Works by Yang, Yuedong

Results: 145

Repurposing the memory-promoting meclofenoxate hydrochloride as a treatment for Parkinson's disease through integrative multi-omics analysis.

Published in:

NPJ Parkinson's Disease, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41531-025-01027-7

By:

Zhang, Huasong;
Fan, Cong;
Li, Ling;
Liu, Feiyi;
Li, Shaoying;
Ma, Linyun;
Yang, Yuanhao;
Cooper, David N.;
Yang, Yuedong;
Hu, Ronggui;
Zhao, Huiying

Publication type:

Article

Predicting the change of exon splicing caused by genetic variant using support vector regression.

Published in:

Human Mutation, 2019, v. 40, n. 9, p. 1235, doi. 10.1002/humu.23785

By:

Chen, Ken;
Lu, Yutong;
Zhao, Huiying;
Yang, Yuedong

Publication type:

Article

Quantitative mapping of genetic similarity in human heritable diseases by shared mutations.

Published in:

Human Mutation, 2018, v. 39, n. 2, p. 292, doi. 10.1002/humu.23358

By:

Zhao, Huiying;
Yang, Yuedong;
Lu, Yutong;
Mort, Matthew;
Cooper, David N.;
Zuo, Zhiyi;
Zhou, Yaoqi

Publication type:

Article

Investigating DNA-, RNA-, and protein-based features as a means to discriminate pathogenic synonymous variants.

Published in:

Human Mutation, 2017, v. 38, n. 10, p. 1336, doi. 10.1002/humu.23283

By:

Livingstone, Mark;
Folkman, Lukas;
Yang, Yuedong;
Zhang, Ping;
Mort, Matthew;
Cooper, David N.;
Liu, Yunlong;
Stantic, Bela;
Zhou, Yaoqi

Publication type:

Article

ExonImpact: Prioritizing Pathogenic Alternative Splicing Events.

Published in:

Human Mutation, 2017, v. 38, n. 1, p. 16, doi. 10.1002/humu.23111

By:

Li, Meng;
Feng, Weixing;
Zhang, Xinjun;
Yang, Yuedong;
Wang, Kejun;
Mort, Matthew;
Cooper, David N;
Wang, Yue;
Zhou, Yaoqi;
Liu, Yunlong

Publication type:

Article

Enrichment of SNPs in Functional Categories Reveals Genes Affecting Complex Traits.

Published in:

Human Mutation, 2016, v. 37, n. 8, p. 820, doi. 10.1002/humu.23007

By:

Zhao, Huiying;
Fan, Dongsheng;
Nyholt, Dale R;
Yang, Yuedong

Publication type:

Article

Structure-based prediction of protein- peptide binding regions using Random Forest.

Published in:

Bioinformatics, 2018, v. 34, n. 3, p. 477, doi. 10.1093/bioinformatics/btx614

By:

Taherzadeh, Ghazaleh;
Zhou, Yaoqi;
Liew, Alan Wee-Chung;
Yang, Yuedong

Publication type:

Article

Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility.

Published in:

Bioinformatics, 2017, v. 33, n. 18, p. 2842, doi. 10.1093/bioinformatics/btx218

By:

Heffernan, Rhys;
Yuedong Yang;
Paliwal, Kuldip;
Yaoqi Zhou

Publication type:

Article

SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library.

Published in:

Bioinformatics, 2017, v. 33, n. 8, p. 1238, doi. 10.1093/bioinformatics/btw829

By:

Litfin, Thomas;
Yaoqi Zhou;
Yuedong Yang

Publication type:

Article

Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks.

Published in:

Bioinformatics, 2017, v. 33, n. 5, p. 685, doi. 10.1093/bioinformatics/btw678

By:

Hanson, Jack;
Yuedong Yang;
Paliwal, Kuldip;
Yaoqi Zhou

Publication type:

Article

LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction.

Published in:

Bioinformatics, 2017, v. 33, n. 5, p. 677, doi. 10.1093/bioinformatics/btw668

By:

Tong Wang;
Yuedong Yang;
Yaoqi Zhou;
Haipeng Gong

Publication type:

Article

Predicting the errors of predicted local backbone angles and non-local solvent-accessibilities of proteins by deep neural networks.

Published in:

Bioinformatics, 2016, v. 32, n. 24, p. 3768, doi. 10.1093/bioinformatics/btw549

By:

Jianzhao Gao;
Yuedong Yang;
Yaoqi Zhou

Publication type:

Article

Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins.

Published in:

Bioinformatics, 2016, v. 32, n. 6, p. 843, doi. 10.1093/bioinformatics/btv665

By:

Heffernan, Rhys;
Dehzangi, Abdollah;
Lyons, James;
Paliwal, Kuldip;
Sharma, Alok;
Jihua Wang;
Sattar, Abdul;
Yaoqi Zhou;
Yuedong Yang

Publication type:

Article

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

Published in:

2016

By:

Brown, Peter;
Pullan, Wayne;
Yuedong Yang;
Yaoqi Zhou

Publication type:

Product Review

DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels.

Published in:

2015

By:

Folkman, Lukas;
Yuedong Yang;
Zhixiu Li;
Stantic, Bela;
Sattar, Abdul;
Mort, Matthew;
Cooper, David N.;
Yunlong Liu;
Yaoqi Zhou

Publication type:

Product Review

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates.

Published in:

Bioinformatics, 2011, v. 27, n. 15, p. 2076, doi. 10.1093/bioinformatics/btr350

By:

Yang, Yuedong;
Faraggi, Eshel;
Zhao, Huiying;
Zhou, Yaoqi

Publication type:

Article

Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function.

Published in:

Bioinformatics, 2010, v. 26, n. 15, p. 1857, doi. 10.1093/bioinformatics/btq295

By:

Huiying Zhao;
Yuedong Yang;
Yaoqi Zhou

Publication type:

Article

Cross‐Modal Graph Contrastive Learning with Cellular Images.

Published in:

Advanced Science, 2024, v. 11, n. 32, p. 1, doi. 10.1002/advs.202404845

By:

Zheng, Shuangjia;
Rao, Jiahua;
Zhang, Jixian;
Zhou, Lianyu;
Xie, Jiancong;
Cohen, Ethan;
Lu, Wei;
Li, Chengtao;
Yang, Yuedong

Publication type:

Article

YesU from Bacillus subtilis preferentially binds fucosylated glycans.

Published in:

Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-31241-8

By:

Tiralongo, Joe;
Cooper, Oren;
Litfin, Tom;
Yang, Yuedong;
King, Rebecca;
Zhan, Jian;
Zhao, Huiying;
Bovin, Nicolai;
Day, Christopher J.;
Zhou, Yaoqi

Publication type:

Article

Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map.

Published in:

Journal of Cheminformatics, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13321-021-00488-1

By:

Chen, Jianwen;
Zheng, Shuangjia;
Zhao, Huiying;
Yang, Yuedong

Publication type:

Article

DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state.

Published in:

Journal of Cheminformatics, 2019, v. 11, n. 1, p. N.PAG, doi. 10.1186/s13321-019-0373-4

By:

Chen, Pin;
Ke, Yaobin;
Lu, Yutong;
Du, Yunfei;
Li, Jiahui;
Yan, Hui;
Zhao, Huiying;
Zhou, Yaoqi;
Yang, Yuedong

Publication type:

Article

QBMG: quasi-biogenic molecule generator with deep recurrent neural network.

Published in:

Journal of Cheminformatics, 2019, v. 11, n. 1, p. 1, doi. 10.1186/s13321-019-0328-9

By:

Zheng, Shuangjia;
Yan, Xin;
Gu, Qiong;
Yang, Yuedong;
Du, Yunfei;
Lu, Yutong;
Xu, Jun

Publication type:

Article

Genetic algorithms for protein conformation sampling and optimization in a discrete backbone dihedral angle space.

Published in:

Journal of Computational Chemistry, 2006, v. 27, n. 13, p. 1593, doi. 10.1002/jcc.20463

By:

Yuedong Yang;
Haiyan Liu

Publication type:

Article

Optimization of Microwave-assisted Extraction of Phenolic Compounds from "Anli" Pear (Pyrus ussuriensis Maxim).

Published in:

Food Science & Technology Research, 2015, v. 21, n. 3, p. 463, doi. 10.3136/fstr.21.463

By:

Fei PENG;
Caihong CHENG;
Ying XIE;
Yuedong YANG

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

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

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 into Improvement for Anti-Rollover Propensity of SUV.

Published in:

Chinese Journal of Mechanical Engineering, 2017, v. 30, n. 3, p. 698, doi. 10.1007/s10033-017-0127-z

By:

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

Publication type:

Article

Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome.

Published in:

PLoS ONE, 2014, v. 9, n. 5, p. 1, doi. 10.1371/journal.pone.0096694

By:

Zhao, Huiying;
Wang, Jihua;
Zhou, Yaoqi;
Yang, Yuedong

Publication type:

Article

Self-derived structure-disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptides.

Published in:

FASEB Journal, 2019, v. 33, n. 2, p. 2095, doi. 10.1096/fj.201700613RR

By:

Jian Zhan;
Husen Jia;
Semchenko, Evgeny A.;
Yunqiang Bian;
Zhou, Amy M.;
Zhixiu Li;
Yuedong Yang;
Jihua Wang;
Sarkar, Sohinee;
Totsika, Makrina;
Blanchard, Helen;
Jen, Freda E.-C.;
Qizhuang Ye;
Haselhorst, Thomas;
Jennings, Michael P.;
Seib, Kate L.;
Yaoqi Zhou

Publication type:

Article

An uncertainty-based interpretable deep learning framework for predicting breast cancer outcome.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05716-7

By:

Chai, Hua;
Lin, Siyin;
Lin, Junqi;
He, Minfan;
Yang, Yuedong;
OuYang, Yongzhong;
Zhao, Huiying

Publication type:

Article

A coarse‐refine segmentation network for COVID‐19 CT images.

Published in:

IET Image Processing (Wiley-Blackwell), 2022, v. 16, n. 2, p. 333, doi. 10.1049/ipr2.12278

By:

Huang, Ziwang;
Li, Liang;
Zhang, Xiang;
Song, Ying;
Chen, Jianwen;
Zhao, Huiying;
Chong, Yutian;
Wu, Hejun;
Yang, Yuedong;
Shen, Jun;
Zha, Yunfei

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

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

Trends in template/fragment-free protein structure prediction.

Published in:

Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2011, v. 128, n. 1, p. 3, doi. 10.1007/s00214-010-0799-2

By:

Zhou, Yaoqi;
Duan, Yong;
Yang, Yuedong;
Faraggi, Eshel;
Lei, Hongxing

Publication type:

Article

Chestnut flower extract as a natural inhibitor of Fusarium graminearum: antifungal activity and mechanisms.

Published in:

Pest Management Science, 2025, v. 81, n. 6, p. 3358, doi. 10.1002/ps.8708

By:

Xie, Qiaoling;
Peng, Fei;
Wang, Xiuping;
Du, Bin;
Yang, Yuedong

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

Imputing spatial transcriptomics through gene network constructed from protein language model.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-06964-2

By:

Zeng, Yuansong;
Song, Yujie;
Zhang, Chengyang;
Li, Haoxuan;
Zhao, Yongkang;
Yu, Weijiang;
Zhang, Shiqi;
Zhang, Hongyu;
Dai, Zhiming;
Yang, Yuedong

Publication type:

Article

Imputing spatial transcriptomics through gene network constructed from protein language model.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-06964-2

By:

Zeng, Yuansong;
Song, Yujie;
Zhang, Chengyang;
Li, Haoxuan;
Zhao, Yongkang;
Yu, Weijiang;
Zhang, Shiqi;
Zhang, Hongyu;
Dai, Zhiming;
Yang, Yuedong

Publication type:

Article

Pyrus ussuriensis Maxim 70% ethanol eluted fraction ameliorates inflammation and oxidative stress in LPS‐induced inflammation in vitro and in vivo.

Published in:

Food Science & Nutrition, 2023, v. 11, n. 1, p. 458, doi. 10.1002/fsn3.3077

By:

Peng, Fei;
Ren, Xin;
Du, Bin;
Yang, Yuedong

Publication type:

Article

Systems-level understanding of ethanol-induced stresses and adaptation in E. coli.

Published in:

Scientific Reports, 2017, p. 44150, doi. 10.1038/srep44150

By:

Cao, Huansheng;
Wei, Du;
Yang, Yuedong;
Shang, Yu;
Li, Gaoyang;
Zhou, Yaoqi;
Ma, Qin;
Xu, Ying

Publication type:

Article

Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.

Published in:

Scientific Reports, 2015, p. 11476, doi. 10.1038/srep11476

By:

Heffernan, Rhys;
Paliwal, Kuldip;
Lyons, James;
Dehzangi, Abdollah;
Sharma, Alok;
Wang, Jihua;
Sattar, Abdul;
Yang, Yuedong;
Zhou, Yaoqi

Publication type:

Article

Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA.

Published in:

PLoS ONE, 2017, v. 12, n. 9, p. 1, doi. 10.1371/journal.pone.0184722

By:

Jegousse, Clara;
Yang, Yuedong;
Zhan, Jian;
Wang, Jihua;
Zhou, Yaoqi

Publication type:

Article

An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles.

Published in:

Proteins, 2009, v. 76, n. 3, p. 718, doi. 10.1002/prot.22384

By:

Xu, Beisi;
Yang, Yuedong;
Liang, Haojun;
Zhou, Yaoqi

Publication type:

Article

Specific interactions for ab initio folding of protein terminal regions with secondary structures.

Published in:

Proteins, 2008, v. 72, n. 2, p. 793, doi. 10.1002/prot.21968

By:

Yang, Yuedong;
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

Preparation and Characterization of 6-Carboxychitosan.

Published in:

Chemistry Letters, 2003, v. 32, n. 8, p. 682, doi. 10.1246/cl.2003.682

By:

Yongguo Zhou;
Yuedong Yang;
Dongjun Wang;
Xiaomin Liu

Publication type:

Article

A narrative review on conformational structure characterization of natural polysaccharides.

Published in:

Food Frontiers, 2022, v. 3, n. 4, p. 631, doi. 10.1002/fft2.150

By:

Du, Bin;
Nie, Shaoping;
Peng, Fei;
Yang, Yuedong;
Xu, Baojun

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