LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

Shujun Ou, Ning Jiang

PLANT PHYSIOLOGY

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

Shujun Ou, Weija Su, Yi Liao, +10

Genome biology

Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing

Michael Alonge, Ludivine Lebeigle, Melanie Kirsche, +7

Genome biology

Plant GeneticsGeneticsNew Rapid-cycling GenotypeMolecular BiologyNew Tomato System +21

Assessing genome assembly quality using the LTR Assembly Index (LAI)

Shujun Ou, Jinfeng Chen, Ning Jiang

Nucleic Acids Research

GeneticsMolecular BiologyGenomicsPlant GenomeMolecular Ecology +16

Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies

Bin Hu, Wei Wang, Shujun Ou, +17

Nature Genetics

BiologyRice SubspeciesBotanyNatural SciencesGenetics +6

Origin and evolution of the octoploid strawberry genome

Patrick P. Edger, Thomas J. Poorten, Robert VanBuren, +26

Nature Genetics

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Matthew B. Hufford, Arun S. Seetharam, Margaret Woodhouse, +43

Science

Structural VariationGeneticsDna MethylationGenomicsPlant Genomics +20

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

Peng Qin, Hongwei Lu, Huilong Du, +26

Cell

BiologyPlant GeneticsGeneticsPan-genome AnalysisGenomic Variations +5

OsNAP connects abscisic acid and leaf senescence by fine-tuning abscisic acid biosynthesis and directly targeting senescence-associated genes in rice

Chengzhen Liang, Yiqin Wang, Yana Zhu, +8

Proceedings of the National Academy of Sciences

Genomic basis of geographical adaptation to soil nitrogen in rice

Yongqiang Liu, Hongru Wang, Zhimin Jiang, +15

Nature

Plant-soil InteractionPrecision AgricultureEngineeringBotanyGeographical Adaptation +7