Yunping Zhu

35 papers B 2Journal 28Unranked 5
YearRankTypeTitle / Venue / Authors
2025 J jnl
MulNet: a scalable framework for reconstructing intra- and intercellular signaling networks from bulk and single-cell RNA-seq data.
Briefings Bioinform.
Mingfei Han, Xiaoqing Chen, Xiao Li, Jie Ma, Tao Chen, Chunyuan Yang, Juan Wang, Yingxing Li, Wenting Guo, Yunping Zhu
2025 J jnl
Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence.
CoRR
Yingying Sun, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Samuel H. Payne, Wout Bittremieux, Markus Ralser, Chen Li, Yi Chen, Zhen Dong, Yasset Pérez-Riverol, Asif Khan, Chris Sander, Ruedi Aebersold, Juan Antonio Vizcaíno, Jonathan R. Krieger, Jianhua Yao, Han Wen, Linfeng Zhang, Yunping Zhu, Yue Xuan, Benjamin Boyang Sun, Liang Qiao, Henning Hermjakob, Haixu Tang, Huanhuan Gao, Yamin Deng, Qing Zhong, Cheng Chang, Nuno Bandeira, Ming Li, Weinan E, Siqi Sun, Yuedong Yang, Gilbert S. Omenn, Yue Zhang, Ping Xu, Yan Fu, Xiaowen Liu, Christopher M. Overall, Yu Wang, Eric W. Deutsch, Luonan Chen, Jürgen Cox, Vadim Demichev, Fuchu He, Jiaxing Huang, Huilin Jin, Chao Liu, Nan Li, Zhongzhi Luan, Jiangning Song, Kaicheng Yu, Wanggen Wan, Tai Wang, Kang Zhang, Le Zhang, Peter A. Bell, Matthias Mann, Bing Zhang, Tiannan Guo
2025 J jnl
π-PhenoDrug: A Comprehensive Deep Learning-Based Pipeline for Phenotypic Drug Screening in High-Content Analysis.
Adv. Intell. Syst.
Xiao Li, Qinxue Ouyang, Mingfei Han, Xiaoqing Liu, Fuchu He, Yunping Zhu, Ling Leng, Jie Ma
2024 — conf
Fetal Cardiac Structure Detection Using Multi-task Learning.
ICIC (LNBI 2)
Jie He, Lei Yang, Yunping Zhu, Donglian Li, Zhixing Ding, Yuhuan Lu, Bocheng Liang, Shengli Li
2024 J jnl
Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data.
Bioinform.
Xiaofan Liu, Yuhuan Tao, Zilin Cai, Pengfei Bao, Hongli Ma, Kexing Li, Mengtao Li, Yunping Zhu, Zhi John Lu
2023 J jnl
COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods.
Bioinform.
Xiaojing Wu, Mingfei Han, Xinyu Song, Song He, Xiaochen Bo, Yunping Zhu
2023 J jnl
The ProteomeXchange consortium at 10 years: 2023 update.
Nucleic Acids Res.
Eric W. Deutsch, Nuno Bandeira, Yasset Pérez-Riverol, Vagisha Sharma, Jeremy Carver, Luis Mendoza, Deepti Jaiswal Kundu, Shengbo Wang, Chakradhar Bandla, Selvakumar Kamatchinathan, Suresh Hewapathirana, Benjamin S. Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Brendan MacLean, Michael J. MacCoss, Yunping Zhu, Yasushi Ishihama, Juan Antonio Vizcaíno
2022 J jnl
iProX in 2021: connecting proteomics data sharing with big data.
Nucleic Acids Res.
Tao Chen, Jie Ma, Yi Liu, Zhiguang Chen, Nong Xiao, Yutong Lu, Yinjin Fu, Chunyuan Yang, Mansheng Li, Songfeng Wu, Xue Wang, Dongsheng Li, Fuchu He, Henning Hermjakob, Yunping Zhu
2020 J jnl
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.
Nucleic Acids Res.
Eric W. Deutsch, Nuno Bandeira, Vagisha Sharma, Yasset Pérez-Riverol, Jeremy Carver, Deepti Jaiswal Kundu, David García-Seisdedos, Andrew F. Jarnuczak, Suresh Hewapathirana, Benjamin S. Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Henning Hermjakob, Brendan MacLean, Michael J. MacCoss, Yunping Zhu, Yasushi Ishihama, Juan Antonio Vizcaíno
2019 — conf
A Complete CPU-FPGA Architecture for Protein Identification with Tandem Mass Spectrometry.
FPT
Moucheng Yang, Tao Chen, Xuegong Zhou, Liang Zhao, Yunping Zhu, Lingli Wang
2019 J jnl
KeggExp: a web server for visual integration of KEGG pathways and expression profile data.
Bioinform.
Xian Liu, Mingfei Han, Chen Zhao, Cheng Chang, Yunping Zhu, Changhui Ge, Ronghua Yin, Yiqun Zhan, Changyan Li, Miao Yu, Fuchu He, Xiaoming Yang
2019 J jnl
PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis.
Bioinform.
Cheng Chang, Mansheng Li, Chaoping Guo, Yuqing Ding, Kaikun Xu, Mingfei Han, Fuchu He, Yunping Zhu
2019 J jnl
SW-Tandem: a highly efficient tool for large-scale peptide identification with parallel spectrum dot product on Sunway TaihuLight.
Bioinform.
Chuang Li, Kenli Li, Tao Chen, Yunping Zhu, Qiang He
2019 J jnl
iProX: an integrated proteome resource.
Nucleic Acids Res.
Jie Ma, Tao Chen, Songfeng Wu, Chunyuan Yang, Mingze Bai, Kunxian Shu, Kenli Li, Guoqing Zhang, Zhong Jin, Fuchu He, Henning Hermjakob, Yunping Zhu
2018 J jnl
PANDA-view: an easy-to-use tool for statistical analysis and visualization of quantitative proteomics data.
Bioinform.
Cheng Chang, Kaikun Xu, Chaoping Guo, Jinxia Wang, Qi Yan, Jian Zhang, Fuchu He, Yunping Zhu
2017 J jnl
LiverWiki: a wiki-based database for human liver.
BMC Bioinform.
Tao Chen, Mansheng Li, Qiang He, Lei Zou, Youhuan Li, Cheng Chang, Dongyan Zhao, Yunping Zhu
2017 J jnl
MRUniNovo: an efficient tool for de novo peptide sequencing utilizing the hadoop distributed computing framework.
Bioinform.
Chuang Li, Tao Chen, Qiang He, Yunping Zhu, Kenli Li
2015 J jnl
Kinematic Analysis of a Partially Decoupled 3-DOF Parallel Wrist.
J. Robotics
Fan Zhang, Yunping Zhu, Tomonari Furukawa, Wanqing Song
2015 J jnl
Web Resources for Mass Spectrometry-based Proteomics.
Genom. Proteom. Bioinform.
Tao Chen, Jie Zhao, Jie Ma, Yunping Zhu
2014 J jnl
SILVER: an efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods.
Bioinform.
Cheng Chang, Jiyang Zhang, Mingfei Han, Jie Ma, Wei Zhang, Songfeng Wu, Kehui Liu, Hongwei Xie, Fuchu He, Yunping Zhu
2013 J jnl
Reconstruction of Signaling Network from Protein Interactions Based on Function Annotations.
IEEE ACM Trans. Comput. Biol. Bioinform.
Wei Liu, Dong Li, Yunping Zhu, Hongwei Xie, Fuchu He
2012 J jnl
Improving X!Tandem on Peptide Identification from Mass Spectrometry by Self-Boosted Percolator.
IEEE ACM Trans. Comput. Biol. Bioinform.
Pengyi Yang, Jie Ma, Penghao Wang, Yunping Zhu, Bing Bing Zhou, Jean Yee Hwa Yang
2012 — conf
Using NMFAS to identify key biological pathways associated with human diseases.
ISB
Hao Guo, Yunping Zhu, Dong Li, Fuchu He, Qijun Liu
2011 J jnl
Modular analysis of the probabilistic genetic interaction network.
Bioinform.
Lin Hou, Lin Wang, Minping Qian, Dong Li, Chao Tang, Yunping Zhu, Minghua Deng, Fangting Li
2010 J jnl
A novel parametric approach to mine gene regulatory relationship from microarray datasets.
BMC Bioinform.
Wanlin Liu, Dong Li, Qijun Liu, Yunping Zhu, Fuchu He
2010 J jnl
Computational identification of rare codons of
BMC Bioinform.
Xianming Wu, Songfeng Wu, Dong Li, Jiyang Zhang, Lin Hou, Jie Ma, Wanlin Liu, Daming Ren, Yunping Zhu, Fuchu He
2009 — conf
A New Recursive Approach for Reconstructing Metabolic Networks from KEGG.
FCST
Tingting Zhou, Samuel K. F. Yung, Zhenghua Wang, Yunping Zhu
2009 — conf
A Semiautomatic Method to Achieve Independent and Intact Gene Ontology Slim (InitGO) and its Cytoscape Plugin Implementation.
BMEI
Qijun Liu, Zhenghua Wang, Hanchang Sun, Hao Guo, Wanlin Liu, Yunping Zhu
2008 J jnl
A nonparametric model for quality control of database search results in shotgun proteomics.
BMC Bioinform.
Jiyang Zhang, Jianqi Li, Xin Liu, Hongwei Xie, Yunping Zhu, Fuchu He
2006 J jnl
A new technique for selecting features from protein sequences.
Int. J. Pattern Recognit. Artif. Intell.
Xing-Ming Zhao, Ji-Xiang Du, Hong-Qiang Wang, Yunping Zhu, Yixue Li
2006 J jnl
Tumor classification based on independent component analysis.
Int. J. Pattern Recognit. Artif. Intell.
Chun-Hou Zheng, Yan Chen, Xiu-Xia Li, Yi-Xue Li, Yunping Zhu
2005 J jnl
Improving protein secondary structure prediction by using the residue conformational classes.
Pattern Recognit. Lett.
Guang-Zheng Zhang, De-Shuang Huang, Yunping Zhu, Yi-Xue Li
2005 B conf
Predicting protein-protein interactions based on protein-domain relationships.
IJCNN
Bing Wang, De-Shuang Huang, Peng Chen, Yunping Zhu, Yixue Li
2005 B conf
Prediction of contact map integrated PNN with conformational energy.
IJCNN
Peng Chen, De-Shuang Huang, Bing Wang, Yunping Zhu, Yixue Li
1999 J jnl
CT reconstruction by using the MLS-ART technique and the KCD imaging system.
IEEE Trans. Medical Imaging
Huaiqun Guan, M. Waleed Gaber, Frank A. DiBianca, Yunping Zhu