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Results: 1 to 20 of 99

1.

Identification of copy number variants in whole-genome data using Reference Coverage Profiles.

Glusman G, Severson A, Dhankani V, Robinson M, Farrah T, Mauldin DE, Stittrich AB, Ament SA, Roach JC, Brunkow ME, Bodian DL, Vockley JG, Shmulevich I, Niederhuber JE, Hood L.

Front Genet. 2015 Feb 17;6:45. doi: 10.3389/fgene.2015.00045. eCollection 2015.

2.

Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression.

Turner KM, Sun Y, Ji P, Granberg KJ, Bernard B, Hu L, Cogdell DE, Zhou X, Yli-Harja O, Nykter M, Shmulevich I, Yung WK, Fuller GN, Zhang W.

Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3421-6. doi: 10.1073/pnas.1414573112. Epub 2015 Mar 3.

PMID:
25737557
3.

Key nodes of a microRNA network associated with the integrated mesenchymal subtype of high-grade serous ovarian cancer.

Sun Y, Guo F, Bagnoli M, Xue FX, Sun BC, Shmulevich I, Mezzanzanica D, Chen KX, Sood AK, Yang D, Zhang W.

Chin J Cancer. 2015 Jan 5;34(1):28-40. doi: 10.5732/cjc.014.10284.

4.

Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers.

Ashworth J, Bernard B, Reynolds S, Plaisier CL, Shmulevich I, Baliga NS.

Nucleic Acids Res. 2014 Dec 1;42(21):12973-83. doi: 10.1093/nar/gku1031. Epub 2014 Nov 5.

5.

Large-scale molecular characterization and analysis of gastric cancer.

Shmulevich I.

Chin J Cancer. 2014 Aug;33(8):369-70. No abstract available.

6.

Clinical significance of CTNNB1 mutation and Wnt pathway activation in endometrioid endometrial carcinoma.

Liu Y, Patel L, Mills GB, Lu KH, Sood AK, Ding L, Kucherlapati R, Mardis ER, Levine DA, Shmulevich I, Broaddus RR, Zhang W.

J Natl Cancer Inst. 2014 Sep 10;106(9). pii: dju245. doi: 10.1093/jnci/dju245. Print 2014 Sep.

PMID:
25214561
7.

Biocellion: accelerating computer simulation of multicellular biological system models.

Kang S, Kahan S, McDermott J, Flann N, Shmulevich I.

Bioinformatics. 2014 Nov 1;30(21):3101-8. doi: 10.1093/bioinformatics/btu498. Epub 2014 Jul 26.

PMID:
25064572
8.

CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer.

Kemp CJ, Moore JM, Moser R, Bernard B, Teater M, Smith LE, Rabaia NA, Gurley KE, Guinney J, Busch SE, Shaknovich R, Lobanenkov VV, Liggitt D, Shmulevich I, Melnick A, Filippova GN.

Cell Rep. 2014 May 22;7(4):1020-9. doi: 10.1016/j.celrep.2014.04.004. Epub 2014 May 1.

9.

Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma.

Li X, Liu Y, Granberg KJ, Wang Q, Moore LM, Ji P, Gumin J, Sulman EP, Calin GA, Haapasalo H, Nykter M, Shmulevich I, Fuller GN, Lang FF, Zhang W.

Oncogene. 2015 Mar 26;34(13):1619-1628. doi: 10.1038/onc.2014.98. Epub 2014 Apr 21.

PMID:
24747968
10.

Multiscale representation of genomic signals.

Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AF, Wessels LF, Laird PW, Aderem A, Shmulevich I.

Nat Methods. 2014 Jun;11(6):689-94. doi: 10.1038/nmeth.2924. Epub 2014 Apr 13.

11.

MiR-506 suppresses proliferation and induces senescence by directly targeting the CDK4/6-FOXM1 axis in ovarian cancer.

Liu G, Sun Y, Ji P, Li X, Cogdell D, Yang D, Parker Kerrigan BC, Shmulevich I, Chen K, Sood AK, Xue F, Zhang W.

J Pathol. 2014 Jul;233(3):308-18. doi: 10.1002/path.4348. Epub 2014 May 21.

PMID:
24604117
12.

Post-transcriptional regulatory network of epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions.

Guo F, Parker Kerrigan BC, Yang D, Hu L, Shmulevich I, Sood AK, Xue F, Zhang W.

J Hematol Oncol. 2014 Mar 5;7:19. doi: 10.1186/1756-8722-7-19. Review.

13.

Quantitative analysis of colony morphology in yeast.

Ruusuvuori P, Lin J, Scott AC, Tan Z, Sorsa S, Kallio A, Nykter M, Yli-Harja O, Shmulevich I, Dudley AM.

Biotechniques. 2014 Jan;56(1):18-27. doi: 10.2144/000114123.

14.

POMO--Plotting Omics analysis results for Multiple Organisms.

Lin J, Kreisberg R, Kallio A, Dudley AM, Nykter M, Shmulevich I, May P, Autio R.

BMC Genomics. 2013 Dec 24;14:918. doi: 10.1186/1471-2164-14-918.

15.

The somatic genomic landscape of glioblastoma.

Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L; TCGA Research Network.

Cell. 2013 Oct 10;155(2):462-77. doi: 10.1016/j.cell.2013.09.034. Erratum in: Cell. 2014 Apr 24;157(3):753.

16.

The Cancer Genome Atlas Pan-Cancer analysis project.

Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM.

Nat Genet. 2013 Oct;45(10):1113-20. doi: 10.1038/ng.2764.

17.

On the limitations of biological knowledge.

Dougherty ER, Shmulevich I.

Curr Genomics. 2012 Nov;13(7):574-87. doi: 10.2174/138920212803251445.

18.

Gene-pair expression signatures reveal lineage control.

Heinäniemi M, Nykter M, Kramer R, Wienecke-Baldacchino A, Sinkkonen L, Zhou JX, Kreisberg R, Kauffman SA, Huang S, Shmulevich I.

Nat Methods. 2013 Jun;10(6):577-83. doi: 10.1038/nmeth.2445. Epub 2013 Apr 21.

19.

Information-theoretic analysis of the dynamics of an executable biological model.

Sadot A, Sarbu S, Kesseli J, Amir-Kroll H, Zhang W, Nykter M, Shmulevich I.

PLoS One. 2013;8(3):e59303. doi: 10.1371/journal.pone.0059303. Epub 2013 Mar 19.

20.

Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer.

Yang D, Sun Y, Hu L, Zheng H, Ji P, Pecot CV, Zhao Y, Reynolds S, Cheng H, Rupaimoole R, Cogdell D, Nykter M, Broaddus R, Rodriguez-Aguayo C, Lopez-Berestein G, Liu J, Shmulevich I, Sood AK, Chen K, Zhang W.

Cancer Cell. 2013 Feb 11;23(2):186-99. doi: 10.1016/j.ccr.2012.12.020. Erratum in: Cancer Cell. 2013 May 13;23(5):705.

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