Xianghong Zhou, Ph.D.

Office Address:
Boyer Hall, Suite 520
CA

Affiliations
Affiliations
Professor, Pathology and Laboratory Medicine
Member, Bioinformatics GPB Home Area, Genetics & Genomics GPB Home Area
Publications

A selected list of publications:

Shin Hanjun, Shi Yi, Dai Chao, Tjong Harianto, Gong Ke, Alber Frank, Zhou Xianghong Jasmine   TopDom: an efficient and deterministic method for identifying topological domains in genomes Nucleic acids research, 2016; 44(7): e70.
Tjong Harianto, Li Wenyuan, Kalhor Reza, Dai Chao, Hao Shengli, Gong Ke, Zhou Yonggang, Li Haochen, Zhou Xianghong Jasmine, Le Gros Mark A, Larabell Carolyn A, Chen Lin, Alber Frank   Population-based 3D genome structure analysis reveals driving forces in spatial genome organization Proceedings of the National Academy of Sciences of the United States of America, 2016; 113(12): E1663-72.
Li Jian-Rong, Sun Chuan-Hu, Li Wenyuan, Chao Rou-Fang, Huang Chieh-Chen, Zhou Xianghong Jasmine, Liu Chun-Chi   Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells Nucleic acids research, 2016; 44(D1): D944-51.
Li Wenyuan, Liu Chun-Chi, Kang Shuli, Li Jian-Rong, Tseng Yu-Ting, Zhou Xianghong Jasmine   Pushing the annotation of cellular activities to a higher resolution: Predicting functions at the isoform level Methods (San Diego, Calif.), 2016; 93(4): 110-8.
Li Wenyuan, Gong Ke, Li Qingjiao, Alber Frank, Zhou Xianghong Jasmine   Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data Bioinformatics (Oxford, England), 2015; 31(6): 960-2.
Gong Ke, Tjong Harianto, Zhou Xianghong Jasmine, Alber Frank   Comparative 3D genome structure analysis of the fission and the budding yeast PloS one, 2015; 10(3): e0119672.
Chen Yongheng, Chen Chunxia, Zhang Zhe, Liu Chun-Chi, Johnson Matthew E, Espinoza Celso A, Edsall Lee E, Ren Bing, Zhou Xianghong Jasmine, Grant Struan F A, Wells Andrew D, Chen Lin   DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions Nucleic acids research, 2015; 43(2): 1268-82.
Liu Chun-Chi, Tseng Yu-Ting, Li Wenyuan, Wu Chia-Yu, Mayzus Ilya, Rzhetsky Andrey, Sun Fengzhu, Waterman Michael, Chen Jeremy J W, Chaudhary Preet M, Loscalzo Joseph, Crandall Edward, Zhou Xianghong Jasmine   DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections Nucleic acids research, 2014; 42(Web Server issue): W137-46.
Li Wenyuan, Dai Chao, Kang Shuli, Zhou Xianghong Jasmine   Integrative analysis of many RNA-seq datasets to study alternative splicing Methods (San Diego, Calif.), 2014; 67(3): 313-24.
Li Wenyuan, Kang Shuli, Liu Chun-Chi, Zhang Shihua, Shi Yi, Liu Yan, Zhou Xianghong Jasmine   High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method Nucleic acids research, 2014; 42(6): e39.
Zhang Shihua, Zhou Xianghong Jasmine   Matrix factorization methods for integrative cancer genomics Methods in molecular biology (Clifton, N.J.), 2014; 1176(6): 229-42.
Zhang Shihua, Liu Chun-Chi, Li Wenyuan, Shen Hui, Laird Peter W, Zhou Xianghong Jasmine   Discovery of multi-dimensional modules by integrative analysis of cancer genomic data Nucleic acids research, 2012; 40(19): 9379-91.
Li Wenyuan, Zhang Shihua, Liu Chun-Chi, Zhou Xianghong Jasmine   Identifying multi-layer gene regulatory modules from multi-dimensional genomic data Bioinformatics (Oxford, England), 2012; 28(19): 2458-66.
Zhou Xianghong Jasmine, Alber Frank   Zooming in on genome organization Nature methods, 2012; 9(10): 961-3.
Yuan Wen, Wu Tong, Fu Hang, Dai Chao, Wu Hui, Liu Nan, Li Xiang, Xu Mo, Zhang Zhuqiang, Niu Tianhui, Han Zhifu, Chai Jijie, Zhou Xianghong Jasmine, Gao Shaorong, Zhu Bing   Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation Science (New York, N.Y.), 2012; 337(6097): 971-5.
Li Wenyuan, Dai Chao, Liu Chun-Chi, Zhou Xianghong Jasmine   Algorithm to identify frequent coupled modules from two-layered network series: application to study transcription and splicing coupling Journal of computational biology : a journal of computational molecular cell biology, 2012; 19(6): 710-30.
Dai Chao, Li Wenyuan, Liu Juan, Zhou Xianghong Jasmine   Integrating many co-splicing networks to reconstruct splicing regulatory modules BMC systems biology, 2012; 6 Suppl 1(6): S17.
Zhang Shihua, Li Qingjiao, Liu Juan, Zhou Xianghong Jasmine   A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules Bioinformatics (Oxford, England), 2011; 27(13): i401-9.
Li Wenyuan, Xu Min, Zhou Xianghong Jasmine   Unraveling complex temporal associations in cellular systems across multiple time-series microarray datasets Journal of biomedical informatics, 2010; 43(4): 550-9.
Huang Haiyan, Liu Chun-Chi, Zhou Xianghong Jasmine   Bayesian approach to transforming public gene expression repositories into disease diagnosis databases Proceedings of the National Academy of Sciences of the United States of America, 2010; 107(15): 6823-8.
Nunez-Iglesias Juan, Liu Chun-Chi, Morgan Todd E, Finch Caleb E, Zhou Xianghong Jasmine   Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer's disease cortex reveals altered miRNA regulation PloS one, 2010; 5(2): e8898.
Mehan Michael R, Nunez-Iglesias Juan, Dai Chao, Waterman Michael S, Zhou Xianghong Jasmine   An integrative modular approach to systematically predict gene-phenotype associations BMC bioinformatics, 2010; 11 Suppl 1(2): S62.
Mehan Michael R, Nunez-Iglesias Juan, Kalakrishnan Mrinal, Waterman Michael S, Zhou Xianghong Jasmine   An integrative network approach to map the transcriptome to the phenome Journal of computational biology : a journal of computational molecular cell biology, 2009; 16(8): 1023-34.
Xu Min, Li Wenyuan, James Gareth M, Mehan Michael R, Zhou Xianghong Jasmine   Automated multidimensional phenotypic profiling using large public microarray repositories Proceedings of the National Academy of Sciences of the United States of America, 2009; 106(30): 12323-8.
Jin Ruoming, McCallen Scott, Liu Chun-Chi, Xiang Yang, Almaas Eivind, Zhou Xianghong Jasmine   Identifying dynamic network modules with temporal and spatial constraints Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2009; 10 Suppl 1(6): 203-14.
Liu Chun-Chi, Hu Jianjun, Kalakrishnan Mrinal, Huang Haiyan, Zhou Xianghong Jasmine   Integrative disease classification based on cross-platform microarray data BMC bioinformatics, 2009; 10 Suppl 1(6): S25.
Xu Min, Kao Ming-Chih J, Nunez-Iglesias Juan, Nevins Joseph R, West Mike, Zhou Xianghong Jasmine   An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer BMC genomics, 2008; 9 Suppl 1(6): S12.
Yan Xifeng, Mehan Michael R, Huang Yu, Waterman Michael S, Yu Philip S, Zhou Xianghong Jasmine   A graph-based approach to systematically reconstruct human transcriptional regulatory modules Bioinformatics (Oxford, England), 2007; 23(13): i577-86.
Huang Yu, Li Haifeng, Hu Haiyan, Yan Xifeng, Waterman Michael S, Huang Haiyan, Zhou Xianghong Jasmine   Systematic discovery of functional modules and context-specific functional annotation of human genome Bioinformatics (Oxford, England), 2007; 23(13): i222-9.
Pan Fei, Chiu Chi-Hsien, Pulapura Sudip, Mehan Michael R, Nunez-Iglesias Juan, Zhang Kangyu, Kamath Kiran, Waterman Michael S, Finch Caleb E, Zhou Xianghong Jasmine   Gene Aging Nexus: a web database and data mining platform for microarray data on aging Nucleic acids research, 2007; 35(Database issue): D756-9.
Hu Jianjun, Li Haifeng, Waterman Michael S, Zhou Xianghong Jasmine   Integrative missing value estimation for microarray data BMC bioinformatics, 2006; 7(Database issue): 449.
Pan Fei, Ma Xiaotu, Zhou Xianghong Jasmine   Removed: Integrative differential gene expression analysis for cross-platform microarray datasets Journal of biomedical informatics, 2006; 7(Database issue): .
Hu Haiyan, Yan Xifeng, Huang Yu, Han Jiawei, Zhou Xianghong Jasmine   Mining coherent dense subgraphs across massive biological networks for functional discovery Bioinformatics (Oxford, England), 2005; 21 Suppl 1(13): i213-21.
Zhou Xianghong Jasmine, Kao Ming-Chih J, Huang Haiyan, Wong Angela, Nunez-Iglesias Juan, Primig Michael, Aparicio Oscar M, Finch Caleb E, Morgan Todd E, Wong Wing Hung   Functional annotation and network reconstruction through cross-platform integration of microarray data Nature biotechnology, 2005; 23(2): 238-43.
Zhou Xianghong Jasmine, Gibson Greg   Cross-species comparison of genome-wide expression patterns Genome biology, 2004; 5(7): 232.