Kai Ye

ORCID

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 20

Top Venues

Genomics, proteomics & bioinformatics

Nature communications

Science (New York, N.Y.)

Journal of cheminformatics

Xi'an Jiaotong University

Leiden University (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Xi'an Jiaotong University

China

professor

Washington University in St. Louis School of Medicine

United States

assistant professor

Education History

Leiden University Jan 01 2004 - Dec 18 2008

Netherlands

PHD

Wuhan University Sep 01 1995 - Jun 30 2003

China

MSC

Publications

Jiang Hu, Zhuo Wang, Fan Yang, Shan-Lin Liu, Kai Ye, De-Peng Wang
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads. Genomics, proteomics & bioinformatics 22 (1) (2024)
Jiang Hu, Zhuo Wang, Fan Yang, Shan-Lin Liu, Kai Ye, De-Peng Wang
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads. Genomics, proteomics & bioinformatics 22 (1) (2024)
Songbo Wang, Jiadong Lin, Peng Jia, Tun Xu, Xiujuan Li, Yuezhuangnan Liu, Dan Xu, Stephen J Bush, Deyu Meng, Kai Ye
De novo and somatic structural variant discovery with SVision-pro. Nature biotechnology (2024)
Xiaofei Yang, Gaoyang Zheng, Peng Jia, Songbo Wang, Kai Ye
Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach. Genomics, proteomics & bioinformatics 22 (1) (2024)
Xiaofei Yang, Gaoyang Zheng, Peng Jia, Songbo Wang, Kai Ye
Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach. Genomics, proteomics & bioinformatics 22 (1) (2024)
Peng Jia, Lianhua Dong, Xiaofei Yang, Bo Wang, Stephen J Bush, Tingjie Wang, Jiadong Lin, Songbo Wang, Xixi Zhao, Tun Xu, Yizhuo Che, Ningxin Dang, Luyao Ren, Yujing Zhang, Xia Wang, Fan Liang, Yang Wang, Jue Ruan, Han Xia, Yuanting Zheng, Leming Shi, Yi Lv, Jing Wang, Kai Ye
Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet. Genome biology 24 (1) (2023)
Xiaofei Yang, Shenghan Gao, Tun Xu, Bo Wang, Yanyan Jia, Kai Ye
Reply to "Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes". Nature communications 14 (1) (2023)
Yang Gao, Xiaofei Yang, Hao Chen, Xinjiang Tan, Zhaoqing Yang, Lian Deng, Baonan Wang, Shuang Kong, Songyang Li, Yuhang Cui, Chang Lei, Yimin Wang, Yuwen Pan, Sen Ma, Hao Sun, Xiaohan Zhao, Yingbing Shi, Ziyi Yang, Dongdong Wu, Shaoyuan Wu, Xing-Ming Zhao, Binyin Shi, Li Jin, Zhi-Bin Hu, null null, Yan Lu, Jiayou Chu, Kai Ye, Shuhua Xu
A pangenome reference of 36 Chinese populations. Nature (2023)
Yizhuo Che, Xiaofei Yang, Peng Jia, Tingjie Wang, Dan Xu, Tianxue Guo, Kai Ye
D<sup>2</sup> Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 9 (30) (2022)
Tun Xu, Xiaofei Yang, Yanyan Jia, Zihang Li, Guangbo Tang, Xiujuan Li, Bo Wang, Tingjie Wang, Jiadong Lin, Li Guo, Kai Ye
A global survey of the transcriptome of the opium poppy (Papaver somniferum) based on single-molecule long-read isoform sequencing. The Plant journal : for cell and molecular biology 110 (2) (2022)
Tingjie Wang, Ningxin Dang, Guangbo Tang, Zihang Li, Xiujuan Li, Bingyin Shi, Zhong Xu, Lei Li, Xiaofei Yang, Chuanrui Xu, Kai Ye
Integrating bulk and single-cell RNA sequencing reveals cellular heterogeneity and immune infiltration in hepatocellular carcinoma. Molecular oncology 16 (11) (2022)
Jiadong Lin, Songbo Wang, Peter A Audano, Deyu Meng, Jacob I Flores, Walter A Kosters, Xiaofei Yang, Peng Jia, Tobias Marschall, Christine R Beck, Kai Ye
SVision: a deep learning approach to resolve complex structural variants. Nature methods 19 (10) (2022)
Shenghan Gao, Xiaofei Yang, Jianyong Sun, Xixi Zhao, Bo Wang, Kai Ye
IAGS: Inferring Ancestor Genome Structure under a Wide Range of Evolutionary Scenarios. Molecular biology and evolution 39 (3) (2022)
Peter Ebert, Peter A Audano, Qihui Zhu, Bernardo Rodriguez-Martin, David Porubsky, Marc Jan Bonder, Arvis Sulovari, Jana Ebler, Weichen Zhou, Rebecca Serra Mari, Feyza Yilmaz, Xuefang Zhao, PingHsun Hsieh, Joyce Lee, Sushant Kumar, Jiadong Lin, Tobias Rausch, Yu Chen, Jingwen Ren, Martin Santamarina, Wolfram Höps, Hufsah Ashraf, Nelson T Chuang, Xiaofei Yang, Katherine M Munson, Alexandra P Lewis, Susan Fairley, Luke J Tallon, Wayne E Clarke, Anna O Basile, Marta Byrska-Bishop, André Corvelo, Uday S Evani, Tsung-Yu Lu, Mark J P Chaisson, Junjie Chen, Chong Li, Harrison Brand, Aaron M Wenger, Maryam Ghareghani, William T Harvey, Benjamin Raeder, Patrick Hasenfeld, Allison A Regier, Haley J Abel, Ira M Hall, Paul Flicek, Oliver Stegle, Mark B Gerstein, Jose M C Tubio, Zepeng Mu, Yang I Li, Xinghua Shi, Alex R Hastie, Kai Ye, Zechen Chong, Ashley D Sanders, Michael C Zody, Michael E Talkowski, Ryan E Mills, Scott E Devine, Charles Lee, Jan O Korbel, Tobias Marschall, Evan E Eichler
Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science (New York, N.Y.) 372 (6537) (2021)
Xiaofei Yang, Shenghan Gao, Li Guo, Bo Wang, Yanyan Jia, Jian Zhou, Yizhuo Che, Peng Jia, Jiadong Lin, Tun Xu, Jianyong Sun, Kai Ye
Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. Nature communications 12 (1) (2021)
Xuhan Liu, Kai Ye, Herman W T van Vlijmen, Michael T M Emmerich, Adriaan P IJzerman, Gerard van Westen
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology. Journal of cheminformatics 13 (1) (2021)
Yongyong Kang, Xinchao Ji, Li Guo, Han Xia, Xiaofei Yang, Zhen Xie, Xiaodan Shi, Rui Wu, Dongyun Feng, Chen Wang, Min Chen, Wenliang Zhang, Hong Wei, Yuanlin Guan, Kai Ye, Gang Zhao
Cerebrospinal Fluid from Healthy Pregnant Women Does Not Harbor a Detectable Microbial Community. Microbiology spectrum 9 (3) (2021)
Like Fokkens, Li Guo, Susanne Dora, Bo Wang, Kai Ye, Clara Sánchez-Rodríguez, Daniel Croll
A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem. G3 (Bethesda, Md.) 10 (10) (2020)
Xuhan Liu, Kai Ye, Herman W T van Vlijmen, Adriaan P IJzerman, Gerard van Westen
An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor. Journal of cheminformatics 11 (1) (2019)
Li Guo, Thilo Winzer, Xiaofei Yang, Yi Li, Zemin Ning, Zhesi He, Roxana Teodor, Ying Lu, Tim A Bowser, Ian A Graham, Kai Ye
The opium poppy genome and morphinan production. Science (New York, N.Y.) 362 (6412) (2018)
Charles Lu, Mingchao Xie, Michael C Wendl, Jiayin Wang, Michael D McLellan, Mark D M Leiserson, Kuan-Lin Huang, Matthew A Wyczalkowski, Reyka G Jayasinghe, Tapahsama Banerjee, Jie Ning, Piyush Tripathi, Qunyuan Zhang, Beifang Niu, Kai Ye, Heather K Schmidt, Robert S Fulton, Joshua F McMichael, Prag Batra, Cyriac Kandoth, Maheetha Bharadwaj, Daniel C Koboldt, Christopher A Miller, Krishna L Kanchi, James M Eldred, David E Larson, John S Welch, Ming You, Bradley A Ozenberger, Ramaswamy Govindan, Matthew J Walter, Matthew J Ellis, Elaine R Mardis, Timothy A Graubert, John F Dipersio, Timothy J Ley, Richard K Wilson, Paul J Goodfellow, Benjamin J Raphael, Feng Chen, Kimberly J Johnson, Jeffrey D Parvin, Li Ding
Patterns and functional implications of rare germline variants across 12 cancer types. Nature communications 6 (2015)

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Publication Activity (10 Years)

Top Topics

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Kai Ye