Publications

2013

J. Lin, R. Kreisberg, A. Kallio, A. M. Dudley, M. Nykter, I. Shmulevich, P. May, R. Autio, “POMO – Plotting Omics analysis results for Multiple Organisms,” BMC Genomics, Vol. 14, No. 1, 918, 2013.

C. W. Brennan, R.G.W. Verhaak, A. McKenna, B. Campos, H. Noushmehr, S. R. Salama, S. Zheng, D. Chakravarty, J. Z. Sanborn, S. H. Berman, R. Beroukhim, B. Bernard, C.J. Wu, G. Genovese, I. Shmulevich, J. Barnholtz-Sloan, L. Zou, R. Vegesna, S. A. Shukla, G. Ciriello, W.K. Yung, W. Zhang, C. Sougnez, T. Mikkelsen, K. Aldape, D. D. Bigner, E. G. Van Meir, M. Prados, A. Sloan, K. L. Black, J. Eschbacher, G. Finocchiaro, W. Friedman, D. W. Andrews, A. Guha, M. Iacocca, B. P. O’Neill, G. Foltz, J. Myers, D. J. Weisenberger, R. Penny, R. Kucherlapati, C. M. Perou, D. N. Hayes, R. Gibbs, M. Marra, G. B. Mills, E. Lander, P. Spellman, R. Wilson, C. Sander, J. Weinstein, M. Meyerson, S. Gabriel, P. W. Laird, D. Haussler, G. Getz, L. Chin, TCGA Research Network, “The Somatic Genomic Landscape of Glioblastoma,” Cell, Vol. 155, No. 2, pp. 462-477, 2013.

The Cancer Genome Atlas Research Network, John N. Weinstein, Eric A. Collisson, Gordon B. Mills, Kenna R. Shaw, Brad A. Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M. Stuart, “The Cancer Genome Atlas Pan-Cancer analysis project,” Nature Genetics, Vol. 45, No. 10, pp. 1113-1120, 2013.

The Cancer Genome Atlas Research Network, “Integrated genomic characterization of endometrial carcinoma,” Nature, Vol. 497, pp. 67–73, 2013.

M. Heinäniemi, M. Nykter, R. Kramer, A. Wienecke-Baldacchino, L. Sinkkonen, J. X. Zhou, R. Kreisberg, S. A. Kauffman, S. Huang, I. Shmulevich, “Gene-pair expression signatures reveal lineage control,” Nature Methods, Vol. 10, pp. 577–583, 2013.

A. Sadot, S. Sarbu, J. Kesseli, H. Amir-Kroll, W. Zhang, M. Nykter, I. Shmulevich, “Information-Theoretic Analysis of the Dynamics of an Executable Biological Model,” PLoS ONE, Vol. 8, No. 3, e59303, 2013.

D. Yang, Y. Sun, L. Hu, H. Zheng, P. Ji, C. V. Pecot, Y. Zhao, S. Reynolds, H. Cheng, R. Rupaimoole, D. Cogdell, M. Nykter, R. Broaddus, C. Rodriguez-Aguayo, G. Lopez-Berestein, J. Liu, I. Shmulevich, A. K. Sood, K. Chen, W. Zhang, “Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer,” Cancer Cell, Vol. 23, No. 2, pp. 186-199, 2013.

A. Larjo, I. Shmulevich, H. Lähdesmäki, “Structure learning for Bayesian networks as models of biological networks,” Methods in Molecular Biology, Vol. 939, pp. 35-45, 2013.

H. Mirzaei, T. A. Knijnenburg, B. Kim, M. Robinson, P. Picotti, G. W. Carter, S. Li, D. J. Dilworth, J. K. Eng, J. D. Aitchison, I. Shmulevich, T. Galitski, R. Aebersold, J. Ranish, “Systematic measurement of transcription factor-DNA interactions by SRM mass spectrometry identifies candidate gene regulatory proteins,” Proceedings of the National Academy of Sciences of the USA, Vol. 110, No. 9, pp. 3645-3650, 2013.

L. M. Moore, V. Kivinen, Y. Liu, M. Annala, D. Cogdell, X. Liu, C.G. Liu, R. Sawaya, O. Yli-Harja, I. Shmulevich, G.N. Fuller, W. Zhang, M. Nykter, “Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma,” The Journal of Pathology, Vol. 229, No. 3, pp. 449-459, 2013.