Works by Zhang, Ziding

Results: 79

SPAR: a random forest-based predictor for self-interacting proteins with fine-grained domain information.

Published in:

Amino Acids, 2016, v. 48, n. 7, p. 1655, doi. 10.1007/s00726-016-2226-z

By:

Liu, Xuhan;
Yang, Shiping;
Li, Chen;
Zhang, Ziding;
Song, Jiangning

Publication type:

Article

Prediction of protein-protein interactions between Ralstonia solanacearum and Arabidopsis thaliana.

Published in:

Amino Acids, 2012, v. 42, n. 6, p. 2363, doi. 10.1007/s00726-011-0978-z

By:

Li, Zhi-Gang;
He, Fei;
Zhang, Ziding;
Peng, You-Liang

Publication type:

Article

MDP25, A Novel Calcium Regulatory Protein, Mediates Hypocotyl Cell Elongation by Destabilizing Cortical Microtubules in Arabidopsis.

Published in:

Plant Cell, 2011, v. 23, n. 12, p. 4411, doi. 10.1105/tpc.111.092684

By:

Li, Jiejie;
Wang, Xianling;
Qin, Tao;
Zhang, Yan;
Liu, Xiaomin;
Sun, Jingbo;
Zhou, Yuan;
Zhu, Lei;
Zhang, Ziding;
Yuan, Ming;
Mao, Tonglin

Publication type:

Article

Prediction and analysis of human-herpes simplex virus type 1 protein-protein interactions by integrating multiple methods.

Published in:

Quantitative Biology, 2020, v. 8, n. 4, p. 312, doi. 10.1007/s40484-020-0222-5

By:

Lian, Xianyi;
Yang, Xiaodi;
Shao, Jiqi;
Hou, Fujun;
Yang, Shiping;
Pan, Dongli;
Zhang, Ziding

Publication type:

Article

Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq.

Published in:

Frontiers in Plant Science, 2021, v. 12, p. 1, doi. 10.3389/fpls.2021.723636

By:

Li, Zhigang;
Yang, Jun;
Peng, Junbo;
Cheng, Zhihua;
Liu, Xinsen;
Zhang, Ziding;
Bhadauria, Vijai;
Zhao, Wensheng;
Peng, You-Liang

Publication type:

Article

Characterization of Calcium-Dependent Protein Kinase 2A, a Potential Drug Target Against Cryptosporidiosis.

Published in:

Frontiers in Microbiology, 2022, v. 13, p. 1, doi. 10.3389/fmicb.2022.883674

By:

Shu, Fanfan;
Li, Yu;
Chu, Wenlun;
Chen, Xuehua;
Zhang, Ziding;
Guo, Yaqiong;
Feng, Yaoyu;
Xiao, Lihua;
Li, Na

Publication type:

Article

Deep Learning-Powered Prediction of Human-Virus Protein-Protein Interactions.

Published in:

Frontiers in Microbiology, 2022, v. 13, p. 1, doi. 10.3389/fmicb.2022.842976

By:

Yang, Xiaodi;
Yang, Shiping;
Ren, Panyu;
Wuchty, Stefan;
Zhang, Ziding

Publication type:

Article

Prp19‐associated splicing factor Cwf15 regulates fungal virulence and development in the rice blast fungus.

Published in:

Environmental Microbiology, 2021, v. 23, n. 10, p. 5901, doi. 10.1111/1462-2920.15616

By:

Liu, Xinsen;
Pan, Xiao;
Chen, Deng;
Yin, Changfa;
Peng, Junbo;
Shi, Wei;
Qi, Linlu;
Wang, Ruijin;
Zhao, Wensheng;
Zhang, Ziding;
Yang, Jun;
Peng, You‐Liang

Publication type:

Article

Deep learning‐assisted prediction of protein–protein interactions in Arabidopsis thaliana.

Published in:

Plant Journal, 2023, v. 114, n. 4, p. 984, doi. 10.1111/tpj.16188

By:

Zheng, Jingyan;
Yang, Xiaodi;
Huang, Yan;
Yang, Shiping;
Wuchty, Stefan;
Zhang, Ziding

Publication type:

Article

The hybrid protein interactome contributes to rice heterosis as epistatic effects.

Published in:

Plant Journal, 2020, v. 102, n. 1, p. 116, doi. 10.1111/tpj.14616

By:

Li, Hong;
Jiang, Shuqin;
Li, Chen;
Liu, Lei;
Lin, Zechuan;
He, Hang;
Deng, Xing‐Wang;
Zhang, Ziding;
Wang, Xiangfeng

Publication type:

Article

Pre-trained protein language model sheds new light on the prediction of Arabidopsis protein–protein interactions.

Published in:

Plant Methods, 2023, v. 19, n. 1, p. 1, doi. 10.1186/s13007-023-01119-6

By:

Zhou, Kewei;
Lei, Chenping;
Zheng, Jingyan;
Huang, Yan;
Zhang, Ziding

Publication type:

Article

Genetic analysis and morphological identification of pilus-like structures in members of the genus Bifidobacterium.

Published in:

Microbial Cell Factories, 2011, v. 10, n. Suppl 1, p. 1, doi. 10.1186/1475-2859-10-S1-S16

By:

Foroni, Elena;
Serafini, Fausta;
Amidani, Davide;
Turroni, Francesca;
Fei He;
Bottacini, Francesca;
Motherway, Mary O'Connell;
Viappiani, Alice;
Ziding Zhang;
Rivetti, Claudio;
van Sinderen, Douwe;
Ventura, Marco

Publication type:

Article

Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-26272-1

By:

Zhu, Feng;
Yin, Zhong-Tao;
Wang, Zheng;
Smith, Jacqueline;
Zhang, Fan;
Martin, Fergal;
Ogeh, Denye;
Hincke, Maxwell;
Lin, Fang-Bing;
Burt, David W.;
Zhou, Zheng-Kui;
Hou, Shui-Sheng;
Zhao, Qiang-Sen;
Li, Xiao-Qin;
Ding, Si-Ran;
Li, Guan-Sheng;
Yang, Fang-Xi;
Hao, Jing-Pin;
Zhang, Ziding;
Lu, Li-Zhi

Publication type:

Article

An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP).

Published in:

SCIENCE CHINA Life Sciences, 2025, v. 68, n. 6, p. 1541, doi. 10.1007/s11427-024-2894-2

By:

Yuan, Junxia;
Yang, Jinlu;
Sun, Yue;
Meng, Yaqi;
He, Ziwei;
Zhang, Wende;
Dang, Lei;
Song, Yan;
Xu, Kanyan;
Lv, Na;
Zhang, Ziding;
Guo, Pei;
Yin, Hong;
Shi, Wenyu

Publication type:

Article

Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs.

Published in:

PLoS ONE, 2015, v. 10, n. 6, p. 1, doi. 10.1371/journal.pone.0129635

By:

Hasan, Md. Mehedi;
Zhou, Yuan;
Lu, Xiaotian;
Li, Jinyan;
Song, Jiangning;
Zhang, Ziding

Publication type:

Article

Operating Mechanism and Molecular Dynamics of Pheromone-Binding Protein ASP1 as Influenced by pH.

Published in:

PLoS ONE, 2014, v. 9, n. 10, p. 1, doi. 10.1371/journal.pone.0110565

By:

Han, Lei;
Zhang, Yong-Jun;
Zhang, Long;
Cui, Xu;
Yu, Jinpu;
Zhang, Ziding;
Liu, Ming S.

Publication type:

Article

PredPPCrys: Accurate Prediction of Sequence Cloning, Protein Production, Purification and Crystallization Propensity from Protein Sequences Using Multi-Step Heterogeneous Feature Fusion and Selection.

Published in:

PLoS ONE, 2014, v. 9, n. 8, p. 1, doi. 10.1371/journal.pone.0105902

By:

Wang, Huilin;
Wang, Mingjun;
Tan, Hao;
Li, Yuan;
Zhang, Ziding;
Song, Jiangning

Publication type:

Article

Structural Propensities of Human Ubiquitination Sites: Accessibility, Centrality and Local Conformation.

Published in:

PLoS ONE, 2013, v. 8, n. 12, p. 1, doi. 10.1371/journal.pone.0083167

By:

Zhou, Yuan;
Liu, Sixue;
Song, Jiangning;
Zhang, Ziding

Publication type:

Article

Using Weakly Conserved Motifs Hidden in Secretion Signals to Identify Type-III Effectors from Bacterial Pathogen Genomes.

Published in:

PLoS ONE, 2013, v. 8, n. 2, p. 1, doi. 10.1371/journal.pone.0056632

By:

Dong, Xiaobao;
Zhang, Yong-Jun;
Zhang, Ziding

Publication type:

Article

An Integrative Computational Framework Based on a Two-Step Random Forest Algorithm Improves Prediction of Zinc-Binding Sites in Proteins.

Published in:

PLoS ONE, 2012, v. 7, n. 11, p. 1, doi. 10.1371/journal.pone.0049716

By:

Cheng Zheng;
Mingjun Wang;
Kazuhiro Takemoto;
Tatsuya Akutsu;
Ziding Zhang;
Jiangning Song

Publication type:

Article

Identification of Catalytic Residues Using a Novel Feature that Integrates the Microenvironment and Geometrical Location Properties of Residues.

Published in:

PLoS ONE, 2012, v. 7, n. 7, p. 1, doi. 10.1371/journal.pone.0041370

By:

Lei Han;
Yong-Jun Zhang;
Jiangning Song;
Ming S. Liu;
Ziding Zhang

Publication type:

Article

Predicting Residue-Residue Contacts and Helix-Helix Interactions in Transmembrane Proteins Using an Integrative Feature-Based Random Forest Approach.

Published in:

PLoS ONE, 2011, v. 6, n. 10, p. 1, doi. 10.1371/journal.pone.0026767

By:

Xiao-Feng Wang;
Zhen Chen;
Chuan Wang;
Ren-Xiang Yan;
Ziding Zhang;
Jiangning Song

Publication type:

Article

Prediction of Ubiquitination Sites by Using the Composition of &kgr;-Spaced Amino Acid Pairs.

Published in:

PLoS ONE, 2011, v. 6, n. 7, p. 1, doi. 10.1371/journal.pone.0022930

By:

Zhen Chen;
Yong-Zi Chen;
Xiao-Feng Wang;
Chuan Wang;
Ren-Xiang Yan;
Ziding Zhang

Publication type:

Article

Phosphatidic acid–regulated SOS2 controls sodium and potassium homeostasis in Arabidopsis under salt stress.

Published in:

EMBO Journal, 2023, v. 42, n. 8, p. 1, doi. 10.15252/embj.2022112401

By:

Li, Jianfang;
Shen, Like;
Han, Xiuli;
He, Gefeng;
Fan, Wenxia;
Li, Yu;
Yang, Shiping;
Zhang, Ziding;
Yang, Yongqing;
Jin, Weiwei;
Wang, Yi;
Zhang, Wenhua;
Guo, Yan

Publication type:

Article

The AtMAP65-1 Cross-Bridge Between Microtubules is Formed by One Dimer.

Published in:

Plant & Cell Physiology, 2007, v. 48, n. 6, p. 866, doi. 10.1093/pcp/pcm059

By:

Hua Li;
Tonglin Mao;
Ziding Zhang;
Ming Yuan

Publication type:

Article

Characterization of Three Calcium-Dependent Protein Kinases of Cryptosporidium parvum.

Published in:

Frontiers in Microbiology, 2021, v. 11, p. N.PAG, doi. 10.3389/fmicb.2020.622203

By:

Zhang, Qiang;
Shao, Qian;
Guo, Yaqiong;
Li, Na;
Li, Yu;
Su, Jiayuan;
Xu, Rui;
Zhang, Ziding;
Xiao, Lihua;
Feng, Yaoyu

Publication type:

Article

Rhizobial migration toward roots mediated by FadL-ExoFQP modulation of extracellular long-chain AHLs.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2023, v. 17, n. 3, p. 417, doi. 10.1038/s41396-023-01357-5

By:

Ji, Yuan-Yuan;
Zhang, Biliang;
Zhang, Pan;
Chen, Liu-Chi;
Si, You-Wei;
Wan, Xi-Yao;
Li, Can;
Wang, Ren-He;
Tian, Yu;
Zhang, Ziding;
Tian, Chang-Fu

Publication type:

Article

The zinc-finger bearing xenogeneic silencer MucR in α-proteobacteria balances adaptation and regulatory integrity.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2022, v. 16, n. 3, p. 738, doi. 10.1038/s41396-021-01118-2

By:

Jiao, Jian;
Zhang, Biliang;
Li, Meng-Lin;
Zhang, Ziding;
Tian, Chang-Fu

Publication type:

Article

Genomic differences of patients with hematologic malignancies in different age groups.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-07293-0

By:

Yang, Xiaodi;
Wang, Qian;
Sun, Yuhua;
Zhang, Ziding;
Wuchty, Stefan;
Liang, Zeyin;
Dong, Yujun

Publication type:

Article

Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection.

Published in:

Scientific Reports, 2016, p. 35064, doi. 10.1038/srep35064

By:

Jiang, Zhenhong;
Dong, Xiaobao;
Li, Zhi-Gang;
He, Fei;
Zhang, Ziding

Publication type:

Article

Crysalis: an integrated server for computational analysis and design of protein crystallization.

Published in:

Scientific Reports, 2016, p. 21383, doi. 10.1038/srep21383

By:

Wang, Huilin;
Feng, Liubin;
Zhang, Ziding;
Webb, Geoffrey I.;
Lin, Donghai;
Song, Jiangning

Publication type:

Article

Network-Based Comparative Analysis of Arabidopsis Immune Responses to Golovinomyces orontii and Botrytis cinerea Infections.

Published in:

Scientific Reports, 2016, p. 19149, doi. 10.1038/srep19149

By:

Jiang, Zhenhong;
Dong, Xiaobao;
Zhang, Ziding

Publication type:

Article

Competition-cooperation relationship networks characterize the competition and cooperation between proteins.

Published in:

Scientific Reports, 2015, p. 11619, doi. 10.1038/srep11619

By:

Li, Hong;
Zhou, Yuan;
Zhang, Ziding

Publication type:

Article

Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features.

Published in:

Scientific Reports, 2014, v. 4, n. 1, p. 1, doi. 10.1038/srep05765

By:

Li, Yuan;
Wang, Mingjun;
Wang, Huilin;
Tan, Hao;
Zhang, Ziding;
Webb, Geoffrey I.;
Song, Jiangning

Publication type:

Article

Network Analysis Reveals a Common Host-Pathogen Interaction Pattern in Arabidopsis Immune Responses.

Published in:

Frontiers in Plant Science, 2017, p. 1, doi. 10.3389/fpls.2017.00893

By:

Hong Li;
Yuan Zhou;
Ziding Zhang

Publication type:

Article

Characterization of Calcium-Dependent Protein Kinases 3, a Protein Involved in Growth of Cryptosporidium parvum.

Published in:

Frontiers in Microbiology, 2020, v. 11, p. 1, doi. 10.3389/fmicb.2020.00907

By:

Zhang, Qiang;
Guo, Yaqiong;
Li, Na;
Li, Yu;
Su, Jiayuan;
Xu, Rui;
Zhang, Ziding;
Feng, Yaoyu;
Xiao, Lihua

Publication type:

Article

Analytic Approaches in Genomic Epidemiological Studies of Parasitic Protozoa.

Published in:

Transboundary & Emerging Diseases, 2024, v. 2024, p. 1, doi. 10.1155/2024/7679727

By:

Wang, Tianpeng;
Zhang, Ziding;
Feng, Yaoyu;
Xiao, Lihua;
Zhang, Long-Xian

Publication type:

Article

Similarity networks of protein binding sites.

Published in:

Proteins, 2006, v. 62, n. 2, p. 470, doi. 10.1002/prot.20752

By:

Zhang, Ziding;
Grigorov, Martin G.

Publication type:

Article

Characterization of the MHC class II α-chain gene in ducks.

Published in:

Immunogenetics, 2011, v. 63, n. 10, p. 667, doi. 10.1007/s00251-011-0545-5

By:

Ren, Liming;
Yang, Zhi;
Wang, Tao;
Sun, Yi;
Guo, Ying;
Zhang, Ziding;
Fei, Jing;
Bao, Yonghua;
Qin, Tong;
Wang, Jing;
Huang, Yinhua;
Hu, Xiaoxiang;
Zhao, Yaofeng;
Li, Ning

Publication type:

Article

Quantitative structure–activity relationship study on antitumour activity of a series of flavonoids.

Published in:

Molecular Simulation, 2012, v. 38, n. 1, p. 38, doi. 10.1080/08927022.2011.600760

By:

Wang, Wei-Xuan;
Si, Hongzong;
Zhang, Ziding

Publication type:

Article

Multi-modal features-based human-herpesvirus protein–protein interaction prediction by using LightGBM.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae005

By:

Yang, Xiaodi;
Wuchty, Stefan;
Liang, Zeyin;
Ji, Li;
Wang, Bingjie;
Zhu, Jialin;
Zhang, Ziding;
Dong, Yujun

Publication type:

Article

SGPPI: structure-aware prediction of protein–protein interactions in rigorous conditions with graph convolutional network.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad020

By:

Huang, Yan;
Wuchty, Stefan;
Zhou, Yuan;
Zhang, Ziding

Publication type:

Article

Current status and future perspectives of computational studies on human–virus protein–protein interactions.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 5, p. 1, doi. 10.1093/bib/bbab029

By:

Lian, Xianyi;
Yang, Xiaodi;
Yang, Shiping;
Zhang, Ziding

Publication type:

Article

HVIDB: a comprehensive database for human–virus protein–protein interactions.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 2, p. 832, doi. 10.1093/bib/bbaa425

By:

Yang, Xiaodi;
Lian, Xianyi;
Fu, Chen;
Wuchty, Stefan;
Yang, Shiping;
Zhang, Ziding

Publication type:

Article

Prediction of protein–protein interactions between fungus (Magnaporthe grisea) and rice (Oryza sativa L.).

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 2, p. 448, doi. 10.1093/bib/bbx132

By:

Ma, Shiwei;
Song, Qi;
Tao, Huan;
Harrison, Andrew;
Wang, Shaobo;
Liu, Wei;
Lin, Shoukai;
Zhang, Ziding;
Ai, Yufang;
He, Huaqin

Publication type:

Article

Critical assessment and performance improvement of plant–pathogen protein–protein interaction prediction methods.

Published in:

Briefings in Bioinformatics, 2019, v. 20, n. 1, p. 274, doi. 10.1093/bib/bbx123

By:

Yang, Shiping;
Li, Hong;
He, Huaqin;
Zhou, Yuan;
Zhang, Ziding

Publication type:

Article

Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features.

Published in:

Briefings in Bioinformatics, 2015, v. 16, n. 4, p. 640, doi. 10.1093/bib/bbu031

By:

Zhen Chen;
Yuan Zhou;
Ziding Zhang;
Jiangning Song

Publication type:

Article

MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins.

Published in:

Database: The Journal of Biological Databases & Curation, 2015, v. 2015, p. 1, doi. 10.1093/database/bav108

By:

Yuan Zhou;
Shiping Yang;
Tonglin Mao;
Ziding Zhang

Publication type:

Article

BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors.

Published in:

Database: The Journal of Biological Databases & Curation, 2015, v. 2015, p. 1, doi. 10.1093/database/bav064

By:

Xiaobao Dong;
Xiaotian Lu;
Ziding Zhang

Publication type:

Article

Toxicity of Ionic Liquids.

Published in:

CLEAN: Soil, Air, Water, 2007, v. 35, n. 1, p. 42, doi. 10.1002/clen.200600015

By:

Dongbin Zhao;
Yongcheng Liao;
Ziding Zhang

Publication type:

Article