De novo assembly of a Chinese soybean genome

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi

(2018) Jens Keilwagen et al.   BMC BIOINFORMATICS

The Rosa genome provides new insights into the domestication of modern roses

(2018) Olivier Raymond et al.   NATURE GENETICS

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

(2017) Bernardo J. Clavijo et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

A Single Nucleotide Deletion in J Encoding GmELF3 Confers Long Juvenility and Is Associated with Adaption of Tropic Soybean

(2017) Yanlei Yue et al.   Molecular Plant

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

(2017) Hélène Badouin et al.   NATURE

Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield

(2017) Sijia Lu et al.   NATURE GENETICS

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

(2017) Maximilian H.-W. Schmidt et al.   PLANT CELL

Photoperiodism dynamics during the domestication and improvement of soybean

(2017) Sheng-Rui Zhang et al.   Science China-Life Sciences

Sequencing and de novo assembly of a near complete indica rice genome

(2017) Huilong Du et al.   Nature Communications

Comparison of Genetic Diversity between Chinese and American Soybean (Glycine max (L.)) Accessions Revealed by High-Density SNPs

(2017) Zhangxiong Liu et al.   Frontiers in Plant Science

A recessive allele for delayed flowering at the soybean maturity locus E9 is a leaky allele of FT2a, a FLOWERING LOCUS T ortholog

(2016) Chen Zhao et al.   BMC PLANT BIOLOGY

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

De novo assembly and phasing of a Korean human genome

(2016) Jeong-Sun Seo et al.   NATURE

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

(2016) Candice N. Hirsch et al.   PLANT CELL

Extensive sequence divergence between the reference genomes of two eliteindicarice varieties Zhenshan 97 and Minghui 63

(2016) Jianwei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterizing and annotating the genome using RNA-seq data

(2016) Geng Chen et al.   Science China-Life Sciences

The effect of transposable elements on phenotypic variation: insights from plants to humans

(2016) Liya Wei et al.   Science China-Life Sciences

Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean

(2016) Bahram Samanfar et al.   THEORETICAL AND APPLIED GENETICS

Long-read sequencing and de novo assembly of a Chinese genome

(2016) Lingling Shi et al.   Nature Communications

Genome sequence and analysis of the Japanese morning glory Ipomoea nil

(2016) Atsushi Hoshino et al.   Nature Communications

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

(2015) Robert VanBuren et al.   NATURE

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

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

AtGGM2014, an Arabidopsis gene co-expression network for functional studies

(2015) ShiSong Ma et al.   Science China-Life Sciences

Genomics progress will facilitate molecular breeding in soybean

(2015) Zheng Wang et al.   Science China-Life Sciences

Transposable elements play an important role during cotton genome evolution and fiber cell development

(2015) Kun Wang et al.   Science China-Life Sciences

TheGlycine maxcv. Enrei Genome for Improvement of Japanese Soybean Cultivars

(2015) Michihiko Shimomura et al.   International Journal of Genomics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A New Dominant Gene Conditions Early Flowering and Maturity in Soybean

(2014) Fanjiang Kong et al.   CROP SCIENCE

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

(2013) Ying-hui Li et al.   BMC GENOMICS

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Nitrogen deprivation promotesPopulusroot growth through global transcriptome reprogramming and activation of hierarchical genetic networks

(2013) Hairong Wei et al.   NEW PHYTOLOGIST

Identification of novel QTL for leaf traits in soybean

(2013) Tae-Hwan Jun et al.   PLANT BREEDING

Yield Trends Are Insufficient to Double Global Crop Production by 2050

(2013) Deepak K. Ray et al.   PLoS One

Towards revealing the functions of all genes in plants

(2013) Seung Yon Rhee et al.   TRENDS IN PLANT SCIENCE

QTL affecting fitness of hybrids between wild and cultivated soybeans in experimental fields

(2013) Yosuke Kuroda et al.   Ecology and Evolution

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

(2012) Chang Liu et al.   BMC GENOMICS

Recent Developments of Genomic Research in Soybean

(2012) Ching Chan et al.   Journal of Genetics and Genomics

Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis

(2012) O. Windram et al.   PLANT CELL

Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering

(2012) Z. Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

A Map-Based Cloning Strategy Employing a Residual Heterozygous Line Reveals that theGIGANTEAGene Is Involved in Soybean Maturity and Flowering

(2011) Satoshi Watanabe et al.   GENETICS

Solutions for a cultivated planet

(2011) Jonathan A. Foley et al.   NATURE

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes

(2011) Kevin L. Childs et al.   PLoS One

Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

(2011) Gabriel Krouk et al.   GENOME BIOLOGY

SoyTEdb: a comprehensive database of transposable elements in the soybean genome

(2010) Jianchang Du et al.   BMC GENOMICS

QTL analysis of net-like cracking in soybean seed coats

(2010) Maurice E. Oyoo et al.   BREEDING SCIENCE

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci

(2010) Ying-Hui Li et al.   NEW PHYTOLOGIST

Control of lateral organ development and flowering time by the Arabidopsis thaliana MADS-box Gene AGAMOUS-LIKE6

(2010) Sung C. Koo et al.   PLANT JOURNAL

Two Coordinately Regulated Homologs of FLOWERING LOCUS T Are Involved in the Control of Photoperiodic Flowering in Soybean

(2010) F. Kong et al.   PLANT PHYSIOLOGY

Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors

(2010) B. H. Le et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Maize Genome Structure Variation: Interplay between Retrotransposon Polymorphisms and Genic Recombination

(2008) H. K. Dooner et al.   PLANT CELL

QTL analysis of cleistogamy in soybean

(2008) Nisar A. Khan et al.   THEORETICAL AND APPLIED GENETICS

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY