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Items: 1 to 50 of 72

1.

Enter the Matrix: Factorization Uncovers Knowledge from Omics.

Stein-O'Brien GL, Arora R, Culhane AC, Favorov AV, Garmire LX, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ.

Trends Genet. 2018 Oct;34(10):790-805. doi: 10.1016/j.tig.2018.07.003. Epub 2018 Aug 22. Review.

2.

Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.

Afsari B, Guo T, Considine M, Florea L, Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Zambo KD, Ha PK, Geman D, Ochs MF, Califano JA, Gaykalova DA, Favorov AV, Fertig EJ.

Bioinformatics. 2018 Jun 1;34(11):1859-1867. doi: 10.1093/bioinformatics/bty004.

3.

Evaluating optimal therapy robustness by virtual expansion of a sample population, with a case study in cancer immunotherapy.

Barish S, Ochs MF, Sontag ED, Gevertz JL.

Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):E6277-E6286. doi: 10.1073/pnas.1703355114. Epub 2017 Jul 17.

4.

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.

Stein-O'Brien GL, Carey JL, Lee WS, Considine M, Favorov AV, Flam E, Guo T, Li S, Marchionni L, Sherman T, Sivy S, Gaykalova DA, McKay RD, Ochs MF, Colantuoni C, Fertig EJ.

Bioinformatics. 2017 Jun 15;33(12):1892-1894. doi: 10.1093/bioinformatics/btx058.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

The present state and future direction of integrated gene function analysis.

Ochs MF.

Methods Mol Biol. 2014;1101:3-9. doi: 10.1007/978-1-62703-721-1_1.

PMID:
24233774
17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

Matrix Factorization for Transcriptional Regulatory Network Inference.

Ochs MF, Fertig EJ.

IEEE Symp Comput Intell Bioinforma Comput Biol Proc. 2012 May;2012:387-396.

27.

Serum microRNA biomarkers for detection of non-small cell lung cancer.

Hennessey PT, Sanford T, Choudhary A, Mydlarz WW, Brown D, Adai AT, Ochs MF, Ahrendt SA, Mambo E, Califano JA.

PLoS One. 2012;7(2):e32307. doi: 10.1371/journal.pone.0032307. Epub 2012 Feb 28.

28.

Hybrid Modeling of Cell Signaling and Transcriptional Reprogramming and Its Application in C. elegans Development.

Fertig EJ, Danilova LV, Favorov AV, Ochs MF.

Front Genet. 2011 Nov 8;2:77. doi: 10.3389/fgene.2011.00077. eCollection 2011.

29.

[Pharmacogenomics of multiple sclerosis: association of immune response genes polymorphism with copaxone treatment efficacy].

Tsareva EIu, Kulakova OG, Makarycheva OIu, Boĭko AN, Shchur SG, Lashch NIu, Popova NF, Gusev EI, Bashinskaia VV, L'vov DV, Favorov AV, Ochs MF, Favorova OO.

Mol Biol (Mosk). 2011 Nov-Dec;45(6):963-72. Russian.

PMID:
22295566
30.

OnionTree XML: a format to exchange gene-related probabilities.

Favorov A, Lvovs D, Speier W, Parmigiani G, Ochs MF.

J Biomol Struct Dyn. 2011 Oct;29(2):417-23. No abstract available.

31.

Promoter methylation in head and neck squamous cell carcinoma cell lines is significantly different than methylation in primary tumors and xenografts.

Hennessey PT, Ochs MF, Mydlarz WW, Hsueh W, Cope L, Yu W, Califano JA.

PLoS One. 2011;6(5):e20584. doi: 10.1371/journal.pone.0020584. Epub 2011 May 26.

32.

Identification of aberrant pathway and network activity from high-throughput data.

Ochs MF, Karchin R, Ressom H, Gentleman R.

Pac Symp Biocomput. 2011:364-8.

33.

A comprehensive statistical model for cell signaling.

Yörük E, Ochs MF, Geman D, Younes L.

IEEE/ACM Trans Comput Biol Bioinform. 2011 May-Jun;8(3):592-606. doi: 10.1109/TCBB.2010.87.

34.

CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.

Fertig EJ, Ding J, Favorov AV, Parmigiani G, Ochs MF.

Bioinformatics. 2010 Nov 1;26(21):2792-3. doi: 10.1093/bioinformatics/btq503. Epub 2010 Sep 1.

35.

Global reactivation of epigenetically silenced genes in prostate cancer.

Ibragimova I, Ibáñez de Cáceres I, Hoffman AM, Potapova A, Dulaimi E, Al-Saleem T, Hudes GR, Ochs MF, Cairns P.

Cancer Prev Res (Phila). 2010 Sep;3(9):1084-92. doi: 10.1158/1940-6207.CAPR-10-0039. Epub 2010 Aug 10.

36.

[Complex analsis of association of inflammation genes with myocardial infarction].

Sudomoina MA, Sukhinina TS, Barsova RM, Favorov AV, Shakhnovich RM, Titov BV, Matveeva NA, Rybalkin IN, Vlasik TN, Ochs MF, Ruda MIa, Favorova OO.

Mol Biol (Mosk). 2010 May-Jun;44(3):463-71. Russian.

PMID:
20608170
37.

Matrix factorisation methods applied in microarray data analysis.

Kossenkov AV, Ochs MF.

Int J Data Min Bioinform. 2010;4(1):72-90. Review.

38.

A resource for analysis of microRNA expression and function in pancreatic ductal adenocarcinoma cells.

Kent OA, Mullendore M, Wentzel EA, López-Romero P, Tan AC, Alvarez H, West K, Ochs MF, Hidalgo M, Arking DE, Maitra A, Mendell JT.

Cancer Biol Ther. 2009 Nov;8(21):2013-24.

39.

Integrative discovery of epigenetically derepressed cancer testis antigens in NSCLC.

Glazer CA, Smith IM, Ochs MF, Begum S, Westra W, Chang SS, Sun W, Bhan S, Khan Z, Ahrendt S, Califano JA.

PLoS One. 2009 Dec 4;4(12):e8189. doi: 10.1371/journal.pone.0008189.

40.

Detection of treatment-induced changes in signaling pathways in gastrointestinal stromal tumors using transcriptomic data.

Ochs MF, Rink L, Tarn C, Mburu S, Taguchi T, Eisenberg B, Godwin AK.

Cancer Res. 2009 Dec 1;69(23):9125-32. doi: 10.1158/0008-5472.CAN-09-1709. Epub 2009 Nov 10.

41.

[Complex analysis of genetic predisposition to ischemic stroke in Russians].

Parfenov MG, Titov BV, Sudomoina MA, Martynov MIu, Favorov AV, Ochs MF, Gusev EI, Favorova OO.

Mol Biol (Mosk). 2009 Sep-Oct;43(5):937-45. Russian.

PMID:
19899640
42.

Matrix factorization for recovery of biological processes from microarray data.

Kossenkov AV, Ochs MF.

Methods Enzymol. 2009;467:59-77. doi: 10.1016/S0076-6879(09)67003-8.

43.

[Genetic predisposition to multiple sclerosis as a polygenic autoimmune disease].

Favorova OO, Favorov AV, Boĭko AN, Sudomoina MA, Andreevskiĭ TV, Alekseenkov AD, Kulakova OG, Gusev EI, Parmigiani G, Ochs MF.

Zh Nevrol Psikhiatr Im S S Korsakova. 2009;109(7 Suppl 2):16-22. Russian.

PMID:
19894308
44.

Knowledge-based data analysis comes of age.

Ochs MF.

Brief Bioinform. 2010 Jan;11(1):30-9. doi: 10.1093/bib/bbp044. Epub 2009 Oct 23.

45.

Gene expression signatures and response to imatinib mesylate in gastrointestinal stromal tumor.

Rink L, Skorobogatko Y, Kossenkov AV, Belinsky MG, Pajak T, Heinrich MC, Blanke CD, von Mehren M, Ochs MF, Eisenberg B, Godwin AK.

Mol Cancer Ther. 2009 Aug;8(8):2172-82. doi: 10.1158/1535-7163.MCT-09-0193. Epub 2009 Aug 11.

46.

Coordinated activation of candidate proto-oncogenes and cancer testes antigens via promoter demethylation in head and neck cancer and lung cancer.

Smith IM, Glazer CA, Mithani SK, Ochs MF, Sun W, Bhan S, Vostrov A, Abdullaev Z, Lobanenkov V, Gray A, Liu C, Chang SS, Ostrow KL, Westra WH, Begum S, Dhara M, Califano J.

PLoS One. 2009;4(3):e4961. doi: 10.1371/journal.pone.0004961. Epub 2009 Mar 23.

47.

Information systems for cancer research.

Ochs MF, Casagrande JT.

Cancer Invest. 2008 Dec;26(10):1060-7. doi: 10.1080/07357900802272729.

48.

The insulin-like growth factor system as a potential therapeutic target in gastrointestinal stromal tumors.

Belinsky MG, Rink L, Cai KQ, Ochs MF, Eisenberg B, Huang M, von Mehren M, Godwin AK.

Cell Cycle. 2008 Oct;7(19):2949-55. Epub 2008 Oct 7. Review.

49.

Gene function analysis. Preface.

Ochs MF.

Methods Mol Biol. 2007;408:vii-ix. No abstract available.

PMID:
18350679
50.

Estimating gene function with least squares nonnegative matrix factorization.

Wang G, Ochs MF.

Methods Mol Biol. 2007;408:35-47. doi: 10.1007/978-1-59745-547-3_3.

PMID:
18314576

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