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2010 | 2009 | 2008 | 2007 | 2006 | 2005

Research using NAViGaTOR

The following papers and publications have used NAViGaTOR or its earlier versions:

Year 2010

  • Radulovich, N., Pham, N. A., Strumpf, D., Leung, L., Xie, W., Jurisica, I., Tsao, M. S. (2010)
    Differential roles of cyclin D1 and D3 in pancreatic ductal adenocarcinoma.
    Mol Cancer, 9(1): 24, 2010.

  • Fortney, K., Kotlyar, M., Jurisica, I.(2010)
    Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging.
    Genome Biol, 11(2): R13, 2010.

  • Niu, Y., Otasek, D., Jurisica, I. (2010)
    Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D.
    Bioinformatics, 26(1):111-119, 2010. Epub: 2009/10/24.

  • Robinson-White, S., Conroy, B., Slavish, K.H., Rosenzweig, M.(2010)
    Patient navigation in breast cancer: a systematic review.
    Cancer Nurs, 33(2):127-40, 2010 Mar-Apr

  • Gehlenborg, N., O'Donoghue, S.I., Baliga, N.S., Goesmann, A., Hibbs, M.A., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D., Gavin, A.C.(2010)
    Visualization of omics data for systems biology.
    Nat Methods. 7(3 Suppl):S56-68. Review., 2010 Mar

Year 2009

  • Deribe, Y.L., P. Wild, A. Chandrashaker, J. Curak, M. H.H. Schmidt, Y. Kalaidzidis, N. Milutinovic, I. Kratchmarova, L. Buerkle, M. J.Fetchko, P. Schmidt, S. Kittanakom, K. R. Brown, I. Jurisica, B. Blagoev, M. Zerial, I. Stagljar, and I. Dikic. (2010)
    Regulation of Epidermal Growth Factor Receptor Trafficking by Lysine Deacetylase HDAC6.
    Sci Signal, 2(102): RA84, 2009. Epub: 2009/12/24.

  • Agarwal, R., Jurisica, I., Cheng K.W., Mills G.B. (2009. In Press)
    The emerging role of the Rab25 small GTPase in cancer.
    Traffic, 2009. E-Pub July 23, 2009. In Press.

  • McGuffin, M., and Jurisica, I.(2009)
    Interaction techniques for selecting and manipulating subgraphs in network visualizations.
    IEEE Transactions on Visualization and Computer Graphics (TVCG), Vol. 15, No. 6, November/December 2009, pages 937-944 (8 pages).
    [ * Honorable Mention ]

  • Savas, S., Geraci, J., Jurisica, I., Liu, G. (2009)
    A comprehensive catalogue of functional genetic variations in the EGFR pathway: Protein-protein interaction analysis reveals novel genes and polymorphisms important for cancer research.
    Int J Cancer, 125, 1257-65, 2009. In press.

  • Cox, B., Kotlyar, M., Evangelou, A., Ignatchenko, V., Ignatchenko, A., Whiteley, K., Jurisica, I., Adamson, L., Rossant, J., Kislinger, T. (2009)
    Comparative systems biology of human and mouse as a tool for modeling human placental pathology.
    Mol Sys Bio, 5, 279, 2009.

  • Mills, G. B., Jurisica, I., Yarden, Y., Norman, J. C. (2009)
    Genomic amplicons target vesicle recycling in breast cancer.
    J Clin Invest, 119, 2123-7, 2009.

  • Dong, J., Kislinger, T., Jurisica, I., Wigle, D. A. (2009)
    Lung cancer: Developmental networks gone awry?
    Cancer Biol Ther, 8(4), 2009.

  • Ihekwaba A.E., Nguyen P.T., Priami C. (2009)
    Elucidation of functional consequences of signalling pathway interactions.
    BMC Bioinformatics, 10:370, Nov 6, 2009

  • Paananen J., Wong G. (2009)
    FORG3D: force-directed 3D graph editor for visualization of integrated genome scale data.
    BMC Syst Biol, 3:36, Feb 24, 2009

Year 2008

  • Tomasini, R., Tsuchihara, K., Wilhelm, M., Fujitani, M., Rufini, A., Cheung, C.C., Khan, F., Itie-Youten, A., Wakeham, A., Tsao, M.-S., Iovanna J. L., Squire, J., Jurisica, I., Kaplan, D., Melino, G., Jurisicova, A. and Mak, T. W. (2008)
    TAp73 knockout shows genomic instability with tumor suppressor.
    Genes Dev, 22(19): 2677-91, 2008. ePub 2008/09/23.

  • Sodek K.L., Evangelou A.I., Ignatchenko A., Brown T.J., Ringuette M., Jurisica I., & Kislinger T.(2008)
    Identification of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identification technology (MudPIT).
    Mol Biosyst, 4(7):762-773, 2008.

  • Gortzak-Uzan, L., Ignatchenko, A., Evangelou, A., Agochiya, M., Brown, K. St.Onge, P., Kireeva, I., Schmitt-Ulms, G., Brown, T., Murphy, J., Rosen, B., Shaw, P., Jurisica, I., Kislinger, T. (2008)
    A proteome resource of ovarian cancer ascites: Integrated proteomic and bioinformatic analyses to identify putative biomarkers.
    Journal of Proteome Research. 7(1): 339-351, 2008.

  • Helena Skalnikova, Petr Vodicka, Steven Pelech, Jan Motlik, Suresh Jivan Gadher, Hana Kovarova. (2008)
    Protein signaling pathways in differentiation of neural stem cells.
    PROTEOMICS. 8(21): 4547-4559, 2008.
    [ Wiley InterScience ]

  • SR Hegde, P Manimaran, SC Mande, L Lai - assets0.pubget.com (2008)
    Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with ...
    ... Sub-Network Visualization: Sub-networks were visualized and analyzed using Cytoscape 2.4.1 [38] and NAViGaTOR (http://ophid.utoronto.ca/ navigator/).....

Year 2007

  • Brown, K. and I. Jurisica.(2007)
    Unequal evolutionary conservation of human protein interactions in interologous networks.
    Genome Biology,8(5), 2007.

  • Cox, B., T. Kislinger, D. A. Wigle, A. Kannan, K. Brown, T. Okubo, B. Hogan, I. Jurisica, B. Frey, J. Rossant and A. Emili. (2007)
    Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes.
    Molecular Systems Biology, 3:109, 2007.

  • Lau, S.K., P. C. Boutros, M. Pintilie, F. H. Blackhall, C.-Q. Zhu, D. Strumpf, M. R. Johnston, G. Darling, S. Keshavjee, T. K. Waddell, N. Liu, D. Lau, L. Z. Penn, F. A. Shepherd, I. Jurisica, S. D. Der, M.-S. Tsao. (2007)
    A three-gene prognostic classifier for early-stage non-small cell lung cancer.
    J Clinical Oncology, 25(35): 5562-5569, 2007.

  • Wu, C., Ma, M. H., Brown, K. R., Geisler, M., Li, L., Tzeng, E., Jia, C. Y., Jurisica, I., Li, S. S.(2007)
    Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening.
    Proteomics, 7(11):1775-85, 2007.

  • Cox, B., T. Kislinger, D. A. Wigle, A. Kannan, K. Brown, T. Okubo, B. Hogan, I. Jurisica, B. Frey, J. Rossant and A. Emili.(2007)
    Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes,
    Molecular Systems Biology, 3:109, 2007.

  • Barrios-Rodiles, M., A. Viloria-Petit, K. R. Brown, I. Jurisica, and J. L. Wrana.(2007)
    High-throughput screening of protein interaction networks in the TGFb interactome: understanding the signaling mechanisms driving tumor progression.
    Cancer Drug Discovery and Development: Transforming Growth Factor-b in Cancer Therapy, Vol 2: Cancer Treatment and Therapy, Edited by Sonia B. Jakowlew, Humana Press Inc., Totowa, N.J., 2007.

  • D. A. Wigle and I. Jurisica.(2007)
    Cancer as a system failure.
    Cancer Informatics. Systems Biology Special Issue editorial. 3(2): 10-18, 2007.

  • Jurisica, I., D. A. Wigle, and B. Wong.(2007)
    Cancer Informatics in the Post-Genomics Era.
    Implementing Information-Based Medicine, Series: Cancer Treatment and Research, Volume 137, Springer Verlag, July 2007.
    [ PubMed ]

  • R Loganantharaj, J Chung - hindawi.com. (2007)
    Integrating Diverse Information to Gain More Insight into Microarray Analysis.
    Biol, vol. 8, pp. R95, 2007. Page 15. [19] "NAViGaTOR 2.0," in http://ophid.utoronto.ca/navigator/index.html, 2008. [20] H. Jeong

Year 2006

  • Jurisica, I. and D. A. Wigle (2006)
    Knowledge Discovery in Proteomics
    Chapman & Hall/CRC Press.
    [ amazon.com ]

  • Motamed-Khorasani, A., I. Jurisica, M. Letarte, P.A. Shaw, R.K. Parkes, X. Zhang, A. Evangelou, B. Rosen, K.J. Murphy, and T.J. Brown. (2006)
    Differentially Androgen-Modulated Genes in Ovarian Epithelial Cells from BRCA Mutation Carriers and Control Patients Predict Ovarian Cancer Survival and Disease Progression.
    Oncogene, 26(2): 198-214.
    [ PubMed ]

  • Seiden-Long, I. M., K. R. Brown, et al. (2006).
    Transcriptional targets of hepatocyte growth factor signaling and Ki-ras oncogene activation in colorectal cancer.
    Oncogene 25(1): 91-102.
    [ PubMed ]

  • Kislinger, T. and I. Jurisica (2006).
    Proteomics and bioinformatics in biomedical research.
    Cancer Genomics and Proteomics 3(1): 11-28.

  • Brierley, M. M., K. L. Marchington, et al. (2006).
    Identification of GAS-dependent interferon-sensitive target genes whose transcription is STAT2-dependent but ISGF3-independent.
    Febs J 273(7): 1569-81.
    [ PubMed ]

Year 2005

  • Brown, K. R. and I. Jurisica (2005)
    Online predicted human interaction database.
    Bioinformatics 21(9): 2076-82.
    [ PubMed ]

  • Barrios-Rodiles, M., K. R. Brown, et al. (2005).
    High-throughput mapping of a dynamic signaling network in mammalian cells.
    Science 307(5715): 1621-5.
    [ PubMed ]