Determination of Local Statistical Significance of Patterns in Markov Sequences with Application to Promoter Element Identification. - Haiyan Huang; Ming-Chih J. Kao; Xianghong Jasmine Zhou; Jun S. Liu; Wing Hung Wong (J. Comput. Biol., 2004)

Mining Closed Relational Graphs with Connectivity Constraints. - Xifeng Yan; Xianghong Jasmine Zhou; Jiawei Han 001 (ICDE, 2005)

Mining coherent dense subgraphs across massive biological networks for functional discovery. - Haiyan Hu; Xifeng Yan; Yu Huang 003; Jiawei Han 001; Xianghong Jasmine Zhou (ISMB (Supplement of Bioinformatics), 2005)

Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data. - Fei Pan; Kiran Kamath; Kangyu Zhang; Sudip Pulapura; Avinash Achar; Juan Nunez-Iglesias; Yu Huang 003; Xifeng Yan; Jiawei Han 001; Haiyan Hu; Min Xu; Jianjun Hu; et al. (Bioinform., 2006)

Integrative missing value estimation for microarray data. - Jianjun Hu; Haifeng Li; Michael S. Waterman; Xianghong Jasmine Zhou (BMC Bioinform., 2006)

Characterizing Disease-specific Pathways and Their Coordination by Integrative Microarray Analysis with Application to Cancer. - Min Xu; Ming-Chih J. Kao; Juan Nunez-Iglesias; Joseph Nevins; Mike West; Xianghong Jasmine Zhou (BIOCOMP, 2007)

Systematic discovery of functional modules and context-specific functional annotation of human genome. - Yu Huang 003; Haifeng Li; Haiyan Hu; Xifeng Yan; Michael S. Waterman; Haiyan Huang; Xianghong Jasmine Zhou (ISMB/ECCB (Supplement of Bioinformatics), 2007)

A graph-based approach to systematically reconstruct human transcriptional regulatory modules. - Xifeng Yan; Michael R. Mehan; Yu Huang 003; Michael S. Waterman; Philip S. Yu; Xianghong Jasmine Zhou (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Gene Aging Nexus: a web database and data mining platform for microarray data on aging. - Fei Pan; Chi-Hsien Chiu; Sudip Pulapura; Michael R. Mehan; Juan Nunez-Iglesias; Kangyu Zhang; Kiran Kamath; Michael S. Waterman; Caleb E. Finch; Xianghong Jasmine Zhou (Nucleic Acids Res., 2007)

Discovering Causal and Temporal Relations in Biomedical Texts. - Rutu Mulkar-Mehta; Jerry R. Hobbs; Chun-Chi Liu; Xianghong Jasmine Zhou (AAAI Spring Symposium: Learning by Reading and Learning to Read, 2009)

Identifying Dynamic Network Modules with Temporal and Spatial Constraints. - Ruoming Jin; Scott McCallen; Chun-Chi Liu; Yang Xiang; Eivind Almaas; Xianghong Jasmine Zhou (Pacific Symposium on Biocomputing, 2009)

Integrative disease classification based on cross-platform microarray data. - Chun-Chi Liu; Jianjun Hu; Mrinal Kalakrishnan; Haiyan Huang; Xianghong Jasmine Zhou (BMC Bioinform., 2009)

An Integrative Network Approach to Map the Transcriptome to the Phenome. - Michael R. Mehan; Juan Nunez-Iglesias; Mrinal Kalakrishnan; Michael S. Waterman; Xianghong Jasmine Zhou (J. Comput. Biol., 2009)

An integrative modular approach to systematically predict gene-phenotype associations. - Michael R. Mehan; Juan Nunez-Iglesias; Chao Dai; Michael S. Waterman; Xianghong Jasmine Zhou (BMC Bioinform., 2010)

Unraveling complex temporal associations in cellular systems across multiple time-series microarray datasets. - Wenyuan Li 006; Min Xu; Xianghong Jasmine Zhou (J. Biomed. Informatics, 2010)

A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. - Shi-Hua Zhang; Qingjiao Li; Juan Liu 007; Xianghong Jasmine Zhou (Bioinform., 2011)

Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation. - Wenyuan Li 006; Chun-Chi Liu; Tong Zhang 001; Haifeng Li; Michael S. Waterman; Xianghong Jasmine Zhou (PLoS Comput. Biol., 2011)

Identifying multi-layer gene regulatory modules from multi-dimensional genomic data. - Wenyuan Li 006; Shi-Hua Zhang; Chun-Chi Liu; Xianghong Jasmine Zhou (Bioinform., 2012)

Integrating many co-splicing networks to reconstruct splicing regulatory modules. - Chao Dai; Wenyuan Li 006; Juan Liu; Xianghong Jasmine Zhou (BMC Syst. Biol., 2012)

Preface: Special Issue. - Ting Chen 006; Paul Marjoram; Fengzhu Sun; Xianghong Jasmine Zhou (J. Comput. Biol., 2012)

Algorithm to Identify Frequent Coupled Modules from Two-Layered Network Series: Application to Study Transcription and Splicing Coupling. - Wenyuan Li 006; Chao Dai; Chun-Chi Liu; Xianghong Jasmine Zhou (J. Comput. Biol., 2012)

DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. - Chun-Chi Liu; Yu-Ting Tseng; Wenyuan Li 006; Chia-Yu Wu; Ilya Mayzus; Andrey Rzhetsky; Fengzhu Sun; Michael S. Waterman; Jeremy J. W. Chen; Preet M. Chaudhary; Joseph Loscalzo; Edward Crandall; et al. (Nucleic Acids Res., 2014)

Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data. - Wenyuan Li 006; Ke Gong; Qingjiao Li; Frank Alber; Xianghong Jasmine Zhou (Bioinform., 2015)

Network tuned multiple rank aggregation and applications to gene ranking. - Wenhui Wang 003; Xianghong Jasmine Zhou; Zhenqiu Liu; Fengzhu Sun (BMC Bioinform., 2015)

IIIDB: a database for isoform-isoform interactions and isoform network modules. - Yu-Ting Tseng; Wenyuan Li 006; Ching-Hsien Chen; Shi-Hua Zhang; Jeremy J. W. Chen; Xianghong Jasmine Zhou; Chun-Chi Liu (BMC Genom., 2015)

Finding Genetic Overlaps Among Diseases Based on Ranked Gene Lists. - Quan Chen; Xianghong Jasmine Zhou; Fengzhu Sun (J. Comput. Biol., 2015)

Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells. - Jianrong Li; Chuan-Hu Sun; Wenyuan Li 006; Rou-Fang Chao; Chieh-Chen Huang; Xianghong Jasmine Zhou; Chun-Chi Liu (Nucleic Acids Res., 2016)

CMEP: a database for circulating microRNA expression profiling. - Jianrong Li; Chun-Yip Tong; Tsai-Jung Sung; Ting-Yu Kang; Xianghong Jasmine Zhou; Chun-Chi Liu (Bioinform., 2019)

Computational Analysis of High-Dimensional DNA Methylation Data for Cancer Prognosis. - Ran Hu; Xianghong Jasmine Zhou; Wenyuan Li 006 (J. Comput. Biol., 2022)