2021

1. Lehmann BD*, Colaprico A, Silva TC,  Chen J, An H, Ban Y, Huang H, Wang 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. (code)
2. Lu MSha YSilva TCColaprico 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 (code)
3. Zhang L, Young JI, Gomez L, Silva TC, Schmidt MA, Cai J, Chen XS, Martin ER, Wang L*   (2021) Sex-specific analysis of DNA methylation changes implicates new loci in Alzheimer’s disease pathology. Acta Pathologica Communications. 9:77 (code)
4. Odom JOColaprico ASilva TCChen XSWang L* (2021) PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched SamplesFrontiers in Genetics 12: 783713 (code) (software)
5. Silva TC, Young JI, Martin ER, Chen XS, Wang L* (2021) MethReg: estimating the regulatory potential of DNA methylation in gene transcription. Preprint.  (code) (software)
6. Zhang L, Odom GJ, Liu L, Silva TC, Wang L* (2021) Predictive modelling using genome-wide DNA methylation data. F1000Research 10:742 (poster
7. 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
8. Szeglin BC, Wu C, Marco MR, Park HS, Zhang Z, Zhang B, Garcia‐Aguilar J, Beauchamp RD, Chen XS*, Smith JJ* (2021) A SMAD4‐modulated gene profile predicts disease‐free survival in stage II and III colorectal cancer Cancer Reports e1423
9. Dosch AR, Singh S, Dai X, Mehra S, ..., Chen XS, Sulagna Banerjee, Nagaraj S. Nagathihalli, Jashodeep Datta and Nipun B. Merchant (2021) Targeting Tumor–Stromal IL6/STAT3 Signaling through IL1 Receptor Inhibition in Pancreatic Cancer. Molecular Cancer Therapeutics 20:2280-90
10. Short SP, Pilat JM, Barrett CW, ..., Chen XS, ..., Burk RF, Rosen MJ, Williams CS (2021) Colonic Epithelial-Derived Selenoprotein P Is the Source for Antioxidant-Mediated Protection in Colitis-Associated Cancer, Gastroenterology, 160: 5 1694-1708.e3
11. Huang C, Chen L, Savage SR, ...,Colaprico A, ...,Chen XS, ...,Zelt R, Zhao G, Zhu J (2021) Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma, Cancer Cell, 39:3, 361-379.e16
12.Wang LB, Karpova A, Gritsenko MA, ...,Colaprico A, ...,Chen XS,...,Zhang Z, Zhao G, Zhu J (2021) Proteogenomic and metabolomic characterization of human glioblastoma, Cancer Cell, 39:4, 509-528.e20
13. Cao L, Huang C, Zhou DC, ..., Chen XS,..., Colaprioco A, ..., Zhao G (2021) Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell 184:19 5031-5052. e26
14. Gowrikumar S, Primeaux M, Pravoverov K, Wu C, Szeglin BC, Sauvé CG, Thapa I, Bastola D, Chen XS, Smith JJ, Singh AB, Dhawan P (2021) A Claudin-Based Molecular Signature Identifies High-Risk, Chemoresistant Colorectal Cancer Patients. Cells, 10(9) 2211
15. Kandimalla R, Shimura T, Mallik S, Sonohara F, Tsai S, Evans DB, Kim SC, Baba H, Kodera Y, Hoff DV, Chen X, Ajay Goel (2021) Identification of Serum miRNA Signature and Establishment of a Nomogram for Risk Stratification in Patients With Pancreatic Ductal Adenocarcinoma. Annals of Surgery.  doi: 10.1097/SLA.0000000000003945
16. Fritsch J, Garces L, Quintero MA, ...,Chen XS, ..., Abreu MT (2021) Low-fat, High-fiber Diet Reduces Markers of Inflammation and Dysbiosis and Improves Quality of Life in Patients With Ulcerative Colitis. Clinical Gastroenterology and Hepatology. 19 (6) 1189-1199. e30
17. Caunca MR, Wang L, Cheung YK, Alperin N, Lee SH, Elkind MSV, Sacco RL, Wright CB, Rundek T. (2021) Machine learning-based estimation of cognitive performance using regional brain MRI markers: the Northern Manhattan Study. Brain Imaging and Behavior. 15(3):1270-1278