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Rui Kuang - Publications

Affiliations: 
Computer Science University of Minnesota, Twin Cities, Minneapolis, MN 
Area:
Computer Science, Bioinformatics Biology
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36 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Zhang W, Petegrosso R, Chang JW, Sun J, Yong J, Chien J, Kuang R. A large-scale comparative study of isoform expressions measured on four platforms. Bmc Genomics. 21: 272. PMID 32228441 DOI: 10.1186/S12864-020-6643-8  0.357
2019 Sun J, Chang JW, Zhang T, Yong J, Kuang R, Zhang W. Platform-integrated mRNA Isoform Quantification. Bioinformatics (Oxford, England). PMID 31834359 DOI: 10.1093/Bioinformatics/Btz932  0.315
2019 Chang JW, Yeh HS, Park M, Erber L, Sun J, Cheng S, Bui AM, Fahmi NA, Nasti R, Kuang R, Chen Y, Zhang W, Yong J. mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control. Nucleic Acids Research. PMID 31504847 DOI: 10.1093/Nar/Gkz761  0.305
2019 Petegrosso R, Li Z, Kuang R. Machine learning and statistical methods for clustering single-cell RNA-sequencing data. Briefings in Bioinformatics. PMID 31243426 DOI: 10.1093/Bib/Bbz063  0.312
2019 Petegrosso R, Li Z, Srour MA, Saad Y, Zhang W, Kuang R. Scalable Remote Homology Detection and Fold Recognition in Massive Protein Networks. Proteins. PMID 30714638 DOI: 10.1002/Prot.25669  0.325
2018 Chang JW, Zhang W, Yeh HS, Park M, Yao C, Shi Y, Kuang R, Yong J. An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response. Nucleic Acids Research. PMID 29733382 DOI: 10.1093/Nar/Gky340  0.335
2017 Roe D, Vierra-Green C, Pyo CW, Eng K, Hall R, Kuang R, Spellman S, Ranade S, Geraghty DE, Maiers M. Revealing complete complex KIR haplotypes phased by long-read sequencing technology. Genes and Immunity. PMID 28569259 DOI: 10.1038/Gene.2017.10  0.348
2017 Zhang H, Cheng F, Xiao YG, Kang XJ, Wang X, Kuang R, Ni M. Global analysis of canola genes targeted by SHORT HYPOCOTYL UNDER BLUE 1 during endosperm and embryo development. The Plant Journal : For Cell and Molecular Biology. PMID 28332746 DOI: 10.1111/Tpj.13542  0.335
2016 Petegrosso R, Park S, Hwang TH, Kuang R. Transfer Learning across Ontologies for Phenome-Genome Association Prediction. Bioinformatics (Oxford, England). PMID 27797759 DOI: 10.1093/Bioinformatics/Btw649  0.582
2016 Liang L, Sun H, Zhang W, Zhang M, Yang X, Kuang R, Zheng H. Meta-Analysis of EMT Datasets Reveals Different Types of EMT. Plos One. 11: e0156839. PMID 27258544 DOI: 10.1371/Journal.Pone.0156839  0.359
2015 Zhang W, Chang JW, Lin L, Minn K, Wu B, Chien J, Yong J, Zheng H, Kuang R. Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis. Plos Computational Biology. 11: e1004465. PMID 26699225 DOI: 10.1371/Journal.Pcbi.1004465  0.378
2015 Cai H, Lilburn TG, Hong C, Gu J, Kuang R, Wang Y. Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments. Bmc Systems Biology. 9: S1. PMID 26100579 DOI: 10.1186/1752-0509-9-S4-S1  0.34
2015 Chang JW, Zhang W, Yeh HS, de Jong EP, Jun S, Kim KH, Bae SS, Beckman K, Hwang TH, Kim KS, Kim DH, Griffin TJ, Kuang R, Yong J. mRNA 3'-UTR shortening is a molecular signature of mTORC1 activation. Nature Communications. 6: 7218. PMID 26074333 DOI: 10.1038/Ncomms8218  0.501
2015 Xie M, Xu Y, Zhang Y, Hwang T, Kuang R. Network-based Phenome-Genome Association Prediction by Bi-Random Walk. Plos One. 10: e0125138. PMID 25933025 DOI: 10.1371/Journal.Pone.0125138  0.58
2015 Johnson N, Zhang H, Fang G, Kumar V, Kuang R. SubPatCNV: approximate subspace pattern mining for mapping copy-number variations. Bmc Bioinformatics. 16: 16. PMID 25591662 DOI: 10.1186/S12859-014-0426-7  0.364
2013 Hwang TH, Atluri G, Kuang R, Kumar V, Starr T, Silverstein KA, Haverty PM, Zhang Z, Liu J. Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers. Bmc Genomics. 14: 440. PMID 23822816 DOI: 10.1186/1471-2164-14-440  0.57
2013 Zhang W, Ota T, Shridhar V, Chien J, Wu B, Kuang R. Network-based survival analysis reveals subnetwork signatures for predicting outcomes of ovarian cancer treatment. Plos Computational Biology. 9: e1002975. PMID 23555212 DOI: 10.1371/Journal.Pcbi.1002975  0.431
2012 Cai H, Hong C, Gu J, Lilburn TG, Kuang R, Wang Y. Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum. Bmc Systems Biology. 6: S5. PMID 23282319 DOI: 10.1186/1752-0509-6-S3-S5  0.316
2012 Hwang T, Atluri G, Xie M, Dey S, Hong C, Kumar V, Kuang R. Co-clustering phenome-genome for phenotype classification and disease gene discovery. Nucleic Acids Research. 40: e146. PMID 22735708 DOI: 10.1093/Nar/Gks615  0.593
2012 Xie M, Hwang TH, Kuang R. Erratum: Reconstructing Disease Phenome-genome Association by Bi-Random Walk (Bioinformatics (2012)) Bioinformatics. 30. PMID 22302570 DOI: 10.1093/Bioinformatics/Bts067  0.511
2012 Zhang W, Johnson N, Wu B, Kuang R. Signed network propagation for detecting differential gene expressions and DNA copy number variations 2012 Acm Conference On Bioinformatics, Computational Biology and Biomedicine, Bcb 2012. 337-344. DOI: 10.1145/2382936.2382979  0.328
2012 Tian Z, Zhang H, Kuang R. Sparse group selection on fused lasso components for identifying group-specific DNA copy number variations Proceedings - Ieee International Conference On Data Mining, Icdm. 665-674. DOI: 10.1109/ICDM.2012.35  0.489
2012 Xie M, Hwang T, Kuang R. Prioritizing disease genes by bi-random walk Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7301: 292-303. DOI: 10.1007/978-3-642-30220-6_25  0.311
2011 Hwang T, Zhang W, Xie M, Liu J, Kuang R. Inferring disease and gene set associations with rank coherence in networks. Bioinformatics (Oxford, England). 27: 2692-9. PMID 21824970 DOI: 10.1093/Bioinformatics/Btr463  0.591
2010 Tian Z, Kuang R. Integrative classification and analysis of multiple arrayCGH datasets with probe alignment. Bioinformatics (Oxford, England). 26: 2313-20. PMID 20660296 DOI: 10.1093/Bioinformatics/Btq428  0.547
2010 Hwang T, Kuang R. A heterogeneous label propagation algorithm for disease gene discovery Proceedings of the 10th Siam International Conference On Data Mining, Sdm 2010. 583-594.  0.304
2009 Tian Z, Hwang T, Kuang R. A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge. Bioinformatics (Oxford, England). 25: 2831-8. PMID 19648139 DOI: 10.1093/Bioinformatics/Btp467  0.671
2009 Kuang R, Gu J, Cai H, Wang Y. Improved prediction of malaria degradomes by supervised learning with SVM and profile kernel. Genetica. 136: 189-209. PMID 19057851 DOI: 10.1007/S10709-008-9336-9  0.345
2009 Tian Z, Hwang T, Kuang R. A hypergraph-based learning algorithm for classifying arraycgh data with spatial prior 2009 Ieee International Workshop On Genomic Signal Processing and Statistics, Gensips 2009. DOI: 10.1109/GENSIPS.2009.5174345  0.53
2008 Hwang T, Sicotte H, Tian Z, Wu B, Kocher JP, Wigle DA, Kumar V, Kuang R. Robust and efficient identification of biomarkers by classifying features on graphs. Bioinformatics (Oxford, England). 24: 2023-9. PMID 18653521 DOI: 10.1093/Bioinformatics/Btn383  0.645
2008 Hwang T, Tian Z, Kuang R, Kocher JP. Learning on weighted hypergraphs to integrate protein interactions and gene expressions for cancer outcome prediction Proceedings - Ieee International Conference On Data Mining, Icdm. 293-302. DOI: 10.1109/ICDM.2008.37  0.561
2007 Melvin I, Ie E, Kuang R, Weston J, Noble WS, Leslie C. SVM-Fold: A tool for discriminative multi-class protein fold and superfamily recognition Bmc Bioinformatics. 8. PMID 17570145 DOI: 10.1186/1471-2105-8-S4-S2  0.34
2006 Weston J, Kuang R, Leslie C, Noble WS. Protein ranking by semi-supervised network propagation. Bmc Bioinformatics. 7: S10. PMID 16723003 DOI: 10.1186/1471-2105-7-S1-S10  0.383
2005 Noble WS, Kuang R, Leslie C, Weston J. Identifying remote protein homologs by network propagation. The Febs Journal. 272: 5119-28. PMID 16218946 DOI: 10.1111/J.1742-4658.2005.04947.X  0.358
2005 Kuang R, Ie E, Wang K, Wang K, Siddiqi M, Freund Y, Leslie C. Profile-based string kernels for remote homology detection and motif extraction. Journal of Bioinformatics and Computational Biology. 3: 527-50. PMID 16108083 DOI: 10.1142/S021972000500120X  0.373
2005 Kuang R, Weston J, Noble WS, Leslie C. Motif-based protein ranking by network propagation. Bioinformatics (Oxford, England). 21: 3711-8. PMID 16076885 DOI: 10.1093/Bioinformatics/Bti608  0.37
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