Fast Kernels for Inexact String Matching. - Christina S. Leslie; Rui Kuang (COLT, 2003)

Profile-Based String Kernels for Remote Homology Detection and Motif Extraction. - Rui Kuang; Eugene Ie; Ke Wang; Kai Wang; Mahira Siddiqi; Yoav Freund; Christina S. Leslie (CSB, 2004)

Protein backbone angle prediction with machine learning approaches. - Rui Kuang; Christina S. Leslie; An-Suei Yang (Bioinform., 2004)

Fast String Kernels using Inexact Matching for Protein Sequences. - Christina S. Leslie; Rui Kuang (J. Mach. Learn. Res., 2004)

Motif-based protein ranking by network propagation. - Rui Kuang; Jason Weston; William Stafford Noble; Christina S. Leslie (Bioinform., 2005)

Protein Ranking by Semi-Supervised Network Propagation. - Jason Weston; Rui Kuang; Christina S. Leslie; William Stafford Noble (BMC Bioinform., 2006)

SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition. - Iain Melvin; Eugene Ie; Rui Kuang; Jason Weston; William Stafford Noble; Christina S. Leslie (BMC Bioinform., 2007)

Learning on Weighted Hypergraphs to Integrate Protein Interactions and Gene Expressions for Cancer Outcome Prediction. - TaeHyun Hwang; Ze Tian; Rui Kuang; Jean-Pierre A. Kocher (ICDM, 2008)

Robust and efficient identification of biomarkers by classifying features on graphs. - TaeHyun Hwang; Hugues Sicotte; Ze Tian; Baolin Wu; Jean-Pierre A. Kocher; Dennis A. Wigle; Vipin Kumar 001; Rui Kuang (Bioinform., 2008)

Partial profile alignment kernels for protein classification. - Thanh T. Ngo; Rui Kuang (GENSiPS, 2009)

A hypergraph-based learning algorithm for classifying arraycgh data with spatial prior. - Ze Tian; TaeHyun Hwang; Rui Kuang (GENSiPS, 2009)

Learning Random-Walk Kernels for Protein Remote Homology Identification and Motif Discovery. - Martin Renqiang Min; Rui Kuang; Anthony J. Bonner; Zhaolei Zhang (SDM, 2009)

A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge. - Ze Tian; TaeHyun Hwang; Rui Kuang (Bioinform., 2009)

Integrative Biomarker Discovery for Breast Cancer Metastasis from Gene Expression and Protein Interaction Data Using Error-tolerant Pattern Mining. - Rohit Gupta 003; Smita Agrawal; Navneet Rao; Ze Tian; Rui Kuang; Vipin Kumar 001 (BICoB, 2010)

Network propagation models for gene selection. - Wei Zhang 076; Baryun Hwang; Baolin Wu; Rui Kuang (GENSiPS, 2010)

Launching: university partnership for health informatics. - Julie A. Jacko; Terrence Adam; Bonnie L. Westra; Marty Witrak; Ron Berkeland; Andrew F. Nelson; Adel L. Ali; Layne Johnson; Rui Kuang; Kathy LaTour; Sandra J. Potthoff; Amy Watters (IHI, 2010)

Subspace Differential Coexpression Analysis: Problem Definition and a General Approach. - Gang Fang; Rui Kuang; Gaurav Pandey 002; Michael S. Steinbach; Chad L. Myers; Vipin Kumar 001 (Pacific Symposium on Biocomputing, 2010)

A Heterogeneous Label Propagation Algorithm for Disease Gene Discovery. - TaeHyun Hwang; Rui Kuang (SDM, 2010)

Integrative classification and analysis of multiple arrayCGH datasets with probe alignment. - Ze Tian; Rui Kuang (Bioinform., 2010)

Inferring disease and gene set associations with rank coherence in networks. - TaeHyun Hwang; Wei Zhang 076; Maoqiang Xie; Jinfeng Liu 003; Rui Kuang (Bioinform., 2011)

Inferring Disease and Gene Set Associations with Rank Coherence in Networks - TaeHyun Hwang; Wei Zhang 076; Maoqiang Xie; Rui Kuang (CoRR, 2011)

Approximate subspace pattern mining for mapping copy-number variations. - Nicholas Johnson 001; Gang Fang; Rui Kuang (BCB, 2012)

Signed network propagation for detecting differential gene expressions and DNA copy number variations. - Wei Zhang 076; Nicholas Johnson 001; Baolin Wu; Rui Kuang (BCB, 2012)

Prediction of novel systems components in cell cycle regulation in malaria parasite by subnetwork alignments. - Hong Cai; Changjin Hong; Jianying Gu; Timothy G. Lilburn; Rui Kuang; Yufeng Wang 002 (BIBM, 2012)

Sparse Group Selection on Fused Lasso Components for Identifying Group-Specific DNA Copy Number Variations. - Ze Tian; Huanan Zhang; Rui Kuang (ICDM, 2012)

Prioritizing Disease Genes by Bi-Random Walk. - Maoqiang Xie; TaeHyun Hwang; Rui Kuang (PAKDD (2), 2012)

Global Linear Neighborhoods for Efficient Label Propagation. - Ze Tian; Rui Kuang (SDM, 2012)

Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum. - Hong Cai; Changjin Hong; Jianying Gu; Timothy G. Lilburn; Rui Kuang; Yufeng Wang 002 (BMC Syst. Biol., 2012)

Transfer Learning across Cancers on DNA Copy Number Variation Analysis. - Huanan Zhang; Ze Tian; Rui Kuang (ICDM, 2013)

A novel subnetwork alignment approach predicts new components of the cell cycle regulatory apparatus in Plasmodium falciparum. - Hong Cai; Changjin Hong; Timothy G. Lilburn; Armando L. Rodriguez; Sheng Chen; Jianying Gu; Rui Kuang; Yufeng Wang 002 (BMC Bioinform., 2013)

Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment. - Wei Zhang 076; Takayo Ota; Viji Shridhar; Jeremy Chien; Baolin Wu; Rui Kuang (PLoS Comput. Biol., 2013)

Network-based Transcript Quantification with RNA-Seq Data. - Wei Zhang 076; Kay Minn; Lilong Lin; Baolin Wu; Jeremy Chien; Hui Zheng; Rui Kuang (CoRR, 2014)

Predicting Small Group Accretion in Social Networks: A topology based incremental approach. - Ankit Sharma 004; Rui Kuang; Jaideep Srivastava; Xiaodong Feng 001; Kartik Singhal 001 (ASONAM, 2015)

SubPatCNV: approximate subspace pattern mining for mapping copy-number variations. - Nicholas Johnson 001; Huanan Zhang; Gang Fang; Vipin Kumar 001; Rui Kuang (BMC Bioinform., 2015)

Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments. - Hong Cai; Timothy G. Lilburn; Changjin Hong; Jianying Gu; Rui Kuang; Yufeng Wang 002 (BMC Syst. Biol., 2015)

Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis. - Wei Zhang 076; Jae-Woong Chang; Lilong Lin; Kay Minn; Baolin Wu; Jeremy Chien; Jeongsik Yong; Hui Zheng; Rui Kuang (PLoS Comput. Biol., 2015)

Dropout Prediction in Home Care Training. - Wenjun Zeng 001; Si-Chi Chin; Brenda Zeimet; Rui Kuang; Chih-Lin Chi (EDM, 2017)

Transfer learning across ontologies for phenome-genome association prediction. - Raphael Petegrosso; Sunho Park; TaeHyun Hwang; Rui Kuang (Bioinform., 2017)

Low-rank Label Propagation for Semi-supervised Learning with 100 Millions Samples. - Raphael Petegrosso; Wei Zhang 076; Zhuliu Li; Yousef Saad; Rui Kuang (CoRR, 2017)

Scalable Label Propagation for Multi-relational Learning on Tensor Product Graph. - Zhuliu Li; Raphael Petegrosso; Shaden Smith; David Sterling; George Karypis; Rui Kuang (CoRR, 2018)

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa. - Huanan Zhang; Catherine A. A. Lee; Zhuliu Li; John R. Garbe; Cindy R. Eide; Raphael Petegrosso; Rui Kuang; Jakub Tolar (PLoS Comput. Biol., 2018)

Learning a Low-Rank Tensor of Pharmacogenomic Multi-relations from Biomedical Networks. - Zhuliu Li; Wei Zhang 076; Rong Stephanie Huang; Rui Kuang (ICDM, 2019)

Detecting Population-Differentiation Copy Number Variants in Human Population Tree by Sparse Group Selection. - Huanan Zhang; David Roe; Rui Kuang (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Path segmentation for movement trajectories with irregular sampling frequency using space-time interpolation and density-based spatial clustering. - Ying Song; Tianci Song; Rui Kuang (Trans. GIS, 2019)

Machine learning and statistical methods for clustering single-cell RNA-sequencing data. - Raphael Petegrosso; Zhuliu Li; Rui Kuang (Briefings Bioinform., 2020)

Platform-integrated mRNA isoform quantification. - Jiao Sun; Jae-Woong Chang; Teng Zhang 002; Jeongsik Yong; Rui Kuang; Wei Zhang 076 (Bioinform., 2020)

QCA-based Hamming code circuit for nano communication network. - Jianhong Huang; Guangjun Xie; Rui Kuang; Feifei Deng; Yongqiang Zhang 006 (Microprocess. Microsystems, 2021)

Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion. - Zhuliu Li; Tianci Song; Jeongsik Yong; Rui Kuang (PLoS Comput. Biol., 2021)

Spars: A Full Flow Quantum-Dot Cellular Automata Circuit Design Tool. - Fei Peng; Yongqiang Zhang 006; Rui Kuang; Guangjun Xie (IEEE Trans. Circuits Syst. II Express Briefs, 2021)

Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network. - Tianci Song; Kathleen K. Markham; Zhuliu Li; Kristen E. Muller; Kathleen Greenham; Rui Kuang (Bioinform., 2022)

Scalable Label Propagation for Multi-Relational Learning on the Tensor Product of Graphs. - Zhuliu Li; Raphael Petegrosso; Shaden Smith; David Sterling; George Karypis; Rui Kuang (IEEE Trans. Knowl. Data Eng., 2022)

Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition. - Charles Broadbent; Tianci Song; Rui Kuang (Bioinform., 2024)

Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs. - Tianci Song; Eric Cosatto; Gaoyuan Wang; Rui Kuang; Mark Gerstein; Martin Renqiang Min; Jonathan Warrell (Bioinform., 2024)

Orchard: Building large cancer phylogenies using stochastic combinatorial search. - Ethan Kulman; Rui Kuang; Quaid Morris (PLoS Comput. Biol., 2024)