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Items: 1 to 20 of 45

1.

Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC.

Gaykalova DA, Zizkova V, Guo T, Tiscareno I, Wei Y, Vatapalli R, Hennessey PT, Ahn J, Danilova L, Khan Z, Bishop JA, Gutkind JS, Koch WM, Westra WH, Fertig EJ, Ochs MF, Califano JA.

Oncotarget. 2017 Feb 28;8(9):15349-15363. doi: 10.18632/oncotarget.14856.

2.

CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network.

Fertig EJ, Ozawa H, Thakar M, Howard JD, Kagohara LT, Krigsfeld G, Ranaweera RS, Hughes RM, Perez J, Jones S, Favorov AV, Carey J, Stein-O'Brien G, Gaykalova DA, Ochs MF, Chung CH.

Oncotarget. 2016 Nov 8;7(45):73845-73864. doi: 10.18632/oncotarget.12075.

3.

Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination.

Stansfield JC, Rusay M, Shan R, Kelton C, Gaykalova DA, Fertig EJ, Califano JA, Ochs MF.

Cancer Inform. 2016 Feb 10;15:15-21. doi: 10.4137/CIN.S32468. eCollection 2016.

4.

Outlier Analysis Defines Zinc Finger Gene Family DNA Methylation in Tumors and Saliva of Head and Neck Cancer Patients.

Gaykalova DA, Vatapalli R, Wei Y, Tsai HL, Wang H, Zhang C, Hennessey PT, Guo T, Tan M, Li R, Ahn J, Khan Z, Westra WH, Bishop JA, Zaboli D, Koch WM, Khan T, Ochs MF, Califano JA.

PLoS One. 2015 Nov 6;10(11):e0142148. doi: 10.1371/journal.pone.0142148. eCollection 2015.

5.

NF-κB and stat3 transcription factor signatures differentiate HPV-positive and HPV-negative head and neck squamous cell carcinoma.

Gaykalova DA, Manola JB, Ozawa H, Zizkova V, Morton K, Bishop JA, Sharma R, Zhang C, Michailidi C, Considine M, Tan M, Fertig EJ, Hennessey PT, Ahn J, Koch WM, Westra WH, Khan Z, Chung CH, Ochs MF, Califano JA.

Int J Cancer. 2015 Oct 15;137(8):1879-89. doi: 10.1002/ijc.29558. Epub 2015 Jun 23.

6.

Correcting transcription factor gene sets for copy number and promoter methylation variations.

Rathi KS, Gaykalova DA, Hennessey P, Califano JA, Ochs MF.

Drug Dev Res. 2014 Sep;75(6):343-7. doi: 10.1002/ddr.21220.

7.

Two clinical phenotypes in polycythemia vera.

Spivak JL, Considine M, Williams DM, Talbot CC Jr, Rogers O, Moliterno AR, Jie C, Ochs MF.

N Engl J Med. 2014 Aug 28;371(9):808-17. doi: 10.1056/NEJMoa1403141.

8.

Outlier Analysis and Top Scoring Pair for Integrated Data Analysis and Biomarker Discovery.

Ochs MF, Farrar JE, Considine M, Wei Y, Meshinchi S, Arceci RJ.

IEEE/ACM Trans Comput Biol Bioinform. 2014 May-Jun;11(3):520-32. doi: 10.1109/TCBB.2013.153.

9.

Expression microarray analysis reveals alternative splicing of LAMA3 and DST genes in head and neck squamous cell carcinoma.

Li R, Ochs MF, Ahn SM, Hennessey P, Tan M, Soudry E, Gaykalova DA, Uemura M, Brait M, Shao C, Westra W, Bishop J, Fertig EJ, Califano JA.

PLoS One. 2014 Mar 27;9(3):e91263. doi: 10.1371/journal.pone.0091263. eCollection 2014.

10.

Novel insight into mutational landscape of head and neck squamous cell carcinoma.

Gaykalova DA, Mambo E, Choudhary A, Houghton J, Buddavarapu K, Sanford T, Darden W, Adai A, Hadd A, Latham G, Danilova LV, Bishop J, Li RJ, Westra WH, Hennessey P, Koch WM, Ochs MF, Califano JA, Sun W.

PLoS One. 2014 Mar 25;9(3):e93102. doi: 10.1371/journal.pone.0093102. eCollection 2014.

11.

Activation of the NOTCH pathway in head and neck cancer.

Sun W, Gaykalova DA, Ochs MF, Mambo E, Arnaoutakis D, Liu Y, Loyo M, Agrawal N, Howard J, Li R, Ahn S, Fertig E, Sidransky D, Houghton J, Buddavarapu K, Sanford T, Choudhary A, Darden W, Adai A, Latham G, Bishop J, Sharma R, Westra WH, Hennessey P, Chung CH, Califano JA.

Cancer Res. 2014 Feb 15;74(4):1091-104. doi: 10.1158/0008-5472.CAN-13-1259. Epub 2013 Dec 18.

12.

Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis.

Fertig EJ, Markovic A, Danilova LV, Gaykalova DA, Cope L, Chung CH, Ochs MF, Califano JA.

PLoS One. 2013 Nov 4;8(11):e78127. doi: 10.1371/journal.pone.0078127. eCollection 2013.

13.

t4 workshop report: Pathways of Toxicity.

Kleensang A, Maertens A, Rosenberg M, Fitzpatrick S, Lamb J, Auerbach S, Brennan R, Crofton KM, Gordon B, Fornace AJ Jr, Gaido K, Gerhold D, Haw R, Henney A, Ma'ayan A, McBride M, Monti S, Ochs MF, Pandey A, Sharan R, Stierum R, Tugendreich S, Willett C, Wittwehr C, Xia J, Patton GW, Arvidson K, Bouhifd M, Hogberg HT, Luechtefeld T, Smirnova L, Zhao L, Adeleye Y, Kanehisa M, Carmichael P, Andersen ME, Hartung T.

ALTEX. 2014;31(1):53-61. doi: 10.14573/altex.1309261. Epub 2013 Oct 15.

14.

Identifying context-specific transcription factor targets from prior knowledge and gene expression data.

Fertig EJ, Favorov AV, Ochs MF.

IEEE Trans Nanobioscience. 2013 Sep;12(3):142-9. doi: 10.1109/TNB.2013.2263390. Epub 2013 May 16.

15.

Implications of systemic dysfunction for the etiology of malignancy.

Knox SS, Ochs MF.

Gene Regul Syst Bio. 2013;7:11-22. doi: 10.4137/GRSB.S10943. Epub 2013 Feb 6.

16.

ZNF-mediated resistance to imatinib mesylate in gastrointestinal stromal tumor.

Rink L, Ochs MF, Zhou Y, von Mehren M, Godwin AK.

PLoS One. 2013;8(1):e54477. doi: 10.1371/journal.pone.0054477. Epub 2013 Jan 25.

17.

A requirement for Nedd9 in luminal progenitor cells prior to mammary tumorigenesis in MMTV-HER2/ErbB2 mice.

Little JL, Serzhanova V, Izumchenko E, Egleston BL, Parise E, Klein-Szanto AJ, Loudon G, Shubina M, Seo S, Kurokawa M, Ochs MF, Golemis EA.

Oncogene. 2014 Jan 23;33(4):411-20. doi: 10.1038/onc.2012.607. Epub 2013 Jan 14.

18.

MAGEB2 is activated by promoter demethylation in head and neck squamous cell carcinoma.

Pattani KM, Soudry E, Glazer CA, Ochs MF, Wang H, Schussel J, Sun W, Hennessey P, Mydlarz W, Loyo M, Demokan S, Smith IM, Califano JA.

PLoS One. 2012;7(9):e45534. doi: 10.1371/journal.pone.0045534. Epub 2012 Sep 24.

19.

Updating annotations with the distributed annotation system and the automated sequence annotation pipeline.

Speier W, Ochs MF.

Bioinformatics. 2012 Nov 1;28(21):2858-9. doi: 10.1093/bioinformatics/bts530. Epub 2012 Sep 3.

20.

Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma.

Fertig EJ, Ren Q, Cheng H, Hatakeyama H, Dicker AP, Rodeck U, Considine M, Ochs MF, Chung CH.

BMC Genomics. 2012 May 1;13:160.

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