Publications

2014

J. Ashworth, B. Bernard, S. Reynolds, C. L. Plaisier, I. Shmulevich, N. S. Baliga, “Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers,” Nucleic Acids Research, Vol. 42, No. 21, pp. 12973-12983, 2014.

The Cancer Genome Atlas Research Network, “Integrated Genomic Characterization of Papillary Thyroid Carcinoma,” Cell, Vol. 159, No. 3, pp. 676–690, 2014.

The Cancer Genome Atlas Research Network, “Comprehensive Molecular Characterization of Gastric Adenocarcinoma,” Nature, Vol. 513, pp. 202–209, 2014.

S. Kang, S. Kahan, J. McDermott, N. Flann, I. Shmulevich, “Biocellion: Accelerating Computer Simulation of Multicellular Biological System Models,” Bioinformatics, Vol. 30, No. 21, pp. 3101-3108, 2014.

T. A. Knijnenburg, S. A. Ramsey, B. P. Berman, K. A. Kennedy, A.F.A. Smit, L. F.A. Wessels, P. W. Laird, A. Aderem, I. Shmulevich, “Multiscale representation of genomic signals,” Nature Methods, Vol. 11, pp. 689–669, 2014.

X. Li, Y. Liu, K. J. Granberg, Q. Wang, L. M. Moore, P. Ji, J. Gumin, E. P. Sulman, G. A. Calin, H. Haapasalo, M. Nykter, I. Shmulevich, G. N. Fuller, F. F. Lang, W. Zhang, “Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma,” Oncogene, Vol. 34, pp. 1619-1628, 2014.

C. J. Kemp, J. M. Moore, R. Moser, B. Bernard, M. Teater, L. E. Smith, N. Rabaia, K. E. Gurley, J. Guinney, S. E. Busch, R. Shaknovich, V. V. Lobanenkov, D. Liggitt, I. Shmulevich, A. Melnick, G. N. Filippova, “CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer,” Cell Reports, Vol. 7, No. 4, pp. 1020–1029, 2014.

The Cancer Genome Atlas Research Network, “Comprehensive molecular characterization of urothelial bladder carcinoma,” Nature, Vol. 507, pp. 315–322, 2014.

G. Liu, Y. Sun, P. Ji, X. Li, D. Cogdell, D. Yang, B. C. Parker-Kerrigan, I. Shmulevich, K. Chen, A. K. Sood, F. Xue, W. Zhang, “MiR-506 Suppresses Proliferation and Induces Senescence by Directly Targeting the CDK4/6-FOXM1 Axis in Ovarian Cancer,” The Journal of Pathology, Vol. 233, No. 3, pp. 308-318, 2014.

Y. Liu , L. Patel , G. B. Mills, K. H. Lu , A. K. Sood , L. Ding, R. Kucherlapati , E. Mardis, D. A. Levine, I. Shmulevich, R. R. Broaddus, W. Zhang, “Clinical Significance of CTNNB1 Mutation and Wnt Pathway Activation in Endometrioid Endometrial Carcinoma,” Journal of the National Cancer Institute, Vol. 106, No. 9, 2014.

F. Guo, B. C. Parker, D. Yang, L. Hu, I. Shmulevich, A. K. Sood, F. Xue, W. Zhang, “Post-Transcriptional Regulatory Network of Epithelial-to-Mesenchymal and Mesenchymal-to-Epithelial Transitions,” Journal of Hematology & Oncology, Vol. 7, No. 19, 2014.

P. Ruusuvuori, Jake Lin, A. C. Scott, Z. Tan, S. Sorsa, A. Kallio, M. Nykter, O. Yli-Harja, I. Shmulevich, A. M. Dudley, “Quantitative analysis of colony morphology in yeast,” BioTechniques, Vol. 56, No. 1, pp. 18–27, 2014.