Computational Biology

Tang, F., Feng, Y., Chiheb, H., and Fan, J. (2021).
The interplay of demographic variables and social distancing scores in deep prediction of U.S. COVID-19 cases.
Journal of American Statistical Association, 116, 492-506.
Zhou, T., etal, Ren, Y. (2019).
Microvascular endothelial cells engulf myelin debris and promote macrophage recruitment and fibrosis after neural injury
Nature Neuroscience, 22, 421-435.
Cheng, Z., Bosco, D.B., Sun, L., Chen, X., Xu, Y., Tai, W., Didier, R., Li, J., Fan, J., He, X. and Ren, Y. (2017).
Neural stem cell-conditioned medium suppresses inflammation and promotes spinal cord injury recovery.
Cell transplantation. 26, 469-482.
Rolfe, A.J., Bosco, D. B., Wang, J., Nowakowski, R. S., Fan, J. and Ren, Y. (2016).
Bioinformatic analysis reveals the expression of unique transcriptomic signatures in Zika virus infected human neural stem cells.
Cell and Bioscience, 6:42, DOI 10.1186/s13578-016-0110-x
Gao, L., Alyssa J. Rolfe, A.J., Wang, X., Tai, W., Cheng, Z., Cao, K., Chen, X., Xu, Y., Sun, D., Li, J., He, X., Young, W., Fan, J. and Ren, Y. (2016).
Rescuing macrophage normal function in spinal cord injury with embryonic stem cell conditioned media. Molecular Brain, 9:48, DOI 10.1186/s13041-016-0233-3.
Wang, X., Cao, K., Sun, X., Chen, Y.X., Duan, Z.X., Sun, L., Guo, L., Bai, P., Sun, D.M., Fan, J., He, X.J., Young, W. and Ren, Y. (2015).
Macrophages in spinal cord injury: phenotypic and functional change from exposure to myelin debris.
Glia , 63, 635-651
Chen, T., Wang, X., Guo, L., Wu, M., Duan, Z., Lv, J., Tai, W., Renganathan, H., Didier, R., Li, J, Sun, D., Chen, X., He, X., Fan, J., Young, W. and Ren, Y. (2014).
Embryonic stem cells promoting macrophage survival and function are crucial for teratoma development.
Frontiers in Immunology , 5, 1-16.
Fan, J. and Liu, H. (2013).
Statistical analysis of big data on pharmacogenomics
Advanced Drug Delivery Reviews , 65, 987-1000. Manuscript
Wang, J., Zhu, H., Fan, J., Giovanello, K., and Lin, W. L. (2013).
Multiscale adaptive smoothing models for the hemodynamic response function in fMRI.
Annals of Applied Statistics, 7, 904-935.
Wang, X., Chen, T., Lin, L., Fan, J., Cao, K., Duan, Z., Zhang, X., Shao, C., Wu, M., Tadmori, I., Li, T., Liang, L., Sun, D., Zheng, S., Meinhardt, A., Young, W., Bucala, R, and Ren, Y. (2012).
MIF Produced by Bone Marrow-Derived Macrophages Contributes to Teratoma Progression after Embryonic Stem Cell Transplantation.
Cancer Research, 71, 2867-2878. Pubmed
Porwancher, R.B., Hagerty, C.G., Fan, J., Landsberg, L, Johnson, B.J.B., Kopnitsky, M., Steere, A.C., Kulas, K. and Wong, S.J. (2011).
Multiplex Immunoassay for Lyme Disease Using VlsE1-IgG and pepC10-IgM Antibodies: Improving Test Performance through Bioinformatics.
Clinical and Vacine Immunology, 18, 851-859.
MAQC Consortium (2010).
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol, 28, 827-838.
Sun, X., Wang, X., Chen, T., Li, T., Cao, K., Lu, A., Chen, Y., Sun, D., Luo, J., Fan, J., Young, W., and Ren, R. (2010).
Myelin Activates FAK/Akt/NF-kB Pathways and Provokes CR3-Dependent Inflammatory Response in Murine System.
PLoS One. 2010; 5(2): e9380.
Xie, Y., Fan, J., Chen, J., Huang, F.-P., Cao, B., Tam, P.K.H., Ren, Y. (2009).
A novel function for dendritic cell: Clearance of VEGF via VEGF receptor-1.
Biochemical and Biophysical Research Communications, 380, 243-248.
Yep, J.S., Fan, J., and Wu, R. (2008).
Nonparametric modeling of longitudinal covariance structure in functional mapping of quantitative trait loci. Biometrics, 65, 1068-1077.Â
Kim, B.-R., Zhang, L., Berg, A., Fan, J. and Wu, R. (2008).
A computational approach to the functional clustering of periodic gene expression profiles.
Genetics, 180, 821-834.
Ren, Y., Xie, Y., Jiang, G., Fan, J., Yeung, J., Li, W., Tam, P., Savill, J. (2008).
Apototic cells protect mice against lipopolysaccharide-induced shock.
The Journal of Immunology, 180, 4978--4985.
Xie, Y., Chan, H., Fan, J., Chen, Y., Young, J., Li, W., Miao, X., Yuan, Z., Wang, H., Tam, P.K., Ren, Y. (2007).
Involvement of visinin like porotein-1 (VSNL-1) in regulating proliferative and invasive properties of neuroblastoma.
Carcinogenesis, 28, 2122-2130.
Fan, J. and Niu, Y. (2007).
Selection and validation of normalization methods for c-DNA microarrays using within-array replications. Bioinformatics,23, 2391-2398.
R-code used for data analysis: Some adaptations are needed
Matlab-code used for simulation studies
Fan, J. and Ren, Y. (2006).
Statistical Analysis of DNA Microarray Data in Cancer Research.
Clinical Cancer Research, 12, 4469--4473. (Invited review article)
Ren, Y., Chan, H.M., Fan, J., Chen, Y.X., Xie, Y., Li, W., Jiang, G.P., Liu, Q., and Tam, P. (2006).
Inhibition of tumor growth and metastasis in vitro and in vivo by targeting macrophage migration inhibitory factor in human neuroblastoma.
Oncogene, 25, 3501-3508.
Fan, J. Chen, Y., Chan, H.M., Tam, P.K.H. and Ren, Y. (2005).
Removing intensity effects and identifying significant genes for Affymetrix arrays in MIF-suppressed neuroblastoma cells.
Proc. Natl. Acad. Sci., 102, 17751-17756.
Fan, J., Huang, T. and Peng, H. (2005).
Semilinear high-dimensional model for normalization of microarray data: a theoretical analysis and partial consistency. (with discussion)
Journal of American Statistical Association, 100, 781--813.
Ren, Y., He, Q.Y., Fan, J., Jones, B., Zhou, Y. Wu, A., Xie, Y., Cheung, C.Y., Chiu, J.F, Peiris, JSM and Tam, P. (2004).
The use of proteomics to identify serum biomarkers for diagnosis of severe acute respiratory syndrome (SARS). Proteomic, 4, 3477-3484.
Fan, J., Tam, P., Vande Woude, G. and Ren, Y. (2004).
Normalization and analysis of cDNA micro-arrays using within-array replications applied to neuroblastoma cell response to a cytokine.
Proc. Natl. Acad. Sci., 101, 1135-1140.