Rui Kuang - Publications

Computer Science University of Minnesota, Twin Cities, Minneapolis, MN 
Computer Science, Bioinformatics Biology

46 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
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  0.56
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  0.56
2018 Hauck AK, Zhou T, Hahn WS, Petegrosso R, Kuang R, Chen Y, Bernlohr DA. Obesity-Induced Protein Carbonylation In Murine Adipose Tissue Regulates The DNA Binding Domain Of Nuclear Zinc-Finger Proteins. The Journal of Biological Chemistry. PMID 30012885 DOI: 10.1074/jbc.RA118.003469  0.56
2018 Xiang X, Wang Y, Zhang H, Piao J, Muthusamy S, Wang L, Deng Y, Zhang W, Kuang R, Billadeau DD, Huang S, Lai J, Urrutia R, Kang N. Vasodilator-stimulated phosphoprotein promotes liver metastasis of gastrointestinal cancer by activating a β1-integrin-FAK-YAP1/TAZ signaling pathway. Npj Precision Oncology. 2: 2. PMID 29872721 DOI: 10.1038/s41698-017-0045-7  0.56
2018 Kang X, Xu G, Lee B, Chen C, Zhang H, Kuang R, Ni M. HRB2 and BBX21 interaction modulates Arabidopsis ABI5 locus and stomatal aperture. Plant, Cell & Environment. PMID 29748960 DOI: 10.1111/pce.13336  0.56
2018 Zhang H, Lee CAA, Li Z, Garbe JR, Eide CR, Petegrosso R, Kuang R, Tolar J. A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa. Plos Computational Biology. 14: e1006053. PMID 29630593 DOI: 10.1371/journal.pcbi.1006053  0.56
2017 Zhang H, Roe D, Kuang R. Detecting Population-differentiation Copy Number Variants in Human Population Tree by Sparse Group Selection. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 29990238 DOI: 10.1109/TCBB.2017.2779481  0.56
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  0.56
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  0.56
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  0.96
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  0.96
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  0.96
2015 Chien J, Sicotte H, Fan JB, Humphray S, Cunningham JM, Kalli KR, Oberg AL, Hart SN, Li Y, Davila JI, Baheti S, Wang C, Dietmann S, Atkinson EJ, Asmann YW, ... ... Kuang R, et al. TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer. Nucleic Acids Research. PMID 25916844 DOI: 10.1093/nar/gkv111  0.96
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  0.96
2015 Sharma A, Kuang R, Srivastava J, Feng X, Singhal K. Predicting small group accretion in social networks: A topology based incremental approach Proceedings of the 2015 Ieee/Acm International Conference On Advances in Social Networks Analysis and Mining, Asonam 2015. 408-415. DOI: 10.1145/2808797.2808914  0.96
2013 Chien J, Kuang R, Landen C, Shridhar V. Platinum-sensitive recurrence in ovarian cancer: the role of tumor microenvironment. Frontiers in Oncology. 3: 251. PMID 24069583 DOI: 10.3389/fonc.2013.00251  0.96
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  0.96
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  0.96
2013 Zhang H, Tian Z, Kuang R. Transfer learning across cancers on DNA copy number variation analysis Proceedings - Ieee International Conference On Data Mining, Icdm. 1283-1288. DOI: 10.1109/ICDM.2013.58  0.96
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  0.6
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  0.96
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  0.96
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  0.96
2012 Tian Z, Kuang R. Global linear neighborhoods for efficient label propagation Proceedings of the 12th Siam International Conference On Data Mining, Sdm 2012. 863-872.  0.96
2011 Cai H, Kuang R, Gu J, Wang Y. Proteases in malaria parasites - a phylogenomic perspective. Current Genomics. 12: 417-27. PMID 22379395 DOI: 10.2174/138920211797248565  0.96
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  0.96
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  0.96
2010 Fang G, Kuang R, Pandey G, Steinbach M, Myers CL, Kumar V. Subspace differential coexpression analysis: problem definition and a general approach. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 145-56. PMID 19908367  0.96
2010 Zhang W, Hwang B, Wu B, Kuang R. Network propagation models for gene selection 2010 Ieee International Workshop On Genomic Signal Processing and Statistics, Gensips 2010. DOI: 10.1109/GENSIPS.2010.5719689  0.96
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.  0.96
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  0.96
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  0.96
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  0.96
2009 Ngo T, Kuang R. Partial profile alignment kernels for protein classification 2009 Ieee International Workshop On Genomic Signal Processing and Statistics, Gensips 2009. DOI: 10.1109/GENSIPS.2009.5174328  0.96
2009 Min R, Kuang R, Bonner A, Zhang Z. Learning random-walk kernels for protein remote homology identification and motif discovery Society For Industrial and Applied Mathematics - 9th Siam International Conference On Data Mining 2009, Proceedings in Applied Mathematics. 1: 132-143.  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
2004 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. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 152-60. PMID 16448009  0.96
2004 Kuang R, Leslie CS, Yang AS. Protein backbone angle prediction with machine learning approaches. Bioinformatics (Oxford, England). 20: 1612-21. PMID 14988121 DOI: 10.1093/bioinformatics/bth136  0.96
2004 Leslie C, Kuang R. Fast string kernels using inexact matching for protein sequences Journal of Machine Learning Research. 5: 1435-1455.  0.96
2003 Leslie C, Kuang R. Fast kernels for inexact string matching Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science). 2777: 114-128.  0.96
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