Publications

• Boninsegna L, Yildirim A, Polles G, Zhan Y, Quinodoz SA, Finn EH, Guttman M, Zhou XJ, Alber F. Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations.. Nature methods, 2022.
• Hu R, Zhou XJ, Li W. Computational Analysis of High-Dimensional DNA Methylation Data for Cancer Prognosis.. Journal of computational biology : a journal of computational molecular cell biology, 2022.
• Li S, Zeng W, Ni X, Zhou Y, Stackpole ML, Noor ZS, Yuan Z, Neal A, Memarzadeh S, Garon EB, Dubinett SM, Li W, Zhou XJ. cfTrack: A Method of Exome-Wide Mutation Analysis of Cell-free DNA to Simultaneously Monitor the Full Spectrum of Cancer Treatment Outcomes Including MRD, Recurrence, and Evolution.. Clinical cancer research : an official journal of the American Association for Cancer Research, 2022.
• Kadara H, Tran LM, Liu B, Vachani A, Li S, Sinjab A, Zhou XJ, Dubinett SM, Krysan K. Early Diagnosis and Screening for Lung Cancer.. Cold Spring Harbor perspectives in medicine, 2021.
• Wang Z, Li S, You R, Zhu S, Zhou XJ, Sun F. ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network.. NAR genomics and bioinformatics, 2021.
• Li S, Noor ZS, Zeng W, Stackpole ML, Ni X, Zhou Y, Yuan Z, Wong WH, Agopian VG, Dubinett SM, Alber F, Li W, Garon EB, Zhou XJ. Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis.. Nature communications, 2021.
• Li W, Zhou XJ. Methylation extends the reach of liquid biopsy in cancer detection.. Nature reviews. Clinical oncology, 2020.
• Court CM, Hou S, Liu L, Winograd P, DiPardo BJ, Liu SX, Chen PJ, Zhu Y, Smalley M, Zhang R, Sadeghi S, Finn RS, Kaldas FM, Busuttil RW, Zhou XJ, Tseng HR, Tomlinson JS, Graeber TG, Agopian VG. Somatic copy number profiling from hepatocellular carcinoma circulating tumor cells.. NPJ precision oncology, 2020.
• Chen P, Li S, Li W, Ren J, Sun F, Liu R, Zhou XJ. Rapid diagnosis and comprehensive bacteria profiling of sepsis based on cell-free DNA.. Journal of translational medicine, 2020.
• An Q, Hu Y, Li Q, Chen X, Huang J, Pellegrini M, Zhou XJ, Rettig M, Fan G. The size of cell-free mitochondrial DNA in blood is inversely correlated with tumor burden in cancer patients.. Precision clinical medicine, 2019.
• Li JR, Tong CY, Sung TJ, Kang TY, Zhou XJ, Liu CC. CMEP: a database for circulating microRNA expression profiling.. Bioinformatics (Oxford, England), 2019.
• Li W, Li Q, Kang S, Same M, Zhou Y, Sun C, Liu CC, Matsuoka L, Sher L, Wong WH, Alber F, Zhou XJ. CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data.. Nucleic acids research, 2018.
• Hua N, Tjong H, Shin H, Gong K, Zhou XJ, Alber F. Producing genome structure populations with the dynamic and automated PGS software.. Nature protocols, 2018.
• Li Q, Tjong H, Li X, Gong K, Zhou XJ, Chiolo I, Alber F. The three-dimensional genome organization of Drosophila melanogaster through data integration.. Genome biology, 2017.
• Kang S, Li Q, Chen Q, Zhou Y, Park S, Lee G, Grimes B, Krysan K, Yu M, Wang W, Alber F, Sun F, Dubinett SM, Li W, Zhou XJ. CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA.. Genome biology, 2017.
• Tjong H, Li W, Kalhor R, Dai C, Hao S, Gong K, Zhou Y, Li H, Zhou XJ, Le Gros MA, Larabell CA, Chen L, Alber F. 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.
• Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.. Cell, 2016.
• Shin H, Shi Y, Dai C, Tjong H, Gong K, Alber F, Zhou XJ. TopDom: an efficient and deterministic method for identifying topological domains in genomes.. Nucleic acids research, 2015.
• Li JR, Sun CH, Li W, Chao RF, Huang CC, Zhou XJ, Liu CC. Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells.. Nucleic acids research, 2015.
• Li W, Liu CC, Kang S, Li JR, Tseng YT, Zhou XJ. Pushing the annotation of cellular activities to a higher resolution: Predicting functions at the isoform level.. Methods (San Diego, Calif.), 2015.
• Gong K, Tjong H, Zhou XJ, Alber F. Comparative 3D genome structure analysis of the fission and the budding yeast.. PloS one, 2015.
• Chen Q, Zhou XJ, Sun F. Finding genetic overlaps among diseases based on ranked gene lists.. Journal of computational biology : a journal of computational molecular cell biology, 2015.
• Chen Y, Chen C, Zhang Z, Liu CC, Johnson ME, Espinoza CA, Edsall LE, Ren B, Zhou XJ, Grant SF, Wells AD, Chen L. DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions.. Nucleic acids research, 2015.
• Li W, Gong K, Li Q, Alber F, Zhou XJ. Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data.. Bioinformatics (Oxford, England), 2014.
• Liu CC, Tseng YT, Li W, Wu CY, Mayzus I, Rzhetsky A, Sun F, Waterman M, Chen JJ, Chaudhary PM, Loscalzo J, Crandall E, Zhou XJ. DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.. Nucleic acids research, 2014.
• Li W, Dai C, Kang S, Zhou XJ. Integrative analysis of many RNA-seq datasets to study alternative splicing.. Methods (San Diego, Calif.), 2014.
• Li W, Kang S, Liu CC, Zhang S, Shi Y, Liu Y, Zhou XJ. High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method.. Nucleic acids research, 2013.
• Pandiyan K, You JS, Yang X, Dai C, Zhou XJ, Baylin SB, Jones PA, Liang G. Functional DNA demethylation is accompanied by chromatin accessibility.. Nucleic acids research, 2013.
• Zhou XJ, Alber F. Zooming in on genome organization.. Nature methods, 2012.
• Zhang S, Liu CC, Li W, Shen H, Laird PW, Zhou XJ. Discovery of multi-dimensional modules by integrative analysis of cancer genomic data.. Nucleic acids research, 2012.
• Li W, Zhang S, Liu CC, Zhou XJ. Identifying multi-layer gene regulatory modules from multi-dimensional genomic data.. Bioinformatics (Oxford, England), 2012.
• Dai C, Li W, Liu J, Zhou XJ. Integrating many co-splicing networks to reconstruct splicing regulatory modules.. BMC systems biology, 2012.
• Li W, Dai C, Liu CC, Zhou XJ. 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.
• Taberlay PC, Kelly TK, Liu CC, You JS, De Carvalho DD, Miranda TB, Zhou XJ, Liang G, Jones PA. Polycomb-repressed genes have permissive enhancers that initiate reprogramming.. Cell, 2011.
• Zhang S, Li Q, Liu J, Zhou XJ. A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules.. Bioinformatics (Oxford, England), 2011.
• Li W, Liu CC, Zhang T, Li H, Waterman MS, Zhou XJ. Integrative analysis of many weighted co-expression networks using tensor computation.. PLoS computational biology, 2011.
• Huang H, Liu CC, Zhou XJ. 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.
• Nunez-Iglesias J, Liu CC, Morgan TE, Finch CE, Zhou XJ. Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer's disease cortex reveals altered miRNA regulation.. PloS one, 2010.
• Mehan MR, Nunez-Iglesias J, Dai C, Waterman MS, Zhou XJ. An integrative modular approach to systematically predict gene-phenotype associations.. BMC bioinformatics, 2010.
• Li W, Xu M, Zhou XJ. Unraveling complex temporal associations in cellular systems across multiple time-series microarray datasets.. Journal of biomedical informatics, 2010.
• Mehan MR, Nunez-Iglesias J, Kalakrishnan M, Waterman MS, Zhou XJ. An integrative network approach to map the transcriptome to the phenome.. Journal of computational biology : a journal of computational molecular cell biology, 2009.
• Xu M, Li W, James GM, Mehan MR, Zhou XJ. Automated multidimensional phenotypic profiling using large public microarray repositories.. Proceedings of the National Academy of Sciences of the United States of America, 2009.
• Liu CC, Hu J, Kalakrishnan M, Huang H, Zhou XJ. Integrative disease classification based on cross-platform microarray data.. BMC bioinformatics, 2009.
• Jin R, McCallen S, Liu CC, Xiang Y, Almaas E, Zhou XJ. Identifying dynamic network modules with temporal and spatial constraints.. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2009.
• Xu M, Kao MC, Nunez-Iglesias J, Nevins JR, West M, Zhou XJ. An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer.. BMC genomics, 2008.
• Huang Y, Li H, Hu H, Yan X, Waterman MS, Huang H, Zhou XJ. Systematic discovery of functional modules and context-specific functional annotation of human genome.. Bioinformatics (Oxford, England), 2007.
• Pan F, Chiu CH, Pulapura S, Mehan MR, Nunez-Iglesias J, Zhang K, Kamath K, Waterman MS, Finch CE, Zhou XJ. Gene Aging Nexus: a web database and data mining platform for microarray data on aging.. Nucleic acids research, 2006.
• Hu J, Li H, Waterman MS, Zhou XJ. Integrative missing value estimation for microarray data.. BMC bioinformatics, 2006.
• Pan F, Ma X, Zhou XJ. Removed: Integrative differential gene expression analysis for cross-platform microarray datasets.. Journal of biomedical informatics, 2006.
• Pan F, Kamath K, Zhang K, Pulapura S, Achar A, Nunez-Iglesias J, Huang Y, Yan X, Han J, Hu H, Xu M, Hu J, Zhou XJ. Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data.. Bioinformatics (Oxford, England), 2006.
• Hu H, Yan X, Huang Y, Han J, Zhou XJ. Mining coherent dense subgraphs across massive biological networks for functional discovery.. Bioinformatics (Oxford, England), 2005.
• Zhou XJ, Kao MC, Huang H, Wong A, Nunez-Iglesias J, Primig M, Aparicio OM, Finch CE, Morgan TE, Wong WH. Functional annotation and network reconstruction through cross-platform integration of microarray data.. Nature biotechnology, 2005.