R. Kuang

发表

Profile-based string kernels for remote homology detection and motif extraction.

Y. Freund, C. Leslie, C. Leslie, 2005, Journal of bioinformatics and computational biology.

Fast String Kernels using Inexact Matching for Protein Sequences

Christina S. Leslie, Rui Kuang, C. Leslie, 2004, J. Mach. Learn. Res..

Scalable remote homology detection and fold recognition in massive protein networks

Yousef Saad, Wei Zhang, Rui Kuang, 2019, Proteins.

Identifying remote protein homologs by network propagation

William Stafford Noble, J. Weston, C. Leslie, 2005, The FEBS journal.

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

Vipin Kumar, R. Kuang, Sanjoy Dey, 2012, Nucleic acids research.

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

Vipin Kumar, R. Kuang, Zemin Zhang, 2013, BMC Genomics.

Protein Ranking by Semi-Supervised Network Propagation

Jason Weston, William Stafford Noble, Christina S. Leslie, 2006, BMC Bioinformatics.

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

R. Kuang, TaeHyun Hwang, Maoqiang Xie, 2015, PloS one.

Retraction. Reconstructing disease phenome-genome association by bi-random walk.

R. Kuang, TaeHyun Hwang, Maoqiang Xie, 2012, Bioinformatics.

TR 13-023 Reconstructing Disease Phenome-genome Association by Bi-Random Walk

R. Kuang, TaeHyun Hwang, Maoqiang Xie, 2013 .

Learning Random-Walk Kernels for Protein Remote Homology Identification and Motif Discovery

Zhaolei Zhang, Martin Renqiang Min, Anthony J. Bonner, 2009, SDM.

Platinum-Sensitive Recurrence in Ovarian Cancer: The Role of Tumor Microenvironment

R. Kuang, J. Chien, C. Landen, 2013, Front. Oncol..

Improved prediction of malaria degradomes by supervised learning with SVM and profile kernel

Rui Kuang, Jianying Gu, Yufeng Wang, 2009, Genetica.

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

R. Kuang, Lei Wang, R. Urrutia, 2018, npj Precision Oncology.

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

Rui Kuang, Raphael Petegrosso, Zhuliu Li, 2019, Briefings Bioinform..

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

S. Ranade, R. Kuang, K. Eng, 2017, Genes and Immunity.

Identifying Clinical and Genetic Markers of Human Disease by Classifying Features on Graphs

Vipin Kumar, R. Kuang, J. Kocher, 2007 .

Model based clustering analysis of 16 S rRNA sequence

Baolin Wu, R. Kuang, Wei Zhang, 2013 .

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

R. Kuang, Zhuliu Li, Tianci Song, 2021, Bioinform..

Proteases in Malaria Parasites - A Phylogenomic Perspective

R. Kuang, Hong Cai, Yufeng Wang, 2011, Current genomics.

Machine Learning with Objective Serum Markers and Algorithmic Deep Learning CT Scan Analysis Predicts Brain Death Due to Trauma and Hypoxia

Tory M. Schaaf, R. Kuang, M. Koller, 2021 .

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

D. Bentley, R. K. Cheetham, S. Humphray, 2015, Nucleic acids research.

Efficient Sequencing, Assembly, and Annotation of Human KIR Haplotypes

R. Kuang, M. Maiers, J. Brouckaert, 2020, Frontiers in immunology.

Efficient Sequencing, Assembly, and Annotation of Human KIR Haplotypes

R. Kuang, M. Maiers, J. Brouckaert, 2020, bioRxiv.

Inferring protein structure with discriminative learning and network diffusion

C. Leslie, R. Kuang, 2006 .

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

R. Kuang, J. Yong, Raphael Petegrosso, 2019, BMC Genomics.

Low-rank Label Propagation for Semi-supervised Learning with 100 Millions Samples pdf

Yousef Saad, Wei Zhang, Rui Kuang, 2017, ArXiv.

A Heterogeneous Label Propagation Algorithm for Disease Gene Discovery

TaeHyun Hwang, Rui Kuang, R. Kuang, 2010, SDM.

Network-based machine learning and graph theory algorithms for precision oncology

Wei Zhang, Jeremy Chien, Jeongsik Yong, 2017, npj Precision Oncology.

A hypergraph-based learning algorithm for classifying arraycgh data with spatial prior

TaeHyun Hwang, Rui Kuang, Ze Tian, 2009, 2009 IEEE International Workshop on Genomic Signal Processing and Statistics.

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

Wei Zhang, Rui Kuang, Zhuliu Li, 2019, 2019 IEEE International Conference on Data Mining (ICDM).

TP 53 mutations , tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer

Julie, D. Bentley, R. K. Cheetham, 2015 .

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa

John R. Garbe, Rui Kuang, Huanan Zhang, 2018, PLoS Comput. Biol..

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

Jeongsik Yong, Rui Kuang, Tianci Song, 2020, bioRxiv.

Meta-Analysis of EMT Datasets Reveals Different Types of EMT

Xiao Yang, Rui Kuang, Wei Zhang, 2016, PloS one.

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

Yufeng Wang, Hong Cai, Rui Kuang, 2015, BMC Systems Biology.

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

Yufeng Wang, Hong Cai, Sheng Chen, 2013, BMC Bioinformatics.

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

Yufeng Wang, Hong Cai, Rui Kuang, 2012, BMC Systems Biology.

Integrative Biomarker Discovery for Breast Cancer Metastasis from Gene Expression and Protein Interaction Data Using Error-tolerant Pattern Mining

Vipin Kumar, Rui Kuang, Navneet Rao, 2010, BICoB.

Inferring disease and gene set associations with rank coherence in networks

TaeHyun Hwang, Wei Zhang, Maoqiang Xie, 2011, Bioinform..

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

Baolin Wu, Wei Zhang, Jeremy Chien, 2013, PLoS Comput. Biol..

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

Vipin Kumar, Gang Fang, Nicholas Johnson, 2015, BMC Bioinformatics.

Predicting KIR Structural Haplotypes with Novel Sequence Signatures from Short-read Whole Genome Sequencing

R. Kuang, D. Roe, 2019, bioRxiv.

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

R. Kuang, Xiaowu Wang, Feng Cheng, 2017, The Plant journal : for cell and molecular biology.

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

TaeHyun Hwang, Rui Kuang, Ze Tian, 2009, Bioinform..

Learning on Weighted Hypergraphs to Integrate Protein Interactions and Gene Expressions for Cancer Outcome Prediction

TaeHyun Hwang, Jean-Pierre A. Kocher, Rui Kuang, 2008, 2008 Eighth IEEE International Conference on Data Mining.

Sparse Group Selection on Fused Lasso Components for Identifying Group-Specific DNA Copy Number Variations

Rui Kuang, Huanan Zhang, Ze Tian, 2012, 2012 IEEE 12th International Conference on Data Mining.

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

Jae-Woong Chang, Rui Kuang, Jeongsik Yong, 2015, Nature Communications.

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

R. Kuang, M. Maiers, D. Geraghty, 2020, bioRxiv.

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

R. Kuang, D. Roe, 2019, Frontiers in Immunology.

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

R. Kuang, J. Trowsdale, M. Maiers, 2016, PloS one.

Obesity-induced protein carbonylation in murine adipose tissue regulates the DNA-binding domain of nuclear zinc finger proteins

R. Kuang, Raphael Petegrosso, D. Bernlohr, 2018, The Journal of Biological Chemistry.

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

Luke H. Hoeppner, R. Kuang, A. Mansfield, 2018, Communications Biology.

DARPP-32 and t-DARPP promote lung cancer growth through IKKα-dependent cell migration and Akt/Erk-mediated cell survival

Luke H. Hoeppner, R. Kuang, A. Mansfield, 2017, bioRxiv.

Platform-integrated mRNA isoform quantification

Jeongsik Yong, Rui Kuang, Wei Zhang, 2019, Bioinform..

Gene expression Platform-integrated mRNA isoform quantification

R. Kuang, J. Yong, Wei Zhang, 2020 .

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

R. Kuang, M. Ni, B. Lee, 2018, Plant, cell & environment.

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

Jae-Woong Chang, Rui Kuang, Jeongsik Yong, 2018, Nucleic acids research.

mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control

R. Kuang, J. Yong, Wei Zhang, 2019, Nucleic acids research.

Protein backbone angle prediction with machine learning approaches

An-Suei Yang, Christina S. Leslie, Rui Kuang, 2004, Bioinform..

Prioritizing Disease Genes by Bi-Random Walk

Maoqiang Xie, TaeHyun Hwang, Rui Kuang, 2012, PAKDD.

Profile-based string kernels for remote homology detection and motif extraction

Ke Wang, Kai Wang, Yoav Freund, 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

Fast Kernels for Inexact String Matching

Christina S. Leslie, Rui Kuang, C. Leslie, 2003, COLT.

Subspace Differential Coexpression Analysis: Problem Definition and a General Approach

Vipin Kumar, Michael S. Steinbach, Gang Fang, 2010, Pacific Symposium on Biocomputing.

Robust and efficient identification of biomarkers by classifying features on graphs

Vipin Kumar, Baolin Wu, TaeHyun Hwang, 2008, Bioinform..

Integrative classification and analysis of multiple arrayCGH datasets with probe alignment

Rui Kuang, Ze Tian, R. Kuang, 2010, Bioinform..

SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition

Jason Weston, William Stafford Noble, Christina S. Leslie, 2007, BMC Bioinformatics.

Launching: university partnership for health informatics

Bonnie L. Westra, Terrence Adam, Julie A. Jacko, 2010, IHI.

Detecting Population-Differentiation Copy Number Variants in Human Population Tree by Sparse Group Selection

Rui Kuang, Huanan Zhang, David Roe, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Transfer Learning across Cancers on DNA Copy Number Variation Analysis

Rui Kuang, Huanan Zhang, Ze Tian, 2013, 2013 IEEE 13th International Conference on Data Mining.

Scalable Label Propagation for Multi-Relational Learning on the Tensor Product of Graphs

George Karypis, Rui Kuang, Raphael Petegrosso, 2021, IEEE Transactions on Knowledge and Data Engineering.

Prediction of novel systems components in cell cycle regulation in malaria parasite by subnetwork alignments

Yufeng Wang, Hong Cai, Rui Kuang, 2012, 2012 IEEE International Conference on Bioinformatics and Biomedicine.

Global Linear Neighborhoods for Efficient Label Propagation

Rui Kuang, Ze Tian, R. Kuang, 2012, SDM.

Scalable Label Propagation for Multi-relational Learning on Tensor Product Graph pdf

George Karypis, Shaden Smith, Rui Kuang, 2018, ArXiv.

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

Luke H. Hoeppner, R. Kuang, A. Mansfield, 2018, Communications Biology.

FIST-nD: A tool for n-dimensional spatial transcriptomics data imputation via graph-regularized tensor completion

R. Kuang, Tianci Song, Thomas Karl Atkins, 2023, bioRxiv.

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

Baolin Wu, Nicholas Johnson, Wei Zhang, 2012, BCB.

Network-based Transcript Quantification with RNA-Seq Data

Baolin Wu, R. Kuang, Wei Zhang, 2014, ArXiv.

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

Baolin Wu, Hui Zheng, Wei Zhang, 2014, PLoS Comput. Biol..

A Heterogeneous Label Propagation Algorithm for Disease Gene Discovery

R. Kuang, TaeHyun Hwang, 2010, SDM.

Transfer learning across ontologies for phenome‐genome association prediction

Sunho Park, TaeHyun Hwang, Rui Kuang, 2016, Bioinform..

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

R. Kuang, Raphael Petegrosso, Tianci Song, 2020, Plant phenomics.

Inferring disease and gene set associations with rank coherence in networks

R. Kuang, Wei Zhang, TaeHyun Hwang, 2011, Bioinform..

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

Jaideep Srivastava, Ankit Sharma, Rui Kuang, 2015, 2015 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM).

SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition

William Stafford Noble, J. Weston, C. Leslie, 2007, BMC Bioinformatics.