Works matching AU Yuedong Yang

Results: 145

Optimal secretion of alkali-tolerant xylanase in Bacillus subtilis by signal peptide screening.

Published in:

Applied Microbiology & Biotechnology, 2016, v. 100, n. 20, p. 8745, doi. 10.1007/s00253-016-7615-4

By:

Zhang, Weiwei;
Yang, Mingming;
Yang, Yuedong;
Zhan, Jian;
Zhou, Yaoqi;
Zhao, Xin

Publication type:

Article

Accurately predicting optimal conditions for microorganism proteins through geometric graph learning and language model.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-07436-3

By:

Zhu, Mingming;
Song, Yidong;
Yuan, Qianmu;
Yang, Yuedong

Publication type:

Article

Genome-scale annotation of protein binding sites via language model and geometric deep learning.

Published in:

eLife, 2024, p. 1, doi. 10.7554/eLife.93695

By:

Qianmu Yuan;
Chong Tian;
Yuedong Yang

Publication type:

Article

Comparative global B cell receptor repertoire difference induced by SARS-CoV-2 infection or vaccination via single-cell V(D)J sequencing.

Published in:

Emerging Microbes & Infections, 2022, v. 11, n. 1, p. 2007, doi. 10.1080/22221751.2022.2105261

By:

He, Bing;
Liu, Shuning;
Xu, Mengxin;
Hu, Yunqi;
Lv, Kexin;
Wang, Yuanyuan;
Ma, Yong;
Zhai, Yanmei;
Yue, Xinyu;
Liu, Lin;
Lu, Hongjie;
Zhou, Siwei;
Li, Pengbin;
Mai, Guoqin;
Huang, Xiaoping;
Li, Chenhang;
Chen, Shifeng;
Ye, Shupei;
Zhao, Pingsen;
Yang, Yuedong

Publication type:

Article

Joints Parameters Identification in Numerical Modeling of Structural Dynamics.

Published in:

Shock & Vibration, 2018, p. 1, doi. 10.1155/2018/2365759

By:

Yang, Yuedong;
Chen, Jiqing;
Lan, Fengchong;
Xiong, Fei;
Zeng, Zicong

Publication type:

Article

Imputing missing RNA-sequencing data from DNA methylation by using a transfer learning–based neural network.

Published in:

GigaScience, 2020, v. 9, n. 7, p. 1, doi. 10.1093/gigascience/giaa076

By:

Zhou, Xiang;
Chai, Hua;
Zhao, Huiying;
Luo, Ching-Hsing;
Yang, Yuedong

Publication type:

Article

Characterization and Anti-Inflammatory Potential of an Exopolysaccharide from Submerged Mycelial Culture of Schizophyllum commune.

Published in:

Frontiers in Pharmacology, 2017, p. 1, doi. 10.3389/fphar.2017.00252

By:

Bin Du;
Yuedong Yang;
Zhaoxiang Bian;
Baojun Xu

Publication type:

Article

Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-53116-5

By:

Chen, Sheng;
Zhang, Sen;
Fang, Xiaoyu;
Lin, Liang;
Zhao, Huiying;
Yang, Yuedong

Publication type:

Article

Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-53116-5

By:

Chen, Sheng;
Zhang, Sen;
Fang, XiaoYu;
Lin, Liang;
Zhao, Huiying;
Yang, Yuedong

Publication type:

Article

Accurately predicting enzyme functions through geometric graph learning on ESMFold-predicted structures.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-52533-w

By:

Song, Yidong;
Yuan, Qianmu;
Chen, Sheng;
Zeng, Yuansong;
Zhao, Huiying;
Yang, Yuedong

Publication type:

Article

Structure-aware protein–protein interaction site prediction using deep graph convolutional network.

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 125, doi. 10.1093/bioinformatics/btab643

By:

Yuan, Qianmu;
Chen, Jianwen;
Zhao, Huiying;
Zhou, Yaoqi;
Yang, Yuedong

Publication type:

Article

Accurate prediction of genome-wide RNA secondary structure profile based on extreme gradient boosting.

Published in:

Bioinformatics, 2020, v. 36, n. 17, p. 4576, doi. 10.1093/bioinformatics/btaa534

By:

Ke, Yaobin;
Rao, Jiahua;
Zhao, Huiying;
Lu, Yutong;
Xiao, Nong;
Yang, Yuedong

Publication type:

Article

An Adaptive Transfer-Learning-Based Deep Cox Neural Network for Hepatocellular Carcinoma Prognosis Prediction.

Published in:

Frontiers in Oncology, 2021, v. 11, p. 1, doi. 10.3389/fonc.2021.692774

By:

Chai, Hua;
Xia, Long;
Zhang, Lei;
Yang, Jiarui;
Zhang, Zhongyue;
Qian, Xiangjun;
Yang, Yuedong;
Pan, Weidong

Publication type:

Article

Development of Chitosan-Based Films Incorporated with Chestnut Flower Essential Oil That Possess Good Anti-Ultraviolet Radiation and Antibacterial Effects for Banana Storage.

Published in:

Coatings (2079-6412), 2024, v. 14, n. 5, p. 548, doi. 10.3390/coatings14050548

By:

Liu, Yanfei;
Zhang, Jingyuan;
Peng, Fei;
Niu, Kui;
Hou, Wenlong;
Du, Bin;
Yang, Yuedong

Publication type:

Article

Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets.

Published in:

Nucleic Acids Research, 2011, v. 39, n. 8, p. 3017, doi. 10.1093/nar/gkq1266

By:

Zhao, Huiying;
Yang, Yuedong;
Zhou, Yaoqi

Publication type:

Article

Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-30970-9

By:

Zheng, Shuangjia;
Zeng, Tao;
Li, Chengtao;
Chen, Binghong;
Coley, Connor W.;
Yang, Yuedong;
Wu, Ruibo

Publication type:

Article

EC-Conf: A ultra-fast diffusion model for molecular conformation generation with equivariant consistency.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00893-2

By:

Fan, Zhiguang;
Yang, Yuedong;
Xu, Mingyuan;
Chen, Hongming

Publication type:

Article

Deep scaffold hopping with multimodal transformer neural networks.

Published in:

Journal of Cheminformatics, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13321-021-00565-5

By:

Zheng, Shuangjia;
Lei, Zengrong;
Ai, Haitao;
Chen, Hongming;
Deng, Daiguo;
Yang, Yuedong

Publication type:

Article

Moraxella catarrhalis phase-variable loci show differences in expression during conditions relevant to disease.

Published in:

PLoS ONE, 2020, v. 15, n. 6, p. 1, doi. 10.1371/journal.pone.0234306

By:

Tan, Aimee;
Blakeway, Luke V.;
Taha;
Yang, Yuedong;
Zhou, Yaoqi;
Atack, John M.;
Peak, Ian R.;
Seib, Kate L.

Publication type:

Article

Characterizing RNA-binding ligands on structures, chemical information, binding affinity and drug-likeness.

Published in:

RNA Biology, 2023, v. 20, n. 1, p. 431, doi. 10.1080/15476286.2023.2231708

By:

Fan, Cong;
Wang, Xin;
Ling, Tianze;
Yang, Yuedong;
Zhao, Huiying

Publication type:

Article

Predicting functional long non-coding RNAs validated by low throughput experiments.

Published in:

RNA Biology, 2019, v. 16, n. 11, p. 1555, doi. 10.1080/15476286.2019.1644590

By:

Zhou, Bailing;
Yang, Yuedong;
Zhan, Jian;
Dou, Xianghua;
Wang, Jihua;
Zhou, Yaoqi

Publication type:

Article

Structural basis for SUMO-E2 interaction revealed by a complex model using docking approach in combination with NMR data.

Published in:

Proteins, 2005, v. 61, n. 4, p. 1050, doi. 10.1002/prot.20695

By:

Ding, Husheng;
Yang, Yuedong;
Zhang, Jiahai;
Wu, Jihui;
Liu, Haiyan;
Shi, Yunyu

Publication type:

Article

Tri©DB: an integrated platform of knowledgebase and reporting system for cancer precision medicine.

Published in:

Journal of Translational Medicine, 2023, v. 21, n. 1, p. 1, doi. 10.1186/s12967-023-04773-5

By:

Jiang, Wei;
Wang, Peng-Ying;
Zhou, Qi;
Lin, Qiu-Tong;
Yao, Yao;
Huang, Xun;
Tan, Xiaoming;
Yang, Shihui;
Ye, Weicai;
Yang, Yuedong;
Bao, Yun-Juan

Publication type:

Article

Accurately Discriminating COVID-19 from Viral and Bacterial Pneumonia According to CT Images Via Deep Learning.

Published in:

Interdisciplinary Sciences: Computational Life Sciences, 2021, v. 13, n. 2, p. 273, doi. 10.1007/s12539-021-00420-z

By:

Zheng, Fudan;
Li, Liang;
Zhang, Xiang;
Song, Ying;
Huang, Ziwang;
Chong, Yutian;
Chen, Zhiguang;
Zhu, Huiling;
Wu, Jiahao;
Chen, Weifeng;
Lu, Yutong;
Yang, Yuedong;
Zha, Yunfei;
Zhao, Huiying;
Shen, Jun

Publication type:

Article

Investigation the Possibility of Using Peptides with a Helical Repeating Pattern of Hydro-Phobic and Hydrophilic Residues to Inhibit IL-10.

Published in:

PLoS ONE, 2016, v. 11, n. 4, p. 1, doi. 10.1371/journal.pone.0153939

By:

Ni, Guoying;
Chen, Shu;
Yang, Yuedong;
Cummins, Scott F.;
Zhan, Jian;
Li, Zhixiu;
Zhu, Bin;
Mounsey, Kate;
Walton, Shelley;
Wei, Ming Q.;
Wang, Yuejian;
Zhou, Yaoqi;
Wang, Tianfang;
Liu, Xiaosong

Publication type:

Article

Identification of Putative Causal Relationships Between Type 2 Diabetes and Blood-Based Biomarkers in East Asians by Mendelian Randomization.

Published in:

American Journal of Epidemiology, 2022, v. 191, n. 11, p. 1867, doi. 10.1093/aje/kwac118

By:

Zhang, Haoyang;
Xiu, Xuehao;
Yang, Yuedong;
Yang, Yuanhao;
Zhao, Huiying

Publication type:

Article

An Insight into Anti-Inflammatory Activities and Inflammation Related Diseases of Anthocyanins: A Review of Both In Vivo and In Vitro Investigations.

Published in:

International Journal of Molecular Sciences, 2021, v. 22, n. 20, p. 11076, doi. 10.3390/ijms222011076

By:

Ma, Zilong;
Du, Bin;
Li, Jun;
Yang, Yuedong;
Zhu, Fengmei

Publication type:

Article

Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids.

Published in:

International Journal of Molecular Sciences, 2018, v. 19, n. 3, p. 885, doi. 10.3390/ijms19030885

By:

Cao, Zanxia;
Bian, Yunqiang;
Hu, Guodong;
Zhao, Liling;
Kong, Zhenzhen;
Yang, Yuedong;
Wang, Jihua;
Zhou, Yaoqi

Publication type:

Article

Genetic evidence for a causal relationship between type 2 diabetes and peripheral artery disease in both Europeans and East Asians.

Published in:

BMC Medicine, 2022, v. 20, n. 1, p. 1, doi. 10.1186/s12916-022-02476-0

By:

Xiu, Xuehao;
Zhang, Haoyang;
Xue, Angli;
Cooper, David N.;
Yan, Li;
Yang, Yuedong;
Yang, Yuanhao;
Zhao, Huiying

Publication type:

Article

Safety Evaluation of Bridge under Moving Abnormal Indivisible Load Based on Fusing Bridge Inspection Data and Load Test Data.

Published in:

Structural Durability & Health Monitoring (SDHM), 2025, v. 19, n. 3, p. 499, doi. 10.32604/sdhm.2025.059070

By:

Zhang, He;
Mu, He-Qing;
Zhang, Xiao;
Yang, Yuedong

Publication type:

Article

Structure, Physicochemical Property, and Functional Activity of Dietary Fiber Obtained from Pear Fruit Pomace (Pyrus ussuriensis Maxim) via Different Extraction Methods.

Published in:

Foods, 2022, v. 11, n. 14, p. 2161, doi. 10.3390/foods11142161

By:

Peng, Fei;
Ren, Xin;
Du, Bin;
Chen, Linan;
Yu, Zuoqing;
Yang, Yuedong

Publication type:

Article

Detecting novel cell type in single-cell chromatin accessibility data via open-set domain adaptation.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 5, p. 1, doi. 10.1093/bib/bbae370

By:

Lin, Yuefan;
Pan, Zixiang;
Zeng, Yuansong;
Yang, Yuedong;
Dai, Zhiming

Publication type:

Article

Comprehensive single-cell RNA-seq analysis using deep interpretable generative modeling guided by biological hierarchy knowledge.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae314

By:

Chen, Hegang;
Lu, Yuyin;
Dai, Zhiming;
Yang, Yuedong;
Li, Qing;
Rao, Yanghui

Publication type:

Article

Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae163

By:

Chen, Ken;
Zhou, Yue;
Ding, Maolin;
Wang, Yu;
Ren, Zhixiang;
Yang, Yuedong

Publication type:

Article

From intuition to AI: evolution of small molecule representations in drug discovery.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad422

By:

McGibbon, Miles;
Shave, Steven;
Dong, Jie;
Gao, Yumiao;
Houston, Douglas R;
Xie, Jiancong;
Yang, Yuedong;
Schwaller, Philippe;
Blay, Vincent

Publication type:

Article

Subgraph extraction and graph representation learning for single cell Hi-C imputation and clustering.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1093/bib/bbad379

By:

Zheng, Jiahao;
Yang, Yuedong;
Dai, Zhiming

Publication type:

Article

Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad360

By:

Song, Yidong;
Yuan, Qianmu;
Zhao, Huiying;
Yang, Yuedong

Publication type:

Article

Fast and accurate protein intrinsic disorder prediction by using a pretrained language model.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 4, p. 1, doi. 10.1093/bib/bbad173

By:

Song, Yidong;
Yuan, Qianmu;
Chen, Sheng;
Chen, Ken;
Zhou, Yaoqi;
Yang, Yuedong

Publication type:

Article

Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad117

By:

Yuan, Qianmu;
Xie, Junjie;
Xie, Jiancong;
Zhao, Huiying;
Yang, Yuedong

Publication type:

Article

Identifying spatial domain by adapting transcriptomics with histology through contrastive learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad048

By:

Zeng, Yuansong;
Yin, Rui;
Luo, Mai;
Chen, Jianing;
Pan, Zixiang;
Lu, Yutong;
Yu, Weijiang;
Yang, Yuedong

Publication type:

Article

EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac583

By:

Zhou, Bailing;
Ding, Maolin;
Feng, Jing;
Ji, Baohua;
Huang, Pingping;
Zhang, Junye;
Yu, Xue;
Cao, Zanxia;
Yang, Yuedong;
Zhou, Yaoqi;
Wang, Jihua

Publication type:

Article

Spatial transcriptomics prediction from histology jointly through Transformer and graph neural networks.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac297

By:

Zeng, Yuansong;
Wei, Zhuoyi;
Yu, Weijiang;
Yin, Rui;
Yuan, Yuchen;
Li, Bingling;
Tang, Zhonghui;
Lu, Yutong;
Yang, Yuedong

Publication type:

Article

parameter-free deep embedded clustering method for single-cell RNA-seq data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac172

By:

Zeng, Yuansong;
Wei, Zhuoyi;
Zhong, Fengqi;
Pan, Zixiang;
Lu, Yutong;
Yang, Yuedong

Publication type:

Article

Capturing large genomic contexts for accurately predicting enhancer-promoter interactions.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbab577

By:

Chen, Ken;
Zhao, Huiying;
Yang, Yuedong

Publication type:

Article

robust and scalable graph neural network for accurate single-cell classification.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbab570

By:

Zeng, Yuansong;
Wei, Zhuoyi;
Pan, Zixiang;
Lu, Yutong;
Yang, Yuedong

Publication type:

Article

AlphaFold2-aware protein–DNA binding site prediction using graph transformer.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbab564

By:

Yuan, Qianmu;
Chen, Sheng;
Rao, Jiahua;
Zheng, Shuangjia;
Zhao, Huiying;
Yang, Yuedong

Publication type:

Article

scAdapt: virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 6, p. 1, doi. 10.1093/bib/bbab281

By:

Zhou, Xiang;
Chai, Hua;
Zeng, Yuansong;
Zhao, Huiying;
Yang, Yuedong

Publication type:

Article

PharmKG: a dedicated knowledge graph benchmark for bomedical data mining.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 4, p. 1, doi. 10.1093/bib/bbaa344

By:

Zheng, Shuangjia;
Rao, Jiahua;
Song, Ying;
Zhang, Jixian;
Xiao, Xianglu;
Fang, Evandro Fei;
Yang, Yuedong;
Niu, Zhangming

Publication type:

Article

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Published in:

Briefings in Bioinformatics, 2018, v. 19, n. 3, p. 482, doi. 10.1093/bib/bbw129

By:

Yuedong Yang;
Jianzhao Gao;
Jihua Wang;
Heffernan, Rhys;
Hanson, Jack;
Paliwal, Kuldip;
Yaoqi Zhou

Publication type:

Article

Mendelian randomization study reveals a population-specific putative causal effect of type 2 diabetes in risk of cataract.

Published in:

2021

By:

Zhang, Haoyang;
Xiu, Xuehao;
Xue, Angli;
Yang, Yuedong;
Yang, Yuanhao;
Zhao, Huiying

Publication type:

journal article