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Analyzing crystals to help fight cancer
By: Help Conquer Cancer research team
28 Aug 2015   

Summary
Behind-the-scenes work continues on the Help Conquer Cancer project - the team is analyzing millions of protein crystallization images processed by World Community Grid volunteers, with the hope of finding patterns that will help researchers build better cancer screening tools.

Dear World Community Grid volunteers:

We continue to analyze the millions of protein-crystallization images that you processed as part of Help Conquer Cancer (HCC), with the end goal of gaining insight into the crystallization process. In turn, this will enable us to crystalize cancer and other disease-related proteins, determine their structure, function, and design drugs accordingly. We aim to identify non-trivial, interesting and ultimately useful patterns in this large and valuable data set.

We strive to integrate more detailed data we have received from Hauptman Woodward Institute which will allow us to interpret patterns we are identifying and linking properties of proteins, conditions, and temporal data to specific images that were processed on World Community Grid. Work is ongoing, albeit more slowly at present, as the Post Doctoral Fellow working on the integration and data mining had to take a leave of absence to expand her teaching skills. Christian continues to dedicate some of his time to the HCC project, but also had to expand on the analysis and streamline infrastructure to support our Mapping Cancer Markers project.

We have been working on some novel analysis angles with a visiting student from Denmark, and a new student is expected to start working on the project in the Fall 2015. We therefore expect to be able to give you more detailed results in the next HCC update, which we will provide in a few months.

In the meantime, here are some recent cancer-related publications and media coverage by our group, which all relate to our effort to identify better algorithms for determining prognostic/predictive signatures and work towards finding and validating novel treatment options for cancer patients. Combined, results from these papers feeds into our new work units for the MCM project, and in turn, results from the MCM projects feed into this research.

Recent publications, presentations and media coverage

MediaPublications
  • Navab, R., Strumpf, D., Jurisica, I., Walker, C. G., Gullberg, D., Tsao, M.S. Integrin a11b1 regulates cancer stromal stiffness and promotes tumorigenecity in non-small cell lung cancer, Oncogene, 2015. In press.
  • Camargo, J. F., Resende, M., Zamel, R., Klement, W., Bhimji, A., Huibner, S., Kumar, D., Humar, A., Jurisica, I., Keshavjee, S., Kaul, R., Husain, S. Potential role of CC chemokine receptor 6 (CCR6) in prediction of late-onset CMV infection following solid organ transplant. Clinical Transplantation, 2015. In press. doi: 10.1111/ctr.12531
  • Tu, W.B., Helander, S., PilstÃ¥l, R., Hickman, K.A., Lourenco, C., Jurisica, I., Raught, B., Wallner, B., Sunnerhagen, M., Penn, L.Z. Myc and its interactors take shape. Biochim Biophys Acta, 1849(5): 469-483, 2015.
  • Dingar, D., Kalkat, M., Chan, M. P-K, Bailey, S.D., Srikumar, T., Tu, W.B., Ponzielli, R., Kotlyar, M., Jurisica, I., Huang, A., Lupien, M., Penn, L.Z., Raught, B. BioID identifies novel c-MYC interacting partners in cultured cells and xenograft tumors, J Proteomics, 2015. doi: 10.1016/j.jprot.2014.09.029
  • Wong, S. W. H., Cercone, N., Jurisica, I. Comparative network analysis via differential graphlet communities, Special Issue of Proteomics dedicated to Signal Transduction, Proteomics, 15(2-3):608-17, 2015. E-pub 2014/10/07. doi: 10.1002/pmic.201400233
  • Kotlyar M., Pastrello C., Pivetta, F., Lo Sardo A., Cumbaa, C., Li, H., Naranian, T., Niu Y., Ding Z., Vafaee F., Broackes-Carter F., Petschnigg, J., Mills, G.B., Jurisicova, A., Stagljar, I., Maestro, R., & Jurisica, I. In silico prediction of physical protein interactions and characterization of interactome orphans, Nat Methods, 12(1):79-84, 2015. E-pub 2014/11/18.
Editorial
  • Hoeng J, Peitsch MC, Meyer, P. and Jurisica, I. Where are we at regarding Species Translation? A review of the sbv IMPROVER Challenge, Bioinformatics, 31(4):451-452, 2015.
Presentations
  • Keynote: Life of an orphan protein, Symposium on Computational Biology, eScience approaches for biomedical data analysis, University of Southern Denmark, Odense, June 10-12
  • Invited highlight presentation: In silico prediction of physical protein interactions and characterization of interactome orphans, [BC]2 Basel Computational Biology Conference, Basel, June 7-10


 


Project Update

Help Conquer Cancer research team

1 Feb 2015
by Randall C. Willis, DDNews