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Most Recent 

  •  Lehmann BD*, Colaprico ASilva TC,  Chen J, An H, Ban Y, Huang HWang L, James JL, Balko JM, Gonzalez-Ericsson PI, Sanders ME, Zhang B, Pietenpol JA, Chen XS* (2021) Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes. Nature Communications 12, 6276.
  • Lu M, Sha Y, Silva TC, Colaprico A, Sun X, Ban Y,  Wang L, Lehmann BD, Chen XS* (2021) LR Hunting: A Random Forest Based Cell–Cell Interaction Discovery Method for Single-Cell Gene Expression Data. Frontiers in genetics 12:708835
  • Zhang L, Young JI, Gomez L, Silva TC, Schmidt MA, Cai J, Chen X, Martin ER, Wang L*   (2021) Sex-specific DNA methylation changes in Alzheimer’s disease pathology. Acta Neuropathologica Communications 9:77  
  • Zhang L, Silva TC, Young JI, Gomez L, Schmidt MA, Hamilton-Nelson KL, Kunkle BW, Chen X, Martin ER, Wang L* (2020). Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer’s disease. Nature Communications 11, 6114
  • Zhang Y, Wang P, Li X, Ning S, Li X*, Cao Y*, Chen XS* (2021) GABC: A Comprehensive Resource and Genome Atlas for Breast Cancer. International Journal of Cancer. 148 (4) 988-994 
  • Colaprico A, Olsen C, Bailey MH, Odom GJ, Terkelsen T, Silva TC, Olsen AV, Cantini L, Zinovyev A, Barillot E, Noushmehr H, Bertoli G, Castiglioni I, Cava C, Bontempi G, Chen XS*, Papaleo E* (2020). Interpreting pathways to discover cancer driver genes with Moonlight. Nature Communications. 11(1):69. 
  • Odom GJ, Ban Y, Colaprico A, Liu L, Silva TC, Sun X, Pico AR, Zhang B, Wang L*, Chen X* (2020) pathwayPCA: an R package for integrative pathway analysis with modern PCA methodology and gene selection. Proteomics. 20(21-22):e1900409
  • Gomez L, Odom GJ, Young JI, Martin ER, Liu L, Chen X, Griswold AJ, Gao Z, Zhang L, Wang L* (2019). coMethDMR: accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies with continuous phenotypes. Nucleic Acids Research. 47(17):e9 
  • Mallik S, Odom GJ, Gao Z, Gomez L, Chen X*, Wang L* (2019). An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays. Brief Bioinform. 20(6):2224-35

 Prediction models for personalized disease risk assessment using genomics data

Methodology and tools for genomics and epi-genomics research

Integrative analysis of genomics data

Cancer genomics analysis