2015) Brad Gulko et al.   NATURE GENETICS

Height-reducing variants and selection for short stature in Sardinia

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Analysis of loss-of-function variants and 20 risk factor phenotypes in 8,554 individuals identifies loci influencing chronic disease

(2015) Alexander H Li et al.   NATURE GENETICS

Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers

(2015) Carlo Sidore et al.   NATURE GENETICS

Identification of a large set of rare complete human knockouts

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

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Omic personality: implications of stable transcript and methylation profiles for personalized medicine

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Aberrant Gene Expression in Humans

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Transcriptome Sequencing of a Large Human Family Identifies the Impact of Rare Noncoding Variants

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

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Rare variant genotype imputation with thousands of study-specific whole-genome sequences: implications for cost-effective study designs

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BAFF and BAFF Receptor Levels Correlate with B Cell Subset Activation and Redistribution in Controlled Human Malaria Infection

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A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes

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A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Loss-of-function mutations in SLC30A8 protect against type 2 diabetes

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Distribution and Medical Impact of Loss-of-Function Variants in the Finnish Founder Population

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Genetic Variants Regulating Immune Cell Levels in Health and Disease

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

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Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

How malaria modulates memory: activation and dysregulation of B cells in Plasmodium infection

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Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

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Malaria infection alters the expression of B-cell activating factor resulting in diminished memory antibody responses and survival

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Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations

(2012) Vincent Segura et al.   NATURE GENETICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Complex effects of nucleotide variants in a mammalian cis-regulatory element

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Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People

(2012) M. R. Nelson et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

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A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

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A Genome-Wide Association Scan on the Levels of Markers of Inflammation in Sardinians Reveals Associations That Underpin Its Complex Regulation

(2012) Silvia Naitza et al.   PLoS Genetics

Complement receptor 1 and malaria

(2011) José A. Stoute   CELLULAR MICROBIOLOGY

Evidence for malaria selection of a CR1 haplotype in Sardinia

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Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis

(2011) Stephen Sawcer et al.   NATURE

Computational methods for transcriptome annotation and quantification using RNA-seq

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Rare and Common Regulatory Variation in Population-Scale Sequenced Human Genomes

(2011) Stephen B. Montgomery et al.   PLoS Genetics

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Deep resequencing reveals excess rare recent variants consistent with explosive population growth

(2010) Alex Coventry et al.   Nature Communications

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

Differential expression analysis for sequence count data

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The Sequence Alignment/Map format and SAMtools

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Detection of nonneutral substitution rates on mammalian phylogenies

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Gene Expression Levels Are a Target of Recent Natural Selection in the Human Genome

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High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation

(2008) Jean-Baptiste Veyrieras et al.   PLoS Genetics