eQTLs play critical roles in regulating gene expression and identifying key regulators in rice

Rice contains a biosynthetic gene cluster associated with production of the casbane‐type diterpenoid phytoalexin ent ‐10‐oxodepressin

(2021) Jin Liang et al.   NEW PHYTOLOGIST

Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton

(2020) Zhonghua Li et al.   NEW PHYTOLOGIST

The coordination of OsbZIP72 and OsMYBS2 with reverse roles regulates the transcription of OsPsbS1 in rice

(2020) Xiangkui Fu et al.   NEW PHYTOLOGIST

Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus

(2020) Shan Tang et al.   Molecular Plant

Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms

(2019) Rebecca L. Walker et al.   CELL

Rewiring of the Fruit Metabolome in Tomato Breeding

(2018) Guangtao Zhu et al.   CELL

Genome-wide Analysis of Transcriptional Variability in a Large Maize-Teosinte Population

(2018) Xufeng Wang et al.   Molecular Plant

Inferring Roles in Defense from Metabolic Allocation of Rice Diterpenoids

(2018) Xuan Lu et al.   PLANT CELL

Comparison of Oryza sativa and Oryza brachyantha genomes reveals selection-driven gene escape from the centromeric regions

(2018) Yi Liao et al.   PLANT CELL

Integrating co-expression networks with GWAS to prioritize causal genes in maize

(2018) Robert Schaefer et al.   PLANT CELL

Genome-wide Association Analyses Reveal the Genetic Basis of Stigma Exsertion in Rice

(2017) Hao Zhou et al.   Molecular Plant

Distant eQTLs and Non-coding Sequences Play Critical Roles in Regulating Gene Expression and Quantitative Trait Variation in Maize

(2017) Haijun Liu et al.   Molecular Plant

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis

(2017) Lei Zhang et al.   Nature Communications

Differentially evolved glucosyltransferases determine natural variation of rice flavone accumulation and UV-tolerance

(2017) Meng Peng et al.   Nature Communications

Integrative approaches for large-scale transcriptome-wide association studies

(2016) Alexander Gusev et al.   NATURE GENETICS

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Feedback regulation of ABA signaling and biosynthesis by a bZIP transcription factor targets drought resistance related genes

(2016) Wei Zong et al.   PLANT PHYSIOLOGY

Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study

(2015) Quanxiu Wang et al.   Molecular Plant

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The role of regulatory variation in complex traits and disease

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

Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection

(2015) Weibo Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of chromosomal translocation hotspots via scan statistics

(2014) Israel T. Silva et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

(2014) Jian-Feng Xiang et al.   CELL RESEARCH

Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism

(2014) Wei Chen et al.   NATURE GENETICS

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

(2014) Claudia Giambartolomei et al.   PLoS Genetics

A Novel Integrated Method for Large-Scale Detection, Identification, and Quantification of Widely Targeted Metabolites: Application in the Study of Rice Metabolomics

(2013) Wei Chen et al.   Molecular Plant

RNA-Guided Genome Editing in Plants Using a CRISPR–Cas System

(2013) Kabin Xie et al.   Molecular Plant

Explaining intraspecific diversity in plant secondary metabolites in an ecological context

(2013) Ben D. Moore et al.   NEW PHYTOLOGIST

PlantGSEA: a gene set enrichment analysis toolkit for plant community

(2013) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

Regulation from a distance: long-range control of gene expression in development and disease

(2013) V. van Heyningen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

RNA sequencing reveals the complex regulatory network in the maize kernel

(2013) Junjie Fu et al.   Nature Communications

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants

(2012) Francisco A Cubillos et al.   CURRENT OPINION IN PLANT BIOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets

(2011) Miao-Xin Li et al.   HUMAN GENETICS

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

(2011) Xuehui Huang et al.   NATURE GENETICS

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription

(2011) Yufeng Wu et al.   PLANT CELL

Thermodynamic models of combinatorial gene regulation by distant enhancers

(2010) J. Narula et al.   IET Systems Biology

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus

(2010) D. R. Drost et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Mutant Resources in Rice for Functional Genomics of the Grasses

(2009) A. Krishnan et al.   PLANT PHYSIOLOGY

Quantitative Genomics: Analyzing Intraspecific Variation Using Global Gene Expression Polymorphisms or eQTLs

(2008) Dan Kliebenstein   Annual Review of Plant Biology

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS