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Xiang Zhou

TitlePostdoctoral Scholar
InstitutionUniversity of Chicago
DepartmentHuman Genetics
AddressChicago IL 60637
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    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. 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. Nat Commun. 2021 07 07; 12(1):4172. PMID: 34234141.
      View in: PubMed
    2. 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 Harb Perspect Med. 2021 May 17. PMID: 34001525.
      View in: PubMed
    3. Li W, Zhou XJ. Methylation extends the reach of liquid biopsy in cancer detection. Nat Rev Clin Oncol. 2020 11; 17(11):655-656. PMID: 32732909.
      View in: PubMed
    4. 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 Precis Oncol. 2020; 4:16. PMID: 32637655.
      View in: PubMed
    5. 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 Precis Oncol. 2020 Jul 02; 4(1):16. PMID: 33594215.
      View in: PubMed
    6. 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. J Transl Med. 2020 01 06; 18(1):5. PMID: 31906978.
      View in: PubMed
    7. 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. Precis Clin Med. 2019 Sep; 2(3):131-139. PMID: 31598384.
      View in: PubMed
    8. Li JR, Tong CY, Sung TJ, Kang TY, Zhou XJ, Liu CC. CMEP: a database for circulating microRNA expression profiling. Bioinformatics. 2019 09 01; 35(17):3127-3132. PMID: 30668638.
      View in: PubMed
    9. Chen P, Chen E, Chen L, Zhou XJ, Liu R. Detecting early-warning signals of influenza outbreak based on dynamic network marker. J Cell Mol Med. 2019 01; 23(1):395-404. PMID: 30338927.
      View in: PubMed
    10. 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 Res. 2018 09 06; 46(15):e89. PMID: 29897492.
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    11. Hua N, Tjong H, Shin H, Gong K, Zhou XJ, Alber F. Producing genome structure populations with the dynamic and automated PGS software. Nat Protoc. 2018 05; 13(5):915-926. PMID: 29622804.
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    12. 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 Biol. 2017 07 31; 18(1):145. PMID: 28760140.
      View in: PubMed
    13. 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 Biol. 2017 03 24; 18(1):53. PMID: 28335812.
      View in: PubMed
    14. 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. Proc Natl Acad Sci U S A. 2016 Mar 22; 113(12):E1663-72. PMID: 26951677.
      View in: PubMed
    15. 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 Feb 11; 164(4):805-17. PMID: 26871637.
      View in: PubMed
    16. 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 Res. 2016 Apr 20; 44(7):e70. PMID: 26704975.
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    17. 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 Res. 2016 Jan 04; 44(D1):D944-51. PMID: 26602695.
      View in: PubMed
    18. 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. 2016 Jan 15; 93:110-8. PMID: 26238263.
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    19. Gallego Romero I, Pavlovic BJ, Hernando-Herraez I, Zhou X, Ward MC, Banovich NE, Kagan CL, Burnett JE, Huang CH, Mitrano A, Chavarria CI, Friedrich Ben-Nun I, Li Y, Sabatini K, Leonardo TR, Parast M, Marques-Bonet T, Laurent LC, Loring JF, Gilad Y. A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics. Elife. 2015 Jun 23; 4:e07103. PMID: 26102527.
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    20. Gong K, Tjong H, Zhou XJ, Alber F. Comparative 3D genome structure analysis of the fission and the budding yeast. PLoS One. 2015; 10(3):e0119672. PMID: 25799503.
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    21. Tung J, Zhou X, Alberts SC, Stephens M, Gilad Y. The genetic architecture of gene expression levels in wild baboons. Elife. 2015 Feb 25; 4. PMID: 25714927.
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    22. Chen Q, Zhou XJ, Sun F. Finding genetic overlaps among diseases based on ranked gene lists. J Comput Biol. 2015 Feb; 22(2):111-23. PMID: 25684200.
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    23. 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 Res. 2015 Jan; 43(2):1268-82. PMID: 25567984.
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    24. 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. 2015 Mar 15; 31(6):960-2. PMID: 25391400.
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    25. 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 Res. 2014 Jul; 42(Web Server issue):W137-46. PMID: 24895436.
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    26. Li W, Dai C, Kang S, Zhou XJ. Integrative analysis of many RNA-seq datasets to study alternative splicing. Methods. 2014 Jun 01; 67(3):313-24. PMID: 24583115.
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    27. Zhou X, Stephens M. Efficient multivariate linear mixed model algorithms for genome-wide association studies. Nat Methods. 2014 Apr; 11(4):407-9. PMID: 24531419.
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    28. Zhang S, Zhou XJ. Matrix factorization methods for integrative cancer genomics. Methods Mol Biol. 2014; 1176:229-42. PMID: 25030932.
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    29. 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 Res. 2014 Apr; 42(6):e39. PMID: 24369432.
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    30. You JS, De Carvalho DD, Dai C, Liu M, Pandiyan K, Zhou XJ, Liang G, Jones PA. SNF5 is an essential executor of epigenetic regulation during differentiation. PLoS Genet. 2013 Apr; 9(4):e1003459. PMID: 23637628.
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    31. 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 Res. 2013 Apr; 41(7):3973-85. PMID: 23408854.
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    32. Zhou X, Carbonetto P, Stephens M. Polygenic modeling with bayesian sparse linear mixed models. PLoS Genet. 2013; 9(2):e1003264. PMID: 23408905.
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    33. Zhou XJ, Alber F. Zooming in on genome organization. Nat Methods. 2012 Oct; 9(10):961-3. PMID: 23018997.
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    34. Yuan W, Wu T, Fu H, Dai C, Wu H, Liu N, Li X, Xu M, Zhang Z, Niu T, Han Z, Chai J, Zhou XJ, Gao S, Zhu B. Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation. Science. 2012 Aug 24; 337(6097):971-5. PMID: 22923582.
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    35. 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 Res. 2012 Oct; 40(19):9379-91. PMID: 22879375.
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    36. Li W, Zhang S, Liu CC, Zhou XJ. Identifying multi-layer gene regulatory modules from multi-dimensional genomic data. Bioinformatics. 2012 Oct 01; 28(19):2458-66. PMID: 22863767.
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    37. Dai C, Li W, Liu J, Zhou XJ. Integrating many co-splicing networks to reconstruct splicing regulatory modules. BMC Syst Biol. 2012; 6 Suppl 1:S17. PMID: 23046974.
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    38. Zhou X, Stephens M. Genome-wide efficient mixed-model analysis for association studies. Nat Genet. 2012 Jun 17; 44(7):821-4. PMID: 22706312.
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    39. 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. J Comput Biol. 2012 Jun; 19(6):710-30. PMID: 22697243.
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    40. Cusanovich DA, Billstrand C, Zhou X, Chavarria C, De Leon S, Michelini K, Pai AA, Ober C, Gilad Y. The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes. Hum Mol Genet. 2012 May 01; 21(9):2111-23. PMID: 22286170.
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    41. 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 Dec 09; 147(6):1283-94. PMID: 22153073.
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    42. 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. 2011 Jul 01; 27(13):i401-9. PMID: 21685098.
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    43. Li W, Liu CC, Zhang T, Li H, Waterman MS, Zhou XJ. Integrative analysis of many weighted co-expression networks using tensor computation. PLoS Comput Biol. 2011 Jun; 7(6):e1001106. PMID: 21698123.
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    44. Huang H, Liu CC, Zhou XJ. Bayesian approach to transforming public gene expression repositories into disease diagnosis databases. Proc Natl Acad Sci U S A. 2010 Apr 13; 107(15):6823-8. PMID: 20360561.
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    45. 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 Feb 01; 5(2):e8898. PMID: 20126538.
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    46. Li W, Xu M, Zhou XJ. Unraveling complex temporal associations in cellular systems across multiple time-series microarray datasets. J Biomed Inform. 2010 Aug; 43(4):550-9. PMID: 20083231.
      View in: PubMed
    47. Mehan MR, Nunez-Iglesias J, Dai C, Waterman MS, Zhou XJ. An integrative modular approach to systematically predict gene-phenotype associations. BMC Bioinformatics. 2010 Jan 18; 11 Suppl 1:S62. PMID: 20122238.
      View in: PubMed
    48. Mehan MR, Nunez-Iglesias J, Kalakrishnan M, Waterman MS, Zhou XJ. An integrative network approach to map the transcriptome to the phenome. J Comput Biol. 2009 Aug; 16(8):1023-34. PMID: 19630539.
      View in: PubMed
    49. Xu M, Li W, James GM, Mehan MR, Zhou XJ. Automated multidimensional phenotypic profiling using large public microarray repositories. Proc Natl Acad Sci U S A. 2009 Jul 28; 106(30):12323-8. PMID: 19590007.
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    50. Liu CC, Hu J, Kalakrishnan M, Huang H, Zhou XJ. Integrative disease classification based on cross-platform microarray data. BMC Bioinformatics. 2009 Jan 30; 10 Suppl 1:S25. PMID: 19208125.
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    51. Jin R, McCallen S, Liu CC, Xiang Y, Almaas E, Zhou XJ. Identifying dynamic network modules with temporal and spatial constraints. Pac Symp Biocomput. 2009; 203-14. PMID: 19209702.
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    52. 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; 9 Suppl 1:S12. PMID: 18366601.
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    53. Yan X, Mehan MR, Huang Y, Waterman MS, Yu PS, Zhou XJ. A graph-based approach to systematically reconstruct human transcriptional regulatory modules. Bioinformatics. 2007 Jul 01; 23(13):i577-86. PMID: 17646346.
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    54. 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. 2007 Jul 01; 23(13):i222-9. PMID: 17646300.
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    55. 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 Res. 2007 Jan; 35(Database issue):D756-9. PMID: 17090592.
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    56. Hu J, Li H, Waterman MS, Zhou XJ. Integrative missing value estimation for microarray data. BMC Bioinformatics. 2006 Oct 12; 7:449. PMID: 17038176.
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    57. Pan F, Ma X, Zhou XJ. Removed: Integrative differential gene expression analysis for cross-platform microarray datasets. J Biomed Inform. 2006 Aug 22. PMID: 17027342.
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    58. 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. 2006 Jul 01; 22(13):1665-7. PMID: 16672260.
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    59. Hu H, Yan X, Huang Y, Han J, Zhou XJ. Mining coherent dense subgraphs across massive biological networks for functional discovery. Bioinformatics. 2005 Jun; 21 Suppl 1:i213-21. PMID: 15961460.
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    60. 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. Nat Biotechnol. 2005 Feb; 23(2):238-43. PMID: 15654329.
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    61. Zhou XJ, Gibson G. Cross-species comparison of genome-wide expression patterns. Genome Biol. 2004; 5(7):232. PMID: 15239823.
      View in: PubMed
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