Dissecting seed pigmentation-associated genomic loci and genes by employing dual approaches of reference-based and k-mer-based GWAS with 438 Glycine accessions

New alleles for chlorophyll content and stay-green traits revealed by a genome wide association study in rice (Oryza sativa)

(2019) Yan Zhao et al.   Scientific Reports

A reference-grade wild soybean genome

(2019) Min Xie et al.   Nature Communications

Resistance gene cloning from a wild crop relative by sequence capture and association genetics

(2019) Sanu Arora et al.   NATURE BIOTECHNOLOGY

Association mapping from sequencing reads using k-mers

(2018) Atif Rahman et al.   eLife

Genotyping of Soybean Cultivars With Medium-Density Array Reveals the Population Structure and QTNs Underlying Maturity and Seed Traits

(2018) Ya-ying Wang et al.   Frontiers in Plant Science

Parallel selection on a dormancy gene during domestication of crops from multiple families

(2018) Min Wang et al.   NATURE GENETICS

Genome-wide association study of maize plant architecture using F1 populations

(2018) Yang Zhao et al.   PLANT MOLECULAR BIOLOGY

A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events

(2018) Magali Jaillard et al.   PLoS Genetics

Metabolism variation and better storability of dark- versus light-coloured soybean (Glycine max L. Merr.) seeds

(2017) Jiang Liu et al.   FOOD CHEMISTRY

The Non-Mendelian Green Cotyledon Gene in Soybean Encodes a Small Subunit of Photosystem II

(2017) Kaori Kohzuma et al.   PLANT PHYSIOLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification and Validation of Loci Governing Seed Coat Color by Combining Association Mapping and Bulk Segregation Analysis in Soybean

(2016) Jian Song et al.   PLoS One

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

(2016) John A. Lees et al.   Nature Communications

GAPIT Version 2: An Enhanced Integrated Tool for Genomic Association and Prediction

(2016) You Tang et al.   Plant Genome

Identifying lineage effects when controlling for population structure improves power in bacterial association studies

(2016) Sarah G. Earle et al.   Nature Microbiology

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

The International Nucleotide Sequence Database Collaboration

(2015) Guy Cochrane et al.   NUCLEIC ACIDS RESEARCH

Fingerprinting Soybean Germplasm and Its Utility in Genomic Research

(2015) Qijian Song et al.   G3-Genes Genomes Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Anil Raj et al.   GENETICS

A Green-Cotyledon/Stay-Green Mutant Exemplifies the Ancient Whole-Genome Duplications in Soybean

(2014) Michiharu Nakano et al.   PLANT AND CELL PHYSIOLOGY

Preventive Effects of Black Soybean Seed Coat Polyphenols against DNA Damage in Salmonella typhimurium

(2013) Tianshun ZHANG et al.   FOOD SCIENCE AND TECHNOLOGY RESEARCH

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

(2013) Stephane E. Castel et al.   NATURE REVIEWS GENETICS

Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks

(2013) Q. Fei et al.   PLANT CELL

Concerted evolution ofD1andD2to regulate chlorophyll degradation in soybean

(2013) Chao Fang et al.   PLANT JOURNAL

The Transition from Primary siRNAs to Amplified Secondary siRNAs That Regulate Chalcone Synthase During Development of Glycine max Seed Coats

(2013) Young B. Cho et al.   PLoS One

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

(2013) S. K. Sheppard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations

(2012) Vincent Segura et al.   NATURE GENETICS

The fate of duplicated genes in a polyploid plant genome

(2012) Anne Roulin et al.   PLANT JOURNAL

Changes in the Activity and Transcription of Antioxidant Enzymes in Response to Al Stress in Black Soybeans

(2012) Konghuan Wu et al.   PLANT MOLECULAR BIOLOGY REPORTER

Large-Scale Identification of Mirtrons in Arabidopsis and Rice

(2012) Yijun Meng et al.   PLoS One

Mirtrons, an emerging class of atypical miRNA

(2012) Helen J. Curtis et al.   Wiley Interdisciplinary Reviews-RNA

Mirtrons: microRNA biogenesis via splicing

(2011) Jakub O. Westholm et al.   BIOCHIMIE

Loss-of-function mutations affecting a specific Glycine max R2R3 MYB transcription factor result in brown hilum and brown seed coats

(2011) Jason D Gillman et al.   BMC PLANT BIOLOGY

A new allele of flower color gene W1 encoding flavonoid 3'5'-hydroxylase is responsible for light purple flowers in wild soybean Glycine soja

(2010) Ryoji Takahashi et al.   BMC PLANT BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

MicroRNA Biogenesis via Splicing and Exosome-Mediated Trimming in Drosophila

(2010) Alex S. Flynt et al.   MOLECULAR CELL

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

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

(2010) Hyun Min Kang et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Endogenous, Tissue-Specific Short Interfering RNAs Silence the Chalcone Synthase Gene Family in Glycine max Seed Coats

(2009) J. H. Tuteja et al.   PLANT CELL

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains

(2008) Q.-H. Zhu et al.   GENOME RESEARCH