代表性文献

慧渡成员发表的代表性文献

液态活检:
 
Detection and Characterization of Circulating Tumour Cells in Multiple Myeloma. Liangxuan Zhang, Sharon Beasley, Natalie L. Prigozhina, Renee Higgins, Shoji Ikeda, Florence Y. Lee, Dena Marrinucci, Shidong Jia. Journal of Circulating Biomarkers. 2016, 5: 1-7

Year of Expanding into Circulating BiomarkersJia S and Kuo WP. Journal of Circulating Biomarkers. 2015, 4: 1-2.

New Year, New Name and New Milestones Scope. Jia S and Kuo WPJournal of Circulating Biomarkers. 2014, 3 (1), 1-2.
 
二代测序:
 
Re: Semiconductor-based sequencing of formalin-fixed, paraffin-embedded colorectal cancer samplesJia S, Zhang L, Latham GJ. Oncologist. 2015;20(5):e12

Profiling cancer gene mutations in clinical formalin-fixed, paraffin-embedded colorectal tumor specimens using targeted next-generation sequencing, Zhang L, Chen L, Sah S, Latham GJ, Patel R, Song Q, Koeppen H, Tam R, Schleifman E, Mashhedi H, Chalasani S, Fu L, Sumiyoshi T, Raja R, Forrest W, Hampton GM, Lackner MR, Hegde P, Jia S. Oncologist. 2014 Apr;19(4):336-43.

Integrative Analysis of Two Cell Lines Derived from a Non-Small-Lung Cancer Patient – A Panomics Approach, Mayba O, Gnad F, Peyton M, Zhang F, Walter K, Du P, Huntley M.A., Jiang Z, Liu J, Haverty P.M., Gentleman R.C., Li R, Minna J.D., Li Y, Shames D.S., Zhang Z, Pacific Symposium on Biocomputing, 19:75-86 (2014).

Functional specialization of the small interfering RNA pathway in response to virus infection. Marques JT, Wang JP, Wang XH, de Oliveira KP, Gao C, Aguiar ER, Jafari N, Carthew RW. PLOS Pathog. 2013;9(8).
 
Chromosomal Instability Estimation Based on Next Generation Sequencing and Single Cell Genome Wide Copy Number Variation Analysis. Greene SB, Dago AE, Leitz LJ, Wang Y, Lee J, Werner SL, Gendreau S, Patel P, Jia S, Zhang L, Tucker EK, Malchiodi M, Graf RP, Dittamore R, Marrinucci D, Landers M. PLoS One. 2016 Nov 16;11(11):
生物信息学:
 
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis, Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L, and Lin SM, BMC Bioinformatics 2010, 11:587.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models, Nature Biotechnology. 2010 Aug;28 (8):827-38. (Du P is one of the major contributors)

A collection of bioconductor methods to visualize gene-list annotations, Feng G*, Du P*, Krett NL, Tessel M, Rosen S, Kibbe WA, Lin SM, BMC Res Notes 2010, 3:10. (co-first author)

From Disease Ontology (DO) to Disease-Ontology Lite (DOLite): statistical methods to adapt a general-purpose ontology for the test of gene-disease associations, Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM, Bioinformatics, 2009 Jun 15;25(12):i63-8.

lumi: a Bioconductor package for processing Illumina microarray, Du P, Kibbe WA and Lin SM, Bioinformatics 2008 24(13):1547-1548.

Model-based Variance-stabilizing Transformation for Illumina Microarray Data, Lin SM*, Du P* and Kibbe WA, Nucleic Acids Res. 2008 36(2):e11. (* co-first authorship)

nuID: A universal naming schema of oligonucleotides for Illumina, Affymetrix, and other microarrays, Du P, Kibbe WA and Lin SM, Biology Direct. (2007, 2:16).

Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching, Du P, Kibbe WA and Lin SM, Bioinformatics, 22, p.p. 2059-2065.

Modeling gene expression networks using fuzzy logic, Du P, Gong J, Wurtele ES and Dickerson JA, IEEE Trans. on Systems, Man, and Cybernetics, Part B, Vol.35, NO.6, pp. 1351-1359, Dec.2005.
药物开发:
 
Development of a robust flow cytometry-based pharmacodynamic assay to detect phospho-protein signals for phosphatidylinositol 3-kinase inhibitors in multiple myeloma. Li C, Takahashi C, Zhang L, Huseni M, Stankovich B, Mashhedi H, Lee J, French D, Anderson JE, Kim D, Howell K, Brauer MJ, Kowanetz M, Yan Y, Humke E, Ebens A, Hampton G, Lackner MR, Hegde P, Jia S. J Transl Med. 2013;11:76. ​

Should individual PI3 kinase isoforms be targeted in cancer? Jia S, Roberts TM, Zhao JJ. Curr Opin Cell Biol. 2009;21(2):199-208.

Essential roles of PI(3)K-p110beta in cell growth, metabolism and tumorigenesis. Jia S*, Liu Z*, Zhang S*, Liu P*, Zhang L, Lee SH, Zhang J, Signoretti S, Loda M, Roberts TM, Zhao JJ. Nature. 2008;454(7205):776-9. (* co-first authorship)

RNA interference directs innate immunity against viruses in adult Drosophila. Wang XH, Aliyari R, Li WX, Li HW, Kim K, Carthew R, Atkinson P, Ding SW. Science. 2006;312(5772):452-4.
耐药性和生物标志物开发:
 
Drug Resistance via Feedback Activation of Stat3 in Oncogene-Addicted Cancer Cells, Lee HJ, Zhuang G, Cao Y, Du P, Kim HJ, and Settleman J, Cancer Cell. 2014;26(2):207-21.

Discovery and development of DNA methylation-based biomarkers for lung cancer, Walter K, Holcomb T, Januario T, Yauch RL, Du P, Bourgon R, Seshagiri S, Amler LC, Hampton GM, and Shames DS, Epigenomics 2014; 6(1):59-72.


Loss of NAPRT1 Expression by Tumor-specific Promoter Methylation Provides a Novel Predictive Biomarker for NAMPT Inhibitors, Shames D, Elkins K, Walter K, Holcomb T, Du P, Mohl D, Xiao Y, Pham T, Haverty P, Liederer B, Liang X, Yauch R, O’Brien T, Bourgon R, Koeppen H, Belmont L. Clin Cancer Res. 2013;19(24):6912-23.

Opposing effects of androgen deprivation and targeted therapy on prostate cancer prevention. Jia S, Gao X, Lee SH, Maira SM, Wu X, Stack EC, Signoretti S, Loda M, Zhao JJ, Roberts TM. Cancer Discov. 2013;3(1):44-51. ​

DNA methylation profiling defines clinically relevant biological subsets of non-small cell lung cancer, Walter K, Holcomb T, Januario T, Du P, Evangelista M, Kartha N, Iniguez L, Soriano R, Huw L, Stern H, Modrusan Z, Seshagiri S, Hampton GM, Amler LC, Bourgon R, Yauch RL, Shames DS, Clin Cancer Res. 2012 Apr 15;18(8):2360-73.

Prostate cancer – a biomarker perspective. Liu Y, Hegde P, Zhang F, Hampton G, Jia S. Front Endocrinol. 2012;3:72.