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Items: 1 to 50 of 52

1.

A Mechanism of Resistance to Antibody-Targeted Immune Attack.

Aldeghaither DS, Zahavi DJ, Murray JC, Fertig EJ, Graham GT, Zhang YW, O'Connell A, Ma J, Jablonski SA, Weiner LM.

Cancer Immunol Res. 2019 Feb;7(2):230-243. doi: 10.1158/2326-6066.CIR-18-0266. Epub 2018 Dec 18.

PMID:
30563830
2.

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.

3.

Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma.

Kelley DZ, Flam EL, Guo T, Danilova LV, Zamuner FT, Bohrson C, Considine M, Windsor EJ, Bishop JA, Zhang C, Koch WM, Sidransky D, Westra WH, Chung CH, Califano JA, Wheelan S, Favorov AV, Florea L, Fertig EJ, Gaykalova DA.

Transl Res. 2018 Dec;202:109-119. doi: 10.1016/j.trsl.2018.07.007. Epub 2018 Jul 26.

PMID:
30118659
4.

Molecular Portrait of Hypoxia in Breast Cancer: A Prognostic Signature and Novel HIF-Regulated Genes.

Ye IC, Fertig EJ, DiGiacomo JW, Considine M, Godet I, Gilkes DM.

Mol Cancer Res. 2018 Dec;16(12):1889-1901. doi: 10.1158/1541-7786.MCR-18-0345. Epub 2018 Jul 23.

PMID:
30037853
5.

Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance.

Stein-O'Brien G, Kagohara LT, Li S, Thakar M, Ranaweera R, Ozawa H, Cheng H, Considine M, Schmitz S, Favorov AV, Danilova LV, Califano JA, Izumchenko E, Gaykalova DA, Chung CH, Fertig EJ.

Genome Med. 2018 May 23;10(1):37. doi: 10.1186/s13073-018-0545-2.

6.

Digitizing omics profiles by divergence from a baseline.

Dinalankara W, Ke Q, Xu Y, Ji L, Pagane N, Lien A, Matam T, Fertig EJ, Price ND, Younes L, Marchionni L, Geman D.

Proc Natl Acad Sci U S A. 2018 May 1;115(18):4545-4552. doi: 10.1073/pnas.1721628115. Epub 2018 Apr 16.

7.

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.

PMID:
29342249
8.

DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma.

Finegersh A, Kulich S, Guo T, Favorov AV, Fertig EJ, Danilova LV, Gaykalova DA, Califano JA, Duvvuri U.

Sci Rep. 2017 Nov 9;7(1):15173. doi: 10.1038/s41598-017-15634-9.

9.

StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data.

Stavrovskaya ED, Niranjan T, Fertig EJ, Wheelan SJ, Favorov AV, Mironov AA.

Bioinformatics. 2017 Oct 15;33(20):3158-3165. doi: 10.1093/bioinformatics/btx379.

10.

Epigenetic regulation of gene expression in cancer: techniques, resources and analysis.

Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Wick HC, Danilova LV, Easwaran H, Favorov AV, Qian J, Gaykalova DA, Fertig EJ.

Brief Funct Genomics. 2018 Jan 1;17(1):49-63. doi: 10.1093/bfgp/elx018.

11.

Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks.

Kelley DZ, Flam EL, Izumchenko E, Danilova LV, Wulf HA, Guo T, Singman DA, Afsari B, Skaist AM, Considine M, Welch JA, Stavrovskaya E, Bishop JA, Westra WH, Khan Z, Koch WM, Sidransky D, Wheelan SJ, Califano JA, Favorov AV, Fertig EJ, Gaykalova DA.

Cancer Res. 2017 Dec 1;77(23):6538-6550. doi: 10.1158/0008-5472.CAN-17-0833. Epub 2017 Sep 25.

12.

An unbiased in vivo functional genomics screening approach in mice identifies novel tumor cell-based regulators of immune rejection.

Shuptrine CW, Ajina R, Fertig EJ, Jablonski SA, Kim Lyerly H, Hartman ZC, Weiner LM.

Cancer Immunol Immunother. 2017 Dec;66(12):1529-1544. doi: 10.1007/s00262-017-2047-2. Epub 2017 Aug 2.

13.

A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers.

Guo T, Sakai A, Afsari B, Considine M, Danilova L, Favorov AV, Yegnasubramanian S, Kelley DZ, Flam E, Ha PK, Khan Z, Wheelan SJ, Gutkind JS, Fertig EJ, Gaykalova DA, Califano J.

Cancer Res. 2017 Oct 1;77(19):5248-5258. doi: 10.1158/0008-5472.CAN-16-3106. Epub 2017 Jul 21.

14.

A Software Application for Mining and Presenting Relevant Cancer Clinical Trials per Cancer Mutation.

Gandy LM, Gumm J, Blackford AL, Fertig EJ, Diaz LA Jr.

Cancer Inform. 2017 Jun 22;16:1176935117711940. doi: 10.1177/1176935117711940. eCollection 2017.

15.

SMAD4 Loss Is Associated with Cetuximab Resistance and Induction of MAPK/JNK Activation in Head and Neck Cancer Cells.

Ozawa H, Ranaweera RS, Izumchenko E, Makarev E, Zhavoronkov A, Fertig EJ, Howard JD, Markovic A, Bedi A, Ravi R, Perez J, Le QT, Kong CS, Jordan RC, Wang H, Kang H, Quon H, Sidransky D, Chung CH.

Clin Cancer Res. 2017 Sep 1;23(17):5162-5175. doi: 10.1158/1078-0432.CCR-16-1686. Epub 2017 May 18.

16.

Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques.

Gandy LM, Gumm J, Fertig B, Thessen A, Kennish MJ, Chavan S, Marchionni L, Xia X, Shankrit S, Fertig EJ.

PLoS One. 2017 Apr 24;12(4):e0175860. doi: 10.1371/journal.pone.0175860. eCollection 2017.

17.

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.

18.

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.

19.

Comparative mutational landscape analysis of patient-derived tumour xenografts.

Brait M, Izumchenko E, Kagohara LT, Long S, Wysocki PT, Faherty B, Fertig EJ, Khor TO, Bruckheimer E, Baia G, Ciznadija D, Sloma I, Ben-Zvi I, Paz K, Sidransky D.

Br J Cancer. 2017 Feb 14;116(4):515-523. doi: 10.1038/bjc.2016.450. Epub 2017 Jan 24.

20.

Systems Approaches to Cancer Biology.

Archer TC, Fertig EJ, Gosline SJ, Hafner M, Hughes SK, Joughin BA, Meyer AS, Piccolo SR, Shajahan-Haq AN.

Cancer Res. 2016 Dec 1;76(23):6774-6777. Epub 2016 Nov 18.

21.

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.

22.

The effects of lacosamide on cognition, quality-of-life measures, and quality of life in patients with refractory partial epilepsy.

Lancman ME, Fertig EJ, Trobliger RW, Perrine K, Myers L, Iyengar SS, Malik M.

Epilepsy Behav. 2016 Aug;61:27-33. doi: 10.1016/j.yebeh.2016.04.049. Epub 2016 Jun 14.

23.

Identification of methylated genes in salivary gland adenoid cystic carcinoma xenografts using global demethylation and methylation microarray screening.

Ling S, Rettig EM, Tan M, Chang X, Wang Z, Brait M, Bishop JA, Fertig EJ, Considine M, Wick MJ, Ha PK.

Int J Oncol. 2016 Jul;49(1):225-34. doi: 10.3892/ijo.2016.3532. Epub 2016 May 18.

24.

Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma.

Guo T, Gaykalova DA, Considine M, Wheelan S, Pallavajjala A, Bishop JA, Westra WH, Ideker T, Koch WM, Khan Z, Fertig EJ, Califano JA.

Int J Cancer. 2016 Jul 15;139(2):373-82. doi: 10.1002/ijc.30081. Epub 2016 Mar 30.

25.

Inferring causal molecular networks: empirical assessment through a community-based effort.

Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.

Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb 22.

26.

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.

27.

Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma.

Rettig EM, Talbot CC Jr, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig EJ, Wheelan SJ, Marchionni L, Considine M, Ling S, Fakhry C, Papadopoulos N, Kinzler KW, Vogelstein B, Ha PK, Agrawal N.

Cancer Prev Res (Phila). 2016 Apr;9(4):265-74. doi: 10.1158/1940-6207.CAPR-15-0316. Epub 2016 Feb 9. Erratum in: Cancer Prev Res (Phila). 2018 Apr;11(4):249.

28.

Epigenetic screening of salivary gland mucoepidermoid carcinoma identifies hypomethylation of CLIC3 as a common alteration.

Wang Z, Ling S, Rettig E, Sobel R, Tan M, Fertig EJ, Considine M, El-Naggar AK, Brait M, Fakhry C, Ha PK.

Oral Oncol. 2015 Dec;51(12):1120-5. doi: 10.1016/j.oraloncology.2015.09.010. Epub 2015 Oct 17.

29.

Analysis of gene expression of secreted factors associated with breast cancer metastases in breast cancer subtypes.

Fertig EJ, Lee E, Pandey NB, Popel AS.

Sci Rep. 2015 Jul 15;5:12133. doi: 10.1038/srep12133.

30.

Decreased SMAD4 expression is associated with induction of epithelial-to-mesenchymal transition and cetuximab resistance in head and neck squamous cell carcinoma.

Cheng H, Fertig EJ, Ozawa H, Hatakeyama H, Howard JD, Perez J, Considine M, Thakar M, Ranaweera R, Krigsfeld G, Chung CH.

Cancer Biol Ther. 2015;16(8):1252-8. doi: 10.1080/15384047.2015.1056418. Epub 2015 Jun 5.

31.

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.

32.

Functional normalization of 450k methylation array data improves replication in large cancer studies.

Fortin JP, Labbe A, Lemire M, Zanke BW, Hudson TJ, Fertig EJ, Greenwood CM, Hansen KD.

Genome Biol. 2014 Dec 3;15(12):503. doi: 10.1186/s13059-014-0503-2.

33.

Learning dysregulated pathways in cancers from differential variability analysis.

Afsari B, Geman D, Fertig EJ.

Cancer Inform. 2014 Oct 23;13(Suppl 5):61-7. doi: 10.4137/CIN.S14066. eCollection 2014. Review.

34.

p16 protein expression and human papillomavirus status as prognostic biomarkers of nonoropharyngeal head and neck squamous cell carcinoma.

Chung CH, Zhang Q, Kong CS, Harris J, Fertig EJ, Harari PM, Wang D, Redmond KP, Shenouda G, Trotti A, Raben D, Gillison ML, Jordan RC, Le QT.

J Clin Oncol. 2014 Dec 10;32(35):3930-8. doi: 10.1200/JCO.2013.54.5228. Epub 2014 Sep 29.

35.

switchBox: an R package for k-Top Scoring Pairs classifier development.

Afsari B, Fertig EJ, Geman D, Marchionni L.

Bioinformatics. 2015 Jan 15;31(2):273-4. doi: 10.1093/bioinformatics/btu622. Epub 2014 Sep 26.

36.

Loss of Trop2 causes ErbB3 activation through a neuregulin-1-dependent mechanism in the mesenchymal subtype of HNSCC.

Zhang K, Jones L, Lim S, Maher CA, Adkins D, Lewis J, Kimple RJ, Fertig EJ, Chung CH, Van Tine BA, Ellis MJ, Herrlich A, Michel LS.

Oncotarget. 2014 Oct 15;5(19):9281-94.

37.

Breast cancer cells condition lymphatic endothelial cells within pre-metastatic niches to promote metastasis.

Lee E, Fertig EJ, Jin K, Sukumar S, Pandey NB, Popel AS.

Nat Commun. 2014 Sep 2;5:4715. doi: 10.1038/ncomms5715.

38.

A 3'-UTR KRAS-variant is associated with cisplatin resistance in patients with recurrent and/or metastatic head and neck squamous cell carcinoma.

Chung CH, Lee JW, Slebos RJ, Howard JD, Perez J, Kang H, Fertig EJ, Considine M, Gilbert J, Murphy BA, Nallur S, Paranjape T, Jordan RC, Garcia J, Burtness B, Forastiere AA, Weidhaas JB.

Ann Oncol. 2014 Nov;25(11):2230-6. doi: 10.1093/annonc/mdu367. Epub 2014 Jul 31. Erratum in: Ann Oncol. 2015 May;26(5):1038-9.

39.

Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction.

Parker HS, Leek JT, Favorov AV, Considine M, Xia X, Chavan S, Chung CH, Fertig EJ.

Bioinformatics. 2014 Oct;30(19):2757-63. doi: 10.1093/bioinformatics/btu375. Epub 2014 Jun 6.

40.

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.

41.

Pattern identification in time-course gene expression data with the CoGAPS matrix factorization.

Fertig EJ, Stein-O'Brien G, Jaffe A, Colantuoni C.

Methods Mol Biol. 2014;1101:87-112. doi: 10.1007/978-1-62703-721-1_6.

PMID:
24233779
42.

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.

43.

Dynamics in hybrid complex systems of switches and oscillators.

Taylor D, Fertig EJ, Restrepo JG.

Chaos. 2013 Sep;23(3):033142. doi: 10.1063/1.4822017.

44.

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.

45.

Inhibition of TGF-β enhances the in vivo antitumor efficacy of EGF receptor-targeted therapy.

Bedi A, Chang X, Noonan K, Pham V, Bedi R, Fertig EJ, Considine M, Califano JA, Borrello I, Chung CH, Sidransky D, Ravi R.

Mol Cancer Ther. 2012 Nov;11(11):2429-39. doi: 10.1158/1535-7163.MCT-12-0101-T. Epub 2012 Aug 27.

46.

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.

47.

Matrix Factorization for Transcriptional Regulatory Network Inference.

Ochs MF, Fertig EJ.

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

48.

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.

49.

Quantifying the dynamics of coupled networks of switches and oscillators.

Francis MR, Fertig EJ.

PLoS One. 2012;7(1):e29497. doi: 10.1371/journal.pone.0029497. Epub 2012 Jan 5.

50.

Application of genomic and proteomic technologies in biomarker discovery.

Fertig EJ, Slebos R, Chung CH.

Am Soc Clin Oncol Educ Book. 2012:377-82. doi: 10.14694/EdBook_AM.2012.32.377.

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