Gene expression networks in the Drosophila Genetic Reference Panel

Systems Genetics of the Drosophila Metabolome

(2019) Shanshan Zhou et al.   GENOME RESEARCH

The functions and unique features of long intergenic non-coding RNA

(2017) Julia D. Ransohoff et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features

(2017) Yu-Jian Kang et al.   NUCLEIC ACIDS RESEARCH

Exploring regulation in tissues with eQTL networks

(2017) Maud Fagny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel

(2017) Trudy F.C. Mackay et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Current Research on Non-Coding Ribonucleic Acid (RNA)

(2017) Jing Wang et al.   Genes

Genotypes, Networks, Phenotypes: Moving Toward Plant Systems Genetics

(2016) Takehiko Ogura et al.   Annual Review of Cell and Developmental Biology

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

FlyBase at 25: looking to the future

(2016) L. Sian Gramates et al.   NUCLEIC ACIDS RESEARCH

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Genetic architecture of natural variation in visual senescence inDrosophila

(2016) Mary Anna Carbone et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diverse Hormone Response Networks in 41 Independent Drosophila Cell Lines

(2016) Marcus Stoiber et al.   G3-Genes Genomes Genetics

The role of regulatory variation in complex traits and disease

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

Genetic basis of transcriptome diversity inDrosophila melanogaster

(2015) Wen Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic architecture of natural variation inDrosophila melanogasteraggressive behavior

(2015) John Shorter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expression quantitative trait locus analysis for translational medicine

(2015) Greg Gibson et al.   Genome Medicine

Quantitative Genetics of Food Intake in Drosophila melanogaster

(2015) Megan E. Garlapow et al.   PLoS One

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

(2014) S. Anders et al.   BIOINFORMATICS

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

(2014) W. Huang et al.   GENOME RESEARCH

Advantages and pitfalls in the application of mixed-model association methods

(2014) Jian Yang et al.   NATURE GENETICS

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

(2014) Ezgi Hacisuleyman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cis and Trans Effects of Human Genomic Variants on Gene Expression

(2014) Julien Bryois et al.   PLoS Genetics

Genome-wide association study of sleep in Drosophila melanogaster

(2013) Susan T Harbison et al.   BMC GENOMICS

Systems genetics approaches to understand complex traits

(2013) Mete Civelek et al.   NATURE REVIEWS GENETICS

Five Years of GWAS Discovery

(2012) Peter M. Visscher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

(2012) Andreas Massouras et al.   PLoS Genetics

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Drosophila melanogaster recombination rate calculator

(2010) Anna-Sophie Fiston-Lavier et al.   GENE

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

(2010) N. C. Riddle et al.   GENOME RESEARCH

Transposable elements in natural populations of Drosophila melanogaster

(2010) Y. C. G. Lee et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

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

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Systems genetics of complex traits in Drosophila melanogaster

(2009) Julien F Ayroles et al.   NATURE GENETICS

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

The genetics of quantitative traits: challenges and prospects

(2009) Trudy F. C. Mackay et al.   NATURE REVIEWS GENETICS

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Gene Network Inference via Structural Equation Modeling in Genetical Genomics Experiments

(2008) B. Liu et al.   GENETICS

Reverse engineering the genotype–phenotype map with natural genetic variation

(2008) Matthew V. Rockman   NATURE

Variations in DNA elucidate molecular networks that cause disease

(2008) Yanqing Chen et al.   NATURE

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE