High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan

Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics

(2020) Wen-Biao Jiao et al.   Nature Communications

All-in-one sequencing: an improved library preparation method for cost-effective and high-throughput next-generation sequencing

(2020) Sheng Zhao et al.   Plant Methods

A platinum standard pan-genome resource that represents the population structure of Asian rice

(2020) Yong Zhou et al.   Scientific Data

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication

(2020) Yixuan Kou et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Strigolactone Biosynthesis Gene Contributed to the Green Revolution in Rice

(2020) Yuexing Wang et al.   Molecular Plant

Quantitative regulation of Waxy expression by CRISPR/Cas9‐based promoter and 5'UTR‐intron editing improves grain quality in rice

(2020) Dongchang Zeng et al.   PLANT BIOTECHNOLOGY JOURNAL

A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice

(2020) Xianrong Xie et al.   Science China-Life Sciences

Sequencing of cultivated peanut, Arachis hypogaea, yields insights into genome evolution and oil improvement

(2019) Xiaoping Chen et al.   Molecular Plant

Structural variants in 3000 rice genomes

(2019) Roven Rommel Fuentes et al.   GENOME RESEARCH

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

iFLinkC: an iterative functional linker cloning strategy for the combinatorial assembly and recombination of linker peptides with functional domains

(2019) Alexander Gräwe et al.   NUCLEIC ACIDS RESEARCH

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

(2018) Todd P. Michael et al.   Nature Communications

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Exploring and exploiting pan-genomics for crop improvement

(2018) Yongfu Tao et al.   Molecular Plant

N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses

(2018) Qian Zhang et al.   Molecular Plant

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser 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

Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice

(2017) Penggen Duan et al.   Molecular Plant

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance

(2017) Yiwen Deng et al.   SCIENCE

Genomic structural variation-mediated allelic suppression causes hybrid male sterility in rice

(2017) Rongxin Shen et al.   Nature Communications

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

(2017) Huilong Du et al.   Nature Communications

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

(2017) Mircea Cretu Stancu et al.   Nature Communications

funRiceGenes dataset for comprehensive understanding and application of rice functional genes

(2017) Wen Yao et al.   GigaScience

Improvement of bacterial blight and brown planthopper resistance in an elite restorer line Huazhan of Oryza

(2016) Youlun Xiao et al.   FIELD CROPS RESEARCH

A pigeonpea gene confers resistance to Asian soybean rust in soybean

(2016) Cintia G Kawashima et al.   NATURE BIOTECHNOLOGY

Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing

(2016) Kamil Witek et al.   NATURE BIOTECHNOLOGY

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

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Copy number variation at the GL7 locus contributes to grain size diversity in rice

(2015) Yuexing Wang et al.   NATURE GENETICS

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Towards plant pangenomics

(2015) Agnieszka A. Golicz et al.   PLANT BIOTECHNOLOGY JOURNAL

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

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

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

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Resequencing rice genomes: an emerging new era of rice genomics

(2013) Xuehui Huang et al.   TRENDS IN GENETICS

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

(2012) Pablo Cingolani et al.   FLY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Acireductone Dioxygenase 1 (ARD1) Is an Effector of the Heterotrimeric G Protein β Subunit inArabidopsis

(2011) Erin J. Friedman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of the blast resistance gene Pit in rice cultivars using functional markers

(2010) K. Hayashi et al.   THEORETICAL AND APPLIED GENETICS

Fine genetic mapping and physical delimitation of the lesion mimic gene spotted leaf 5 (spl5) in rice (Oryza sativa L.)

(2009) Xifeng Chen et al.   MOLECULAR BREEDING

Identification and characterization ofBph14, a gene conferring resistance to brown planthopper in rice

(2009) Bo Du et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

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

(2008) Brian J Haas et al.   GENOME BIOLOGY