Publications

69 entries « 1 of 2 »

2022

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

Detecting Spatially Co-expressed Gene Clusters with Functional Coherence by Graph-regularized Convolutional Neural Network Journal Article

In: Bioinformatics, 38 (5), pp. 1344–1352, 2022.

Links | BibTeX | Tags: Network-based Learning, Spatial Clustering, Spatial Transcriptomics

2021

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

Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion Journal Article

In: PLoS computational biology, 17 (4), pp. e1008218, 2021.

Links | BibTeX | Tags: Network-based Learning, Spatial Transcriptomics, Tensor Completion

Li, Zhuliu; Petegrosso, Raphael; Smith, Shaden; Sterling, David; Karypis, George; Kuang, Rui

Scalable Label Propagation for Multi-relational Learning on the Tensor Product of Graphs Journal Article

In: IEEE Transactions on Knowledge and Data Engineering, 2021.

Links | BibTeX | Tags: Multi-relational learning, Network-based Learning, Protein-Protein Interaction Network, Tensor Completion

2020

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

Platform-integrated mRNA Isoform Quantification Journal Article

In: Bioinformatics, 36 (8), pp. 2466–2473, 2020.

Links | BibTeX | Tags: Isoform Quantification

Petegrosso, Raphael; Song, Tianci; Kuang, Rui

Hierarchical Canonical Correlation Analysis Reveals Phenotype, Genotype, and Geoclimate Associations in Plants Journal Article

In: Plant Phenomics, 2020 (1969142), 2020.

Links | BibTeX | Tags: Phenome-genome Association

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

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

In: BMC Bioinformatics, 21 (272), 2020.

Links | BibTeX | Tags: Isoform Quantification

Roe, David; Kuang, Rui

Accurate and Efficient KIR Gene and Haplotype Inference from Genome Sequencing Reads with Novel K-mer Signatures Journal Article

In: Frontiers in immunology, 11 , pp. 3102, 2020.

Links | BibTeX | Tags: KIR Haplotype Inference

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

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

In: Frontiers in immunology, 11 , 2020.

Links | BibTeX | Tags: KIR Haplotype Inference

Roe, David; Williams, Jonathan; Ivery, Keyton; Brouckaert, Jenny; Downey, Nick; Locklear, Chad; Kuang, Rui; Maiers, Martin

Efficient Sequencing, Assembly, and Annotation of Human KIR Haplotypes Journal Article

In: Frontiers in immunology, 11 , 2020.

Links | BibTeX | Tags: KIR Haplotype Inference

2019

Li, Zhuliu; Zhang, Wei; Huang, R Stephanie; Kuang, Rui

Learning a Low-rank Tensor of Pharmacogenomic Multi-relations from Biomedical Networks Proceeding

IEEE International Conference on Data Mining 2019.

Abstract | Links | BibTeX | Tags: Multi-relational learning, Tensor Completion

Petegrosso, Raphael; Li, Zhuliu; Kuang, Rui

Machine Learning and Statistical Methods for Clustering Single-cell RNA-sequencing Data Journal Article

In: Briefings in Bioinformatics, 2019.

Abstract | Links | BibTeX | Tags: scRNA-Seq, scRNA-Seq Clustering

Song, Ying; Song, Tianci; Kuang, Rui

Path segmentation for movement trajectories with irregular sampling frequency using space-time interpolation and density-based spatial clustering Journal Article

In: Transactions in GIS, 23 (3), pp. 558–578, 2019.

Abstract | Links | BibTeX | Tags: Spatial Clustering

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

Scalable Remote Homology Detection and Fold Recognition in Massive Protein Networks Journal Article

In: PROTEINS: Structure, Function, and Bioinformatics, 87 (6), pp. 478-491, 2019.

Abstract | Links | BibTeX | Tags: Protein Remote Homology Detection

2018

Hauck, Amy K; Zhou, Tong; Hahn, Wendy S; Petegrosso, Raphael; Kuang, Rui; Chen, Yue; Bernlohr, David A

Obesity-Induced Protein Carbonylation In Murine Adipose Tissue Regulates The DNA Binding Domain Of Nuclear Zinc-Finger Proteins Journal Article

In: Journal of Biological Chemistry, 2018.

Abstract | Links | BibTeX | Tags:

Jae-Woong; Zhang Chang, Wei; Yeh; Yong, Jeongsik#

An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response Journal Article

In: Nucleic Acids Research, 46 (12), pp. P5996–6008, 2018.

Abstract | BibTeX | Tags: Transcriptome

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

HRB2 and BBX21 interaction modulates Arabidopsis ABI5 locus and stomatal aperture Journal Article

In: Plant, Cell & Environment, (41), pp. 1912-1925, 2018.

Abstract | Links | BibTeX | Tags:

Zhang, Huanan; Lee, Catherine A. A.; Li, Zhuliu; Garbe, John R.; Eide, Cindy R.; Petegrosso, Raphael; Kuang, Rui; Tolar, Jakub

A Multitask Clustering Approach for Single-cell RNA-Seq Analysis in Recessive Dystrophic Epidermolysis Bullosa Journal Article

In: PLOS Computational Biology, 14 (4), 2018.

Abstract | Links | BibTeX | Tags: Multitask learning, scRNA-Seq

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

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

In: npj Precision Oncology, 2018.

Abstract | Links | BibTeX | Tags:

2017

Zhang, Huanan; Roe, David; Kuang, Rui

Detecting Population-differentiation Copy Number Variants in Human Population Tree by Sparse Group Selection Journal Article

In: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16 (2), pp. 538 - 549, 2017.

Abstract | Links | BibTeX | Tags: DNA Copy Number Variation, Sparse Group Learning

Zhang, Wei; Chien, Jeremy; Yong, Jeongsik; Kuang, Rui

Network-based Machine Learning and Graph Theory Algorithms for Precision Oncology Journal Article

In: NPJ Precision Oncology, (25), 2017.

Abstract | Links | BibTeX | Tags: Cancer Genomics, Network-based Learning, Phenome-genome Association, Protein-Protein Interaction Network, Semi-supervised Learning

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

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

In: The Plant Journal, 91 (1), pp. 158-171, 2017.

Abstract | Links | BibTeX | Tags:

Roe, David; Vierra-Green, Cynthia; Pyo, C-W; Eng, K; Hall, R; Kuang, Rui; Spellman, Stephen; Ranade, S; Geraghty, D E; Maiers, Martin

Revealing complete complex KIR haplotypes phased by long-read sequencing technology Journal Article

In: Genes Immunity, 1-8 , 2017.

Abstract | Links | BibTeX | Tags: KIR Haplotype Inference

2016

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

Transfer Learning across Ontologies for Phenome-Genome Association Prediction Journal Article

In: Bioinformatics, 33 (4), pp. 529-536, 2016.

Abstract | Links | BibTeX | Tags: Phenome-genome Association, Semi-supervised Learning, Transfer Learning

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

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

In: PloS one, 11 (10), pp. e0163973, 2016.

Abstract | Links | BibTeX | Tags: KIR Haplotype Inference

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

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

In: PloS one, 11 (6), pp. e0156839–e0156839, 2016.

Abstract | Links | BibTeX | Tags: Gene Expression, Transcriptome

2015

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

Network-based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis Journal Article

In: PLoS Computational Biology, e1004465 , 2015.

Abstract | Links | BibTeX | Tags: Cancer Genomics, Isoform Quantification, Network-based Learning

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; others,

mRNA 3'-UTR shortening is a molecular signature of mTORC1 activation Journal Article

In: Nature communications, 6 , 2015.

Abstract | Links | BibTeX | Tags:

Xie, MaoQiang; Xu, YingJie; Zhang, YaoGong; Hwang, TaeHyun; Kuang, Rui

Network-based Phenome-Genome Association Prediction by Bi-Random Walk Journal Article

In: PloS one, 10 (5), pp. e0125138, 2015.

Abstract | Links | BibTeX | Tags: Phenome-genome Association, Semi-supervised Learning

Chien, Jeremy; Sicotte, Hugues; Fan, Jian-Bing; Humphray, Sean; Cunningham, Julie M; Kalli, Kimberly R; Oberg, Ann L; Hart, Steven N; Li, Ying; Davila, Jaime I; others,

TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer Journal Article

In: Nucleic acids research, pp. gkv111, 2015.

Abstract | Links | BibTeX | Tags: Cancer Genomics

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

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

In: BMC bioinformatics, 16 (1), pp. 1, 2015, ISSN: 1471-2105.

Abstract | Links | BibTeX | Tags: Cancer Genomics, DNA Copy Number Variation

Sharma, Ankit; Kuang, Rui; Srivastava, Jaideep; Feng, Xiaodong; Singhal, Kartik

Predicting small group accretion in social networks: A topology based incremental approach Inproceedings

In: 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), pp. 408–415, IEEE 2015, ISBN: 978-1-4503-3854-7/15/08.

Abstract | Links | BibTeX | Tags: Semi-supervised Learning

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

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

In: BMC systems biology, 9 (4), pp. 1, 2015.

BibTeX | Tags: Network Alignment, Protein-Protein Interaction Network

2013

Zhang, Huanan; Tian, Ze; Kuang, Rui

Transfer learning across cancers on DNA copy number variation analysis Inproceedings

In: 2013 IEEE 13th International Conference on Data Mining, pp. 1283–1288, IEEE IEEE, 2013, ISBN: 978-0-7695-5108-1.

Abstract | Links | BibTeX | Tags: Cancer Genomics, DNA Copy Number Variation, Transfer Learning

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

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

In: BMC bioinformatics, 14 (12), pp. 1, 2013, ISSN: 1471-2105.

Abstract | Links | BibTeX | Tags: Network Alignment

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

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

In: Frontiers in oncology, 3 , pp. 251, 2013.

Abstract | Links | BibTeX | Tags: Cancer Genomics

Hwang, TaeHyun; Atluri, Gowtham; Kuang, Rui; Kumar, Vipin; Starr, Timothy; Silverstein, Kevin AT; Haverty, Peter M; Zhang, Zemin; Liu, Jinfeng

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

In: BMC genomics, 14 (1), pp. 440, 2013.

Abstract | Links | BibTeX | Tags: Cancer Genomics, DNA Copy Number Variation, Network-based Learning

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

Network-based survival analysis reveals subnetwork signatures for predicting outcomes of ovarian cancer treatment Journal Article

In: PLoS Comput Biol, 9 (3), pp. e1002975, 2013.

Abstract | Links | BibTeX | Tags: Cancer Genomics, Network-based Learning, Survival Analysis, Transcriptome

2012

Tian, Ze; Zhang, Huanan; Kuang, Rui

Sparse group selection on fused lasso components for identifying group-specific DNA copy number variations Inproceedings

In: 2012 IEEE 12th International Conference on Data Mining, pp. 665–674, IEEE IEEE, 2012, ISBN: 978-1-4673-4649-8.

Abstract | Links | BibTeX | Tags: DNA Copy Number Variation, Sparse Group Learning

Zhang, Wei; Johnson, Nicholas; Wu, Baolin; Kuang, Rui

Signed network propagation for detecting differential gene expressions and DNA copy number variations Inproceedings

In: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, pp. 337–344, ACM 2012.

Abstract | Links | BibTeX | Tags: DNA Copy Number Variation, Gene Expression, Semi-supervised Learning

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

Co-clustering phenome--genome for phenotype classification and disease gene discovery Journal Article

In: Nucleic acids research, 40 (19), pp. e146–e146, 2012.

Abstract | Links | BibTeX | Tags: Network-based Learning, Phenome-genome Association, Semi-supervised Learning

Xie, Maoqiang; Hwang, Taehyun; Kuang, Rui

Prioritizing disease genes by bi-random walk Inproceedings

In: Pacific-Asia Conference on Knowledge Discovery and Data Mining, pp. 292–303, Springer 2012.

Abstract | Links | BibTeX | Tags: Phenome-genome Association, Semi-supervised Learning

Tian, Ze; Kuang, Rui

Global Linear Neighborhoods for Efficient Label Propagation. Inproceedings

In: SDM, pp. 863–872, SIAM 2012, ISBN: 978-1-61197-232-0.

Abstract | Links | BibTeX | Tags: Semi-supervised Learning

2011

Cai, Hong; Kuang, Rui; Gu, Jianying; Wang, Yufeng

Proteases in malaria parasites-a phylogenomic perspective Journal Article

In: Current genomics, 12 (6), pp. 417–427, 2011.

Abstract | Links | BibTeX | Tags:

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

Inferring disease and gene set associations with rank coherence in networks Journal Article

In: Bioinformatics, 27 (19), pp. 2692–2699, 2011.

Abstract | Links | BibTeX | Tags: Phenome-genome Association, Semi-supervised Learning

Jacko, Julie A; Johnson, Layne M; Adam, Terrence J; Ali, Adel L; Chan, Daniel; Kuang, Rui; Nelson, Andrew F; Watters, Amy; Westra, Bonnie; Fauchald, Sally; others,

Community engagement and outreach as curricular and pedagogical tools for consortial delivery of health informatics curricula Journal Article

In: International Journal of Information and Operations Management Education, 4 (3-4), pp. 284–308, 2011, ISSN: 1744-2311.

Abstract | Links | BibTeX | Tags:

2010

Zhang, Wei; Hwang, Baryun; Wu, Baolin; Kuang, Rui

Network propagation models for gene selection Inproceedings

In: 2010 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), IEEE, 2010, ISBN: 978-1-61284-791-7.

Abstract | Links | BibTeX | Tags: Cancer Genomics, Gene Expression, Semi-supervised Learning

Tian, Ze; Kuang, Rui

Integrative classification and analysis of multiple arrayCGH datasets with probe alignment Journal Article

In: Bioinformatics, 26 (18), pp. 2313–2320, 2010, ISSN: 1460-2059.

Abstract | Links | BibTeX | Tags: DNA Copy Number Variation, Kernel Method

Hwang, TaeHyun; Kuang, Rui

A Heterogeneous Label Propagation Algorithm for Disease Gene Discovery Inproceedings

In: Society for Industrial and Applied Mathematics. Proceedings of the SIAM International Conference on Data Mining, pp. 583, Society for Industrial and Applied Mathematics 2010.

Abstract | Links | BibTeX | Tags: Phenome-genome Association, Semi-supervised Learning

Fang, Gang; Kuang, Rui; Pandey, Gaurav; Steinbach, Michael; Myers, Chad L; Kumar, Vipin

Subspace differential coexpression analysis: problem definition and a general approach. Inproceedings

In: Pacific symposium on biocomputing, pp. 145–56, 2010.

Abstract | Links | BibTeX | Tags: Gene Expression, Transcriptome

Jacko, Julie A.; Adam, Terrence; Westra, Bonnie; Witrak, Marty; Berkeland, Ron; Nelson, Andrew F.; Ali, Adel L.; Johnson, Layne; Kuang, Rui; LaTour, Kathy; Potthoff, Sandra; Watters, Amy

Launching: university partnership for health informatics Inproceedings

In: Proceedings of the 1st ACM International Health Informatics Symposium, ACM 2010, ISBN: 978-1-4503-0030-8.

Abstract | Links | BibTeX | Tags:

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