Yi Zheng

Plant Genomics · Bioinformatics · Horticultural Crops

Yazhouwan National Laboratory
崖州湾国家实验室

Professor, Beijing University of Agriculture (2020–2024)

Positions

2025 – present

Researcher / Professor

Yazhouwan National Laboratory, Sanya, China

2020 – 2024

Professor

College of Plant Science and Technology, Beijing University of Agriculture

2013 – 2020

Postdoctoral Researcher & Consultant

Boyce Thompson Institute, Cornell University, USA

2005 – 2012

Ph.D., Ornamental Horticulture

China Agricultural University

2001 – 2005

B.S., Landscape Architecture

College of Landscape Architecture, Beijing University of Agriculture

Research Areas

Horticultural Crop Genomics

Genome assembly, annotation, and comparative genomics of horticultural crops including tomato, watermelon, melon, cucumber, spinach, rose, kiwifruit, apple, and chestnut.

Multi-omics Data Integration

Integration of genomics, transcriptomics, epigenomics, and metabolomics data to understand gene regulatory networks in horticultural crops and to power genome-based breeding.

Bioinformatics Tools & Databases

Development of widely-used bioinformatics tools (iTAK, VirusDetect, iAssembler) and crop-specific genomics databases (CuGenDB, SpinachBase, KGD, HSE, and more).

Selected Contributions

89 publications, 6,300+ citations, h-index 36

01
iTAK — genome-wide prediction of plant transcription factors, transcriptional regulators, and protein kinases. Molecular Plant, 2016 · 1,114 citations
02
PGED — Plant Genome Editing Database, a centralized resource for information about genome-edited plant mutants. Molecular Plant, 2019
03
Tomato genome — the genome sequence of tomato provides insights into fleshy fruit evolution. Nature, 2012 · 3,677 citations
04
Watermelon genome — draft genome and resequencing of 20 diverse accessions. Nature Genetics, 2013 · 971 citations
05
CuGenDB — the cucurbit genomics database and its updated version CuGenDBv2. Nucleic Acids Research, 2019 · 220 citations
06
Spinach genome & SpinachBase — draft genome and transcriptome diversity of 120 accessions, plus a central portal for spinach genomics. Nature Communications, 2017 · Database, 2019
07
iAssembler — a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics, 2011 · 144 citations
08
VirusDetect — automated pipeline for virus discovery using deep sequencing of small RNAs. Virology, 2017 · 265 citations
09
Apple (Malus) genomes — haplotype-resolved assembly of 'Red Fuji' and chromosomal-level assemblies of two crabapple cultivars Flame and Royalty, plus dwarfing interstock 'SH6'. Scientific Data, 2024
10
HortGenome Search Engine — universal genomic search covering 500+ horticultural crops. Horticulture Research, 2024