Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects

Plant metabolic gene clusters in the multi-omics era

(2022) Chuansong Zhan et al.   TRENDS IN PLANT SCIENCE

Triangulation supports agricultural spread of the Transeurasian languages

(2021) Martine Robbeets et al.   NATURE

Reference Genome for the Highly Transformable Setaria viridis ME034V

(2020) Peter M. Thielen et al.   G3-Genes Genomes Genetics

Understanding the Role of Interleukin-6 (IL-6) in the Joint and Beyond: A Comprehensive Review of IL-6 Inhibition for the Management of Rheumatoid Arthritis

(2020) Ennio G. Favalli   Rheumatology and Therapy

A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci

(2020) Sujan Mamidi et al.   NATURE BIOTECHNOLOGY

In Vivo Anti-inflammatory and Antiallergic Activity of Pure Naringenin, Naringenin Chalcone, and Quercetin in Mice

(2019) Elvira Escribano-Ferrer et al.   JOURNAL OF NATURAL PRODUCTS

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Genome-wide Dissection of Co-selected UV-B Responsive Pathways in the UV-B Adaptation of Qingke

(2019) Xingquan Zeng et al.   Molecular Plant

Rewiring of the Fruit Metabolome in Tomato Breeding

(2018) Guangtao Zhu et al.   CELL

Domestication and Improvement in the Model C4 Grass, Setaria

(2018) Hao Hu et al.   Frontiers in Plant Science

Metabolic GWAS-based dissection of genetic bases underlying the diversity of plant metabolism

(2018) Chuanying Fang et al.   PLANT JOURNAL

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

Maftools: efficient and comprehensive analysis of somatic variants in cancer

(2018) Anand Mayakonda et al.   GENOME RESEARCH

Evaluation of intensity drift correction strategies using MetaboDrift, a normalization tool for multi-batch metabolomics data

(2017) Chanisa Thonusin et al.   JOURNAL OF CHROMATOGRAPHY A

A chemical genetic roadmap to improved tomato flavor

(2017) Denise Tieman et al.   SCIENCE

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

(2017) Meng Peng et al.   Nature Communications

Evaluation of O2PLS in Omics data integration

(2016) Said el Bouhaddani et al.   BMC BIOINFORMATICS

Integrative approaches for large-scale transcriptome-wide association studies

(2016) Alexander Gusev et al.   NATURE GENETICS

Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals

(2016) Wei Chen et al.   Nature Communications

Immunoregulatory Pathways Involved in Inflammatory Bowel Disease

(2015) Gabriela Fonseca-Camarillo et al.   INFLAMMATORY BOWEL DISEASES

A Robust CRISPR/Cas9 System for Convenient, High-Efficiency Multiplex Genome Editing in Monocot and Dicot Plants

(2015) Xingliang Ma et al.   Molecular Plant

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Combining Quantitative Genetics Approaches with Regulatory Network Analysis to Dissect the Complex Metabolism of the Maize Kernel

(2015) Weiwei Wen et al.   PLANT PHYSIOLOGY

Role of Chlorogenic Acids in Controlling Oxidative and Inflammatory Stress Conditions

(2015) Ningjian Liang et al.   Nutrients

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

(2014) Tae-Ho Lee et al.   BMC GENOMICS

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

selscan: An Efficient Multithreaded Program to Perform EHH-Based Scans for Positive Selection

(2014) Z. A. Szpiech et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Wei Chen et al.   NATURE GENETICS

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism

(2014) Fumio Matsuda et al.   PLANT JOURNAL

Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights

(2014) Weiwei Wen et al.   Nature Communications

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

(2013) Y. Liao et al.   BIOINFORMATICS

Encapsulation of the Most Potent Antioxidant Betalains in Edible Matrixes as Powders of Different Colors

(2013) Fernando Gandía-Herrero et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

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

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

(2012) Gengyun Zhang et al.   NATURE BIOTECHNOLOGY

Integrating heterogeneous high-throughput data for meta-dimensional pharmacogenomics and disease-related studies

(2012) Emily R Holzinger et al.   PHARMACOGENOMICS

Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize

(2012) C. Riedelsheimer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early millet use in northern China

(2012) X. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

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

Combining Genome-Wide Association Mapping and Transcriptional Networks to Identify Novel Genes Controlling Glucosinolates in Arabidopsis thaliana

(2011) Eva K. F. Chan et al.   PLOS BIOLOGY

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Mixed linear model approach adapted for genome-wide association studies

(2010) Zhiwu Zhang et al.   NATURE GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

The Complex Genetic Architecture of the Metabolome

(2010) Eva K. F. Chan et al.   PLoS Genetics

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

Pathogenic perspectives for the role of inflammation in diabetic nephropathy

(2009) Antonio Rivero et al.   CLINICAL SCIENCE

Understanding the Evolution of Defense Metabolites in Arabidopsis thaliana Using Genome-wide Association Mapping

(2009) E. K. F. Chan et al.   GENETICS

Transcriptional Control of SET DOMAIN GROUP 8 and CAROTENOID ISOMERASE during Arabidopsis Development

(2009) Christopher I. Cazzonelli et al.   Molecular Plant

The Role of Inflammatory Cytokines in Diabetic Nephropathy

(2008) J. F. Navarro-Gonzalez et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites

(2008) Fumio Matsuda et al.   PLANT JOURNAL