Shipshaw Labs is a bioinformatics research company based in Montreal which develops software and hardware solutions for the analysis of genomic data.
Leif™ Microbiome Analyzer The Leif Microbiome Analyzer is a bioinformatics package optimized to analyze microbiomes using unbiased high-throughput sequencing (Lipkin 2010). This software rapidly catalogs both known and unknown microbial sequences without any need for cluster computing.
Unlike primer based assays such as IBIS or PCR, Leif is based on an assay which can detect all microbes, even microbes for which primers have not yet been developed. While Leif was designed specifically to survey the microbiome of the human prostate, it performs well with most mixed DNA/RNA samples. A beta version is currently available for download.
Prostate Cancer Research Recent discoveries suggest the presence of an as yet unrecognized microbe which is associated with prostate cancer, yet no complete survey of the prostate microbiome has ever been published. This is partly due to the lack of suitable bioinformatics tools, which motivated the development of the Leif Microbiome Analyzer.
Important peer reviewed articles related to the prostate microbiome and its association with prostate cancer: - Strickler, H. D., & Goedert, J. J. (2001). Sexual behavior and evidence for an infectious cause of prostate cancer. Epidemiologic reviews, 23(1), 144-151.
- Dennis, L. K., & Dawson, D. V. (2002). Meta-analysis of measures of sexual activity and prostate cancer. Epidemiology, 13(1), 72-79.
- Wright, J. L., Lin, D. W., & Stanford, J. L. (2012). Circumcision and the risk of prostate cancer. Cancer, 118(18), 4437-4443.
- Hrbacek, J., Urban, M., Hamsikova, E., Tachezy, R., & Heracek, J. (2012). Thirty years of research on infection and prostate cancer: No conclusive evidence for a link. A systematic review. In Urologic Oncology: Seminars and Original Investigations. Elsevier.
Research directly linked to Shipshaw Labs' findings: - Stott‐Miller, M., Wright, J. L., & Stanford, J. L. (2013). MSMB gene variant alters the association between prostate cancer and number of sexual partners.The Prostate, 73(16), 1803-1809.
- Sutcliffe, S., De Marzo, A.M., Sfanos, K.S. & Laurence, M (2014). MSMB variation and prostate cancer risk: Clues towards a possible fungal etiology. The Prostate, 74(6), 569-578.
- Laurence M., Hatzis C., Brash D.E. (2014). Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes. PLoS ONE 9(5): e97876.
- Laurence, M. & Benito-León, J. (2017). Epstein–Barr Virus and Multiple Sclerosis: Updating Pender's Hypothesis. Mult Scler Relat Disord, 16, 8-14.
- Benito-León, J. & Laurence, M. (2017). The Role of Fungi in the Etiology of Multiple Sclerosis. Front Neurol, 8, 535.
- Laurence, M., Asquith, M., Rosenbaum, J.T. (2018). Spondyloarthritis, Acute Anterior Uveitis and Fungi: Updating the Catterall King Hypothesis.
Front Med. 5, 80. - Laurence, M. (2018). PSP94, what is it good for? Sixth edition. Montreal, Canada.
- Benito-León, J., Laurence, M. (2019). Malassezia in the central nervous system and multiple sclerosis. Infection 47(1):135-136
- Laurence, M., Benito-León, J. & Calon, F (2019). Malassezia and Parkinson's disease. Front Neurol, 10, 758.
- Laurence, M. (draft). No microbe left behind. First edition (draft). Montreal, Canada.
|
|
