Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease

Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator

(2021) Lila Allou et al.   NATURE

Widespread Transcriptional Scanning in the Testis Modulates Gene Evolution Rates

(2020) Bo Xia et al.   CELL

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

(2020) Konrad J. Karczewski et al.   NATURE

A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer

(2020) Kaivalya Walavalkar et al.   Nature Communications

Transcriptomic signatures across human tissues identify functional rare genetic variation

(2020) Nicole M. Ferraro et al.   SCIENCE

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity

(2019) Kaia Mattioli et al.   GENOME RESEARCH

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

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

An expanded landscape of human long noncoding RNA

(2019) Shuai Jiang et al.   NUCLEIC ACIDS RESEARCH

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Paediatric genomics: diagnosing rare disease in children

(2018) Caroline F. Wright et al.   NATURE REVIEWS GENETICS

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites

(2018) Ying Liu et al.   NATURE BIOTECHNOLOGY

Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

(2018) Sarah M. Urbut et al.   NATURE GENETICS

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology

(2017) Eugene J. Gardner et al.   GENOME RESEARCH

Quantifying the regulatory effect size ofcis-acting genetic variation using allelic fold change

(2017) Pejman Mohammadi et al.   GENOME RESEARCH

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon et al.   NATURE

Annotation-free quantification of RNA splicing using LeafCutter

(2017) Yang I. Li et al.   NATURE GENETICS

The impact of structural variation on human gene expression

(2017) Colby Chiang et al.   NATURE GENETICS

An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome

(2017) Bernard Ng et al.   NATURE NEUROSCIENCE

C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis

(2017) Kaido Lepik et al.   PLoS Computational Biology

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Colocalization of GWAS and eQTL Signals Detects Target Genes

(2016) Farhad Hormozdiari et al.   AMERICAN JOURNAL OF HUMAN GENETICS

FINEMAP: efficient variable selection using summary data from genome-wide association studies

(2016) Christian Benner et al.   BIOINFORMATICS

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

(2016) Marta Melé et al.   GENOME RESEARCH

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

(2016) Zhihong Zhu et al.   NATURE GENETICS

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

Unique features of long non-coding RNA biogenesis and function

(2016) Jeffrey J. Quinn et al.   NATURE REVIEWS GENETICS

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu et al.   SCIENCE

Oral pathology in inflammatory bowel disease

(2016) Miranda Muhvić-Urek et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Homeobox NKX2-3 promotes marginal-zone lymphomagenesis by activating B-cell receptor signalling and shaping lymphocyte dynamics

(2016) Eloy F. Robles et al.   Nature Communications

Rare variant phasing and haplotypic expression from RNA sequencing with phASER

(2016) Stephane E. Castel et al.   Nature Communications

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads

(2015) Hung-I Chen et al.   BMC GENOMICS

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

(2015) Fabian Grubert et al.   CELL

Mutations within theLINC-HELLPnon-coding RNA differentially bind ribosomal and RNA splicing complexes and negatively affect trophoblast differentiation

(2015) Marie van Dijk et al.   HUMAN MOLECULAR GENETICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

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

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs

(2015) Viren Amin et al.   Nature Communications

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

Influence of RNA extraction methods and library selection schemes on RNA-seq data

(2014) Marc Sultan et al.   BMC GENOMICS

Cell Type-Specific Expression Analysis to Identify Putative Cellular Mechanisms for Neurogenetic Disorders

(2014) X. Xu et al.   JOURNAL OF NEUROSCIENCE

Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins

(2014) Alfonso Buil et al.   NATURE GENETICS

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

(2014) Xiu Cheng Quek et al.   NUCLEIC ACIDS RESEARCH

The role of long non-coding RNAs in neurodevelopment, brain function and neurological disease

(2014) T. C. Roberts et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Long non-coding RNAs in the regulation of the immune response

(2014) James A. Heward et al.   TRENDS IN IMMUNOLOGY

Contribution of NKX2-3 Polymorphisms to Inflammatory Bowel Diseases: A Meta-Analysis of 35358 subjects

(2014) XiaoCheng Lu et al.   Scientific Reports

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

(2014) Claudia Giambartolomei et al.   PLoS Genetics

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs

(2013) Liuqing Yang et al.   NATURE

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

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

(2013) Maria Gutierrez-Arcelus et al.   eLife

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

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

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

(2012) Oliver Stegle et al.   Nature Protocols

Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants

(2012) A. Keinan et al.   SCIENCE

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

(2011) Noa Novershtern et al.   CELL

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

Long noncoding RNAs and human disease

(2011) Orly Wapinski et al.   TRENDS IN CELL BIOLOGY

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

Analytical approaches to RNA profiling data for the identification of genes enriched in specific cells

(2010) Joseph D. Dougherty et al.   NUCLEIC ACIDS RESEARCH

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase

(2008) Mohammad Ali Faghihi et al.   NATURE MEDICINE