Publications in
Computational
Biology
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- 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-¦ĘB Pathways and Provokes CR3-Dependent Inflammatory Response in Murine System. PLoS One. 2010; 5(2): e9380.
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- 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.
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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.
- 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.
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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
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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.