Selected Publications

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Paris, P.L. et al. High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays. Am J Pathol 162, 763-70 (2003).

Paris, P.L. et al. Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum Mol Genet 13, 1303-13 (2004).

Paris, P.L. et al. Preliminary evaluation of prostate cancer metastatic risk biomarkers. Int J Biol Markers 20, 141-5 (2005).

Raphael, B.J. et al. A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol 9, R59 (2008).

Paris, P.L. et al. A group of genome-based biomarkers that add to a Kattan nomogram for predicting progression in men with high-risk prostate cancer. Clin Cancer Res 16, 195-202 (2010).

Paris, P.L. et al. Genomic profiling of hormone-naive lymph node metastases in patients with prostate cancer. Neoplasia 8, 1083-9 (2006).

Paris, P.L. et al. High resolution oligonucleotide CGH using DNA from archived prostate tissue. Prostate 67, 1447-55 (2007).

Lapuk, A. et al. Exon-level microarray analyses identify alternative splicing programs in breast cancer. Mol Cancer Res 8, 961-74 (2010).

Yu, M. et al. Superficial, nodular, and morpheiform basal-cell carcinomas exhibit distinct gene expression profiles. J Invest Dermatol 128, 1797-805 (2008).

Yu, M. et al. Lichen planopilaris and pseudopelade of Brocq involve distinct disease associated gene expression patterns by microarray. J Dermatol Sci 57, 27-36 (2010).

van Duin, M. et al. Construction and application of a full-coverage, high-resolution, human chromosome 8q genomic microarray for comparative genomic hybridization. Cytometry A 63, 10-9 (2005).

Paris, P.L. et al. An oncogenic role for the multiple endocrine neoplasia type 1 gene in prostate cancer. Prostate Cancer Prostatic Dis 12, 184-91 (2009).

Volik, S. et al. End-sequence profiling: sequence-based analysis of aberrant genomes. Proc Natl Acad Sci U S A 100, 7696-701 (2003).

Bashir, A., Volik, S., Collins, C., Bafna, V. & Raphael, B.J. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol 4, e1000051 (2008).

Chin, K. et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 10, 529-41 (2006).

Hajirasouliha, I. et al. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics 26, 1277-83 (2010).

Alkan, C. et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 41, 1061-7 (2009).

Hach, F. et al. mrsFAST: a cache-oblivious algorithm for short-read mapping. Nat Methods 7, 576-7.

Manju Sharma, Shawn A. Anderson, Roland Schoop, James B. Hudson. Induction of multiple pro-inflammatory cytokines by respiratory viruses and reversal by standardized Echinacea, a potent antiviral herbal extract. Antiviral Research. Volume 83, Issue 2, August 2009, 165-170

Sharma M, Anderson S, Schoop R, Hudson JB. Bactericidal and anti-inflammatory properties of a standardized Echinacea extract (Echinaforce): dual actions against respiratory bacteria. Phytomedicine. 2010 Jul;17(8-9):563-8. Epub 2009 Dec 29.

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