Author

Sharon Wei

Cold Spring Harbor LaboratoryORCID 0000-0002-4585-3264Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:experimental assay· 5 Assay:whole-genome sequencing· 5 Research Focus:gene regulatory network inference· 3 Research Focus:genome assembly· 3 Organism:plant (other)· 3 Approach:statistical model· 3 Organism:zebrafish· 3 Research Focus:variant calling· 2

Frequent Co-Authors

Doreen WareiD· 6 shared Kapeel M. ChouguleiD· 5 shared Andrew J. OlsoniD· 4 shared Bo WangiD· 3 shared Kevin A. FengleriD· 3 shared R. Kelly DaweiD· 3 shared Víctor LlacaiD· 3 shared Amanda M. Gilbert· 2 shared

Activity by Year

2017-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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6 shared papersGenomics

Doreen WareORCID

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Author profile →

7 papers

Recent·Most cited

A pan-gene catalogue of Asian cultivated rice

Bruno Contreras‐Moreira, Eshan Sharma, Shradha Saraf, Guy Naamati, Parul Gupta, Justin L. Elser, Dmytro Chebotarov, Kapeel M. Chougule, Zhenyuan Lu, Sharon Wei, Andrew J. Olson, Ian Tsang, Disha Lodha, Yong Zhou, Zhichao Yu, , Andrew R. Jones

The paper develops a pan-gene catalogue for Asian cultivated rice by creating a reference panel of 16 cultivars and identifying core and cultivar-specific genes.

bioRxiv · Feb 17, 2025 · PreprintGenomics

HPC-based genome variant calling workflow (HPC-GVCW)

Yong Zhou, Nagarajan Kathiresan, Zhichao Yu, Luis F. Rivera, Manjula Thimma, Keerthana Manickam, Dmytro Chebotarov, Ramil Mauleon, Kapeel M. Chougule, Sharon Wei, Tingting Gao, Carl D. Green, Andrea Zuccolo, Doreen Ware, Jianwei Zhang, , Rod A. Wing

The paper presents an HPC-based workflow for genome variant calling using GATK, demonstrating SNP detection in four plant species and identifying novel SNPs in rice.

bioRxiv · Jun 25, 2023 · PreprintGenomics

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

Matthew B. Hufford, Arun Somwarpet Seetharam, Margaret Roth Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A. Ricci, Tingting Guo, Andrew J. Olson, Yinjie Qiu, Rafael Della Coletta, Silas B. Tittes, Asher I. Hudson, Alexandre P. Marand, Sharon Wei, , R. Kelly Dawe

A multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.

Science · Aug 5, 2021Peer-reviewedGenomics

Pan-genome Analysis in Sorghum Highlights the Extent of Genomic Variation and Sugarcane Aphid Resistance Genes

Bo Wang, Yinping Jiao, Kapeel M. Chougule, Andrew J. Olson, Jian Huang, Víctor Llaca, Kevin A. Fengler, Xuehong Wei, Liya Wang, Xiao‐Fei Wang, Michael Regulski, Jörg Drenkow, T Gingeras, Chad M. Hayes, John Scott Armstrong, , Doreen Ware

This study constructs high-quality sorghum genome assemblies and identifies structural variations and resistance genes associated with sugarcane aphid resistance.

bioRxiv · Jan 3, 2021 · PreprintGenomics

Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358

Shujun Ou, Jianing Liu, Kapeel M. Chougule, Arkarachai Fungtammasan, Arun Somwarpet Seetharam, Joshua C. Stein, Víctor Llaca, Nancy Manchanda, Amanda M. Gilbert, Sharon Wei, Chen-Shan Chin, David E. Hufnagel, Sarah Pedersen, Samantha J. Snodgrass, Kevin A. Fengler, , Doreen Ware

This study evaluates the impact of sequence depth and read length on long-read assembly quality for the maize genome, finding that lower depths and shorter reads result in fragmented assemblies.

Nature Communications · May 8, 2020Peer-reviewedGenomics

Effect of recombinant phycocyanin on photosynthetic system in Chlamydomonas reinhardtii

F. L. Zhang, Xiaomei Cong, Zhendong Wang, Yalin Guo, Lulu Hou, Rui Li, Menghui Shang, Xuehong Wei, Zhaxi Yangzong, Xiaoting Xu, Xiaonan Zang

Recombinant phycocyanin from Arthrospira platensis FACHB 314 expressed in Chlamydomonas reinhardtii enhances early growth and photosynthesis under low-light conditions but inhibits final biomass accumulation.

bioRxiv · Oct 21, 2019 · PreprintMolecular Biology

Improved maize reference genome with single molecule technologies

Yinping Jiao, Paul S. Peluso, Jinghua Shi, Tiffany Y Liang, Michelle C. Stitzer, Bo Wang, Michael S. Campbell, Joshua C. Stein, Xuehong Wei, Chen-Shan Chin, Katherine E. Guill, Michael Regulski, Sunita Kumari, Andrew J. Olson, Jonathan Isaiah Gent, , Doreen Ware

The paper improves the maize reference genome using single molecule technologies, resulting in longer contigs and better annotation of repetitive elements and genes.

Nature · Jun 1, 2017Peer-reviewedGenomics