Genetic architecture of microRNA expression and its link to complex diseases in the Japanese population

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases

(2020) Kazuyoshi Ishigaki et al.   NATURE GENETICS

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

Global landscape and genetic regulation of RNA editing in cortical samples from individuals with schizophrenia

(2019) Michael S. Breen et al.   NATURE NEUROSCIENCE

ncRNA-eQTL: a database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types

(2019) Jiang Li et al.   NUCLEIC ACIDS RESEARCH

Characterizing rare and low-frequency height-associated variants in the Japanese population

(2019) Masato Akiyama et al.   Nature Communications

OUP accepted manuscript

(2018)   BIOINFORMATICS

A miRNA-145/TGF-β1 negative feedback loop regulates the cancer-associated fibroblast phenotype

(2018) Genevieve E Melling et al.   CARCINOGENESIS

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

(2018) Yukinori Okada et al.   Nature Communications

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

(2018) Alvaro N. Barbeira et al.   Nature Communications

A One-Penny Imputed Genome from Next-Generation Reference Panels

(2018) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Evidence for a potential role of miR-1908-5p and miR-3614-5p in autoimmune disease risk using integrative bioinformatics

(2018) Inken Wohlers et al.   JOURNAL OF AUTOIMMUNITY

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Integration of genetics and miRNA–target gene network identified disease biology implicated in tissue specificity

(2018) Saori Sakaue et al.   NUCLEIC ACIDS RESEARCH

Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers

(2017) Yumeng Wang et al.   GENOME RESEARCH

An integrated expression atlas of miRNAs and their promoters in human and mouse

(2017) Derek de Rie et al.   NATURE BIOTECHNOLOGY

Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis

(2017) Kazuyoshi Ishigaki et al.   NATURE GENETICS

Genome-wide association study identifies 112 new loci for body mass index in the Japanese population

(2017) Masato Akiyama et al.   NATURE GENETICS

The impact of structural variation on human gene expression

(2017) Colby Chiang et al.   NATURE GENETICS

A comprehensive, cell specific microRNA catalogue of human peripheral blood

(2017) Simonas Juzenas et al.   NUCLEIC ACIDS RESEARCH

Accurate detection for a wide range of mutation and editing sites of microRNAs from small RNA high-throughput sequencing profiles

(2016) Yun Zheng et al.   NUCLEIC ACIDS RESEARCH

Significant impact of miRNA–target gene networks on genetics of human complex traits

(2016) Yukinori Okada et al.   Scientific Reports

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

Large multiallelic copy number variations in humans

(2015) Robert E Handsaker et al.   NATURE GENETICS

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

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

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

(2015) et al.   SCIENCE

Genome-wide identification of microRNA expression quantitative trait loci

(2015) Tianxiao Huan et al.   Nature Communications

Comprehensive analysis of human small RNA sequencing data provides insights into expression profiles and miRNA editing

(2015) Jing Gong et al.   RNA Biology

A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection

(2014) K. J. Siddle et al.   GENOME RESEARCH

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

(2014) Claudia Giambartolomei et al.   PLoS Genetics

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

(2013) Y. Liao et al.   BIOINFORMATICS

Genetic regulation of human adipose microRNA expression and its consequences for metabolic traits

(2013) Mete Civelek et al.   HUMAN MOLECULAR GENETICS

IL-1 Receptor Regulates microRNA-135b Expression in a Negative Feedback Mechanism during Cigarette Smoke-Induced Inflammation

(2013) S. Halappanavar et al.   JOURNAL OF IMMUNOLOGY

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Adenosine-to-inosine RNA editing and human disease

(2013) William Slotkin et al.   Genome Medicine

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Systematic identification of edited microRNAs in the human brain

(2012) S. Alon et al.   GENOME RESEARCH

Cutting Edge: A Variant of the IL-23R Gene Associated with Inflammatory Bowel Disease Induces Loss of MicroRNA Regulation and Enhanced Protein Production

(2012) A. Zwiers et al.   JOURNAL OF IMMUNOLOGY

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

(2012) Oliver Stegle et al.   Nature Protocols

Evolution of the human-specific microRNA miR-941

(2012) Hai Yang Hu et al.   Nature Communications

Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue

(2012) Leopold Parts et al.   PLoS Genetics

Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miRNAome

(2011) Cailin E. Joyce et al.   HUMAN MOLECULAR GENETICS

A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease

(2011) Patrick Brest et al.   NATURE GENETICS

Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3′ UTRs

(2011) Brad R Rosenberg et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

(2010) M. J.L. de Hoon et al.   GENOME RESEARCH

Identification of cis- and trans-regulatory variation modulating microRNA expression levels in human fibroblasts

(2010) C. Borel et al.   GENOME RESEARCH

Molecular diversity through RNA editing: a balancing act

(2010) Sanaz Farajollahi et al.   TRENDS IN GENETICS

Causes and consequences of microRNA dysregulation in cancer

(2009) Carlo M. Croce   NATURE REVIEWS GENETICS

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE

MicroRNA regulation of a cancer network: Consequences of the feedback loops involving miR-17-92, E2F, and Myc

(2008) B. D. Aguda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA