Publications

64 entries « 1 of 3 »

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: Geoclimate, 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

2019

Li, Zhuliu; Zhang, Wei; Huang, Stephanie R; 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: Tensor

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: Path Segmentation, 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: Fold Recognition, Protein Networks, 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 Forthcoming

In: Journal of Biological Chemistry, Forthcoming.

Abstract | Links | BibTeX | Tags:

Chang Jae-Woong; Zhang, Wei; Yeh Hsin Sung; Park Meeyeon; Yao Chengguo; Shi Yongsheng; Kuang Rui# ; 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: clustering, 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 Forthcoming

In: npj Precision Oncology, Forthcoming.

Abstract | Links | BibTeX | Tags:

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

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

arXiv, 2018.

Abstract | Links | BibTeX | Tags: Network Alignment, Network-based Learning, Semi-supervised Learning

2017

Zhang, Huanan; Roe, David; Kuang, Rui

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

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

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, RNA-Seq

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

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

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

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

64 entries « 1 of 3 »