Works by Kuang, Rui

Results: 67

Global analysis of canola genes targeted by SHORT HYPOCOTYL UNDER BLUE 1 during endosperm and embryo development.

Published in:

Plant Journal, 2017, v. 91, n. 1, p. 158, doi. 10.1111/tpj.13542

By:

Zhang, Huanan;
Cheng, Feng;
Xiao, Yuguo;
Kang, Xiaojun;
Wang, Xiaowu;
Kuang, Rui;
Ni, Min

Publication type:

Article

Synthesis of cysteamine-coated CdTe quantum dots for the detection of bisphenol A.

Published in:

Microchimica Acta, 2010, v. 169, n. 1/2, p. 109, doi. 10.1007/s00604-010-0323-3

By:

Rui Kuang;
Xuan Kuang;
Siyi Pan;
Xiaodong Zheng;
Jiacai Duan;
Yaqing Duan

Publication type:

Article

Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs.

Published in:

Bioinformatics, 2024, v. 40, p. ii111, doi. 10.1093/bioinformatics/btae383

By:

Song, Tianci;
Cosatto, Eric;
Wang, Gaoyuan;
Kuang, Rui;
Gerstein, Mark;
Min, Martin Renqiang;
Warrell, Jonathan

Publication type:

Article

Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition.

Published in:

Bioinformatics, 2024, v. 40, p. i529, doi. 10.1093/bioinformatics/btae245

By:

Broadbent, Charles;
Song, Tianci;
Kuang, Rui

Publication type:

Article

Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network.

Published in:

Bioinformatics, 2022, v. 38, n. 5, p. 1344, doi. 10.1093/bioinformatics/btab812

By:

Song, Tianci;
Markham, Kathleen K;
Li, Zhuliu;
Muller, Kristen E;
Greenham, Kathleen;
Kuang, Rui

Publication type:

Article

Different forms of entropy dimension for zero entropy systems.

Published in:

Dynamical Systems: An International Journal, 2014, v. 29, n. 2, p. 239, doi. 10.1080/14689367.2014.881778

By:

Kuang, Rui;
Cheng, Wen-Chiao;
Ma, Dongkui;
Li, Bing

Publication type:

Article

Topological entropy dimension for noncompact sets.

Published in:

Dynamical Systems: An International Journal, 2012, v. 27, n. 3, p. 303, doi. 10.1080/14689367.2012.682646

By:

Ma, Dongkui;
Kuang, Rui;
Li, Bing

Publication type:

Article

Acoustoelastic Theory and Mode Analysis of Bolted Structures Under Preload.

Published in:

Machines, 2024, v. 12, n. 11, p. 822, doi. 10.3390/machines12110822

By:

Zhao, Lei;
Kuang, Rui;
Tian, Guizhong;
Shi, Xiaona;
Sun, Li

Publication type:

Article

Co-clustering phenome–genome for phenotype classification and disease gene discovery.

Published in:

Nucleic Acids Research, 2012, v. 40, n. 19, p. e146, doi. 10.1093/nar/gks615

By:

Hwang, TaeHyun;
Atluri, Gowtham;
Xie, MaoQiang;
Dey, Sanjoy;
Hong, Changjin;
Kumar, Vipin;
Kuang, Rui

Publication type:

Article

A large-scale comparative study of isoform expressions measured on four platforms.

Published in:

BMC Genomics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12864-020-6643-8

By:

Zhang, Wei;
Petegrosso, Raphael;
Chang, Jae-Woong;
Sun, Jiao;
Yong, Jeongsik;
Chien, Jeremy;
Kuang, Rui

Publication type:

Article

Identifying remote protein homologs by network propagation.

Published in:

FEBS Journal, 2005, v. 272, n. 20, p. 5119, doi. 10.1111/j.1742-4658.2005.04947.x

By:

Noble, William S.;
Rui Kuang;
Leslie, Christina;
Weston, Jason

Publication type:

Article

Orchard: Building large cancer phylogenies using stochastic combinatorial search.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 12, p. 1, doi. 10.1371/journal.pcbi.1012653

By:

Kulman, Ethan;
Kuang, Rui;
Morris, Quaid

Publication type:

Article

Motif-based protein ranking by network propagation.

Published in:

Bioinformatics, 2005, v. 21, n. 19, p. 3711, doi. 10.1093/bioinformatics/bti608

By:

Rui Kuang;
Jason Weston;
William Stafford Noble;
Christina Leslie

Publication type:

Article

Protein backbone angle prediction with machine learning approaches.

Published in:

Bioinformatics, 2004, v. 20, n. 10, p. 1612, doi. 10.1093/bioinformatics/bth136

By:

Rui Kuang;
Christina S. Leslie;
An-Suei Yang

Publication type:

Article

DARPP-32 and t-DARPP promote non-small cell lung cancer growth through regulation of IKKα-dependent cell migration.

Published in:

Communications Biology, 2018, v. 1, n. 1, p. N.PAG, doi. 10.1038/s42003-018-0050-6

By:

Alam, Sk. Kayum;
Astone, Matteo;
Liu, Ping;
Hall, Stephanie R.;
Coyle, Abbygail M.;
Dankert, Erin N.;
Hoffman, Dane K.;
Zhang, Wei;
Kuang, Rui;
Roden, Anja C.;
Mansfield, Aaron S.;
Hoeppner, Luke H.

Publication type:

Article

Hepcidin Protects Yellow Catfish (Pelteobagrus fulvidraco) against Aeromonas veronii -Induced Ascites Disease by Regulating Iron Metabolism.

Published in:

Antibiotics (2079-6382), 2021, v. 10, n. 7, p. 848, doi. 10.3390/antibiotics10070848

By:

Fu, Manquan;
Kuang, Rui;
Wang, Weicheng;
Yu, Yunzhen;
Ai, Taoshan;
Liu, Xiaoling;
Su, Jianguo;
Yuan, Gailing

Publication type:

Article

Estimating KIR Haplotype Frequencies on a Cohort of 10,000 Individuals: A Comprehensive Study on Population Variations, Typing Resolutions, and Reference Haplotypes.

Published in:

PLoS ONE, 2016, v. 11, n. 10, p. 1, doi. 10.1371/journal.pone.0163973

By:

Vierra-Green, Cynthia;
Roe, David;
Jayaraman, Jyothi;
Trowsdale, John;
Traherne, James;
Kuang, Rui;
Spellman, Stephen;
Maiers, Martin

Publication type:

Article

Meta-Analysis of EMT Datasets Reveals Different Types of EMT.

Published in:

PLoS ONE, 2016, v. 11, n. 6, p. 1, doi. 10.1371/journal.pone.0156839

By:

Liang, Lining;
Sun, Hao;
Zhang, Wei;
Zhang, Mengdan;
Yang, Xiao;
Kuang, Rui;
Zheng, Hui

Publication type:

Article

Vasodilator-stimulated phosphoprotein promotes liver metastasis of gastrointestinal cancer by activating a β1-integrin-FAK-YAP1/TAZ signaling pathway.

Published in:

NPJ Precision Oncology, 2018, v. 2, n. 1, p. N.PAG, doi. 10.1038/s41698-017-0045-7

By:

Xiang, Xiaoyu;
Wang, Yuanguo;
Zhang, Hongbin;
Piao, Jinhua;
Muthusamy, Selvaraj;
Wang, Lei;
Deng, Yibin;
Zhang, Wei;
Kuang, Rui;
Billadeau, Daniel D.;
Huang, Shengbing;
Lai, Jinping;
Urrutia, Raul;
Kang, Ningling

Publication type:

Article

Machine learning and statistical methods for clustering single-cell RNA-sequencing data.

Published in:

Briefings in Bioinformatics, 2020, v. 21, n. 4, p. 1209, doi. 10.1093/bib/bbz063

By:

Petegrosso, Raphael;
Li, Zhuliu;
Kuang, Rui

Publication type:

Article

Structural neuroimaging markers of normal pressure hydrocephalus versus Alzheimer's dementia and Parkinson's disease, and hydrocephalus versus atrophy in chronic TBI--a narrative review.

Published in:

Frontiers in Neurology, 2024, p. 1, doi. 10.3389/fneur.2024.1347200

By:

Sridhar, Sharada Kadaba;
Robb, Jen Dysterheft;
Gupta, Rishabh;
Cheong, Scarlett Cheong;
Kuang, Rui;
Samadani, Uzma

Publication type:

Article

Shadowable Points of Free Semigroup Actions.

Published in:

Bulletin of the Malaysian Mathematical Sciences Society, 2024, v. 47, n. 4, p. 1, doi. 10.1007/s40840-024-01718-z

By:

Li, Ritong;
Ma, Dongkui;
Kuang, Rui;
Ye, Xiaojiang

Publication type:

Article

Platform-integrated mRNA isoform quantification.

Published in:

Bioinformatics, 2020, v. 36, n. 8, p. 2466, doi. 10.1093/bioinformatics/btz932

By:

Sun, Jiao;
Chang, Jae-Woong;
Zhang, Teng;
Yong, Jeongsik;
Kuang, Rui;
Zhang, Wei

Publication type:

Article

Transfer learning across ontologies for phenome-genome association prediction.

Published in:

Bioinformatics, 2017, v. 33, n. 4, p. 529, doi. 10.1093/bioinformatics/btw649

By:

Petegrosso, Raphael;
Sunho Park;
Tae Hyun Hwang;
Rui Kuang

Publication type:

Article

Inferring disease and gene set associations with rank coherence in networks.

Published in:

Bioinformatics, 2011, v. 27, n. 19, p. 2692, doi. 10.1093/bioinformatics/btr463

By:

Hwang, TaeHyun;
Zhang, Wei;
Xie, Maoqiang;
Liu, Jinfeng;
Kuang, Rui

Publication type:

Article

Integrative classification and analysis of multiple arrayCGH datasets with probe alignment.

Published in:

Bioinformatics, 2010, v. 26, n. 18, p. 2313, doi. 10.1093/bioinformatics/btq428

By:

Ze Tian;
Rui Kuang

Publication type:

Article

A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge.

Published in:

Bioinformatics, 2009, v. 25, n. 21, p. 2831, doi. 10.1093/bioinformatics/btp467

By:

Ze Tian;
Tae Hyun Hwang;
Rui Kuang

Publication type:

Article

Robust and efficient identification of biomarkers by classifying features on graphs.

Published in:

Bioinformatics, 2008, v. 24, n. 18, p. 2023, doi. 10.1093/bioinformatics/btn383

By:

TaeHyun Hwang;
Hugues Sicotte;
Ze Tian;
Baolin Wu;
Jean-Pierre Kocher;
Dennis A. Wigle;
Vipin Kumar;
Rui Kuang

Publication type:

Article

GNTD: reconstructing spatial transcriptomes with graph-guided neural tensor decomposition informed by spatial and functional relations.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-44017-0

By:

Song, Tianci;
Broadbent, Charles;
Kuang, Rui

Publication type:

Article

Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments.

Published in:

BMC Systems Biology, 2015, v. 9, p. 1, doi. 10.1186/1752-0509-9-S4-S1

By:

Hong Cai;
Lilburn, Timothy G.;
Changjin Hong;
Jianying Gu;
Rui Kuang;
Yufeng Wang

Publication type:

Article

Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum.

Published in:

BMC Systems Biology, 2012, v. 6, n. Suppl 3, p. 1, doi. 10.1186/1752-0509-6-S3-S5

By:

Hong Cai;
Changjin Hong;
Jianying Gu;
Lilburn, Timothy G.;
Rui Kuang;
Yufeng Wang

Publication type:

Article

Scalable remote homology detection and fold recognition in massive protein networks.

Published in:

Proteins, 2019, v. 87, n. 6, p. 478, doi. 10.1002/prot.25669

By:

Petegrosso, Raphael;
Li, Zhuliu;
Srour, Molly A.;
Saad, Yousef;
Zhang, Wei;
Kuang, Rui

Publication type:

Article

Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers.

Published in:

BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-440

By:

Tae Hyun Hwang;
Gowtham Atluri;
Rui Kuang;
Kumar, Vipin;
Starr, Timothy;
Silverstein, Kevin A.T.;
Haverty, Peter M.;
Zemin Zhang;
Jinfeng Liu

Publication type:

Article

Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.

Published in:

BMC Genomics, 2012, v. 13, n. 1, p. 374, doi. 10.1186/1471-2164-13-374

By:

Chun-yu Li;
Gui-ming Deng;
Jing Yang;
Viljoen, Altus;
Yan Jin;
Rui-bin Kuang;
Cun-wu Zuo;
Zhi-cheng Lv;
Qiao-song Yang;
Ou Sheng;
Yue-rong Wei;
Chun-hua Hu;
Tao Dong;
Gan-jun Yi

Publication type:

Article

SubPatCNV: approximate subspace pattern mining for mapping copy-number variations.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-014-0426-7

By:

Johnson, Nicholas;
Huanan Zhang;
Gang Fang;
Kumar, Vipin;
Rui Kuang

Publication type:

Article

SubPatCNV: approximate subspace pattern mining for mapping copy-number variations.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 131, doi. 10.1186/s12859-014-0426-7

By:

Johnson, Nicholas;
Huanan Zhang;
Gang Fang;
Kumar, Vipin;
Rui Kuang

Publication type:

Article

Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 4, p. 1, doi. 10.1371/journal.pcbi.1008218

By:

Li, Zhuliu;
Song, Tianci;
Yong, Jeongsik;
Kuang, Rui

Publication type:

Article

HRB2 and BBX21 interaction modulates Arabidopsis ABI5 locus and stomatal aperture.

Published in:

Plant, Cell & Environment, 2018, v. 41, n. 8, p. 1912, doi. 10.1111/pce.13336

By:

Kang, Xiaojun;
Xu, Gang;
Lee, Byungha;
Chen, Chen;
Zhang, Huanan;
Kuang, Rui;
Ni, Min

Publication type:

Article

mRNA 3′-UTR shortening is a molecular signature of mTORC1 activation.

Published in:

Nature Communications, 2015, v. 6, n. 6, p. 7218, doi. 10.1038/ncomms8218

By:

Chang, Jae-Woong;
Zhang, Wei;
Yeh, Hsin-Sung;
de Jong, Ebbing P.;
Jun, Semo;
Kim, Kwan-Hyun;
Bae, Sun S.;
Beckman, Kenneth;
Hwang, Tae Hyun;
Kim, Kye-Seong;
Kim, Do-Hyung;
Griffin, Timothy J.;
Kuang, Rui;
Yong, Jeongsik

Publication type:

Article

A novel subnetwork alignment approach predicts new components of the cell cycle regulatory apparatus in Plasmodium falciparum.

Published in:

BMC Bioinformatics, 2013, v. 14, n. Suppl 12, p. 1, doi. 10.1186/1471-2105-14-S12-S2

By:

Hong Cai;
Changjin Hong;
Lilburn, Timothy G.;
Rodriguez, Armando L.;
Chen, Sheng;
Jianying Gu;
Rui Kuang;
Yufeng Wang

Publication type:

Article

Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 12, p. 1, doi. 10.1371/journal.pcbi.1004465

By:

Zhang, Wei;
Chang, Jae-Woong;
Lin, Lilong;
Minn, Kay;
Wu, Baolin;
Chien, Jeremy;
Yong, Jeongsik;
Zheng, Hui;
Kuang, Rui

Publication type:

Article

Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002975

By:

Zhang, Wei;
Ota, Takayo;
Shridhar, Viji;
Chien, Jeremy;
Wu, Baolin;
Kuang, Rui

Publication type:

Article

PROFILE-BASED STRING KERNELS FOR REMOTE HOMOLOGY DETECTION AND MOTIF EXTRACTION.

Published in:

Journal of Bioinformatics & Computational Biology, 2005, v. 3, n. 3, p. 527, doi. 10.1142/S021972000500120X

By:

Kuang, Rui;
Ie, Eugene;
Wang, Ke;
Wang, Kai;
Siddiqi, Mahira;
Freund, Yoav;
Leslie, Christina

Publication type:

Article

Effect of Particle Size, Sphericity, and Distribution on Seepage in Granular Porous Media.

Published in:

Geotechnical & Geological Engineering, 2025, v. 43, n. 3, p. 1, doi. 10.1007/s10706-025-03095-1

By:

Xiong, Bo-bo;
Kuang, Rui;
Zhang, Ping;
Tian, Bin;
Gao, Hong-hu;
Zheng, Qian;
Li, Yu-qin

Publication type:

Article

Antiproliferative Evaluation of (E)-3-(3-(Allyloxy)-2-Methoxyphenyl)-1-(2,4,6-Trimethoxyphenyl)Prop-2-En-1-One as a Novel Apoptosis Inducer Against Prostate Cancer PC-3 Cells.

Published in:

Pharmaceutical Chemistry Journal, 2019, v. 52, n. 11, p. 917, doi. 10.1007/s11094-019-01926-z

By:

Fu, Dong-Jun;
Li, Ping;
Kuang, Yi-Rui;
Jiang, Li-Le;
Zhu, Ming-Chao;
Li, Si-Chen;
Zheng, Guo;
Zhang, Rui;
Zhang, Sai-Yang;
Li, Jiang-Feng

Publication type:

Article

Scrambled sets and chain recurrence points of generic graph maps.

Published in:

Journal of Difference Equations & Applications, 2022, v. 28, n. 11/12, p. 1507, doi. 10.1080/10236198.2022.2159397

By:

Feng, Jiahui;
Kuang, Rui

Publication type:

Article

Platinum-sensitive recurrence in ovarian cancer: the role of tumor microenvironment.

Published in:

Frontiers in Oncology, 2013, v. 3, p. 1, doi. 10.3389/fonc.2013.00251

By:

Chien, Jeremy;
Kuang, Rui;
Landen, Charles;
Shridhar, Viji

Publication type:

Article

Corrigendum: A Detailed View of KIR Haplotype Structures and Gene Families as Provided by a New Motif-Based Multiple Sequence Alignment.

Published in:

2021

By:

Roe, David;
Vierra-Green, Cynthia;
Pyo, Chul-Woo;
Geraghty, Daniel E.;
Spellman, Stephen R.;
Maiers, Martin;
Kuang, Rui

Publication type:

Correction Notice

Accurate and Efficient KIR Gene and Haplotype Inference From Genome Sequencing Reads With Novel K-mer Signatures.

Published in:

Frontiers in Immunology, 2020, v. 11, p. N.PAG, doi. 10.3389/fimmu.2020.583013

By:

Roe, David;
Kuang, Rui

Publication type:

Article

A Detailed View of KIR Haplotype Structures and Gene Families as Provided by a New Motif-Based Multiple Sequence Alignment.

Published in:

Frontiers in Immunology, 2020, v. 11, p. N.PAG, doi. 10.3389/fimmu.2020.585731

By:

Roe, David;
Vierra-Green, Cynthia;
Pyo, Chul-Woo;
Geraghty, Daniel E.;
Spellman, Stephen R.;
Maiers, Martin;
Kuang, Rui

Publication type:

Article