Elana J. Fertig, Ph.D. - Publications

2007 Applied Mathematics and Scientific Computation University of Maryland, College Park, College Park, MD 
Atmospheric Sciences, Remote Sensing

44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Ling S, Rettig EM, Tan M, Chang X, Wang Z, Brait M, Bishop JA, Fertig EJ, Considine M, Wick MJ, Ha PK. Identification of methylated genes in salivary gland adenoid cystic carcinoma xenografts using global demethylation and methylation microarray screening. International Journal of Oncology. PMID 27212063 DOI: 10.3892/Ijo.2016.3532  0.48
2016 Guo T, Gaykalova DA, Considine M, Wheelan S, Pallavajjala A, Bishop JA, Westra WH, Ideker T, Koch WM, Khan Z, Fertig EJ, Califano JA. Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma. International Journal of Cancer. PMID 26949921 DOI: 10.1002/Ijc.30081  0.48
2016 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, ... ... Fertig EJ, et al. Inferring causal molecular networks: empirical assessment through a community-based effort. Nature Methods. PMID 26901648 DOI: 10.1038/Nmeth.3773  0.48
2016 Stansfield JC, Rusay M, Shan R, Kelton C, Gaykalova DA, Fertig EJ, Califano JA, Ochs MF. Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination. Cancer Informatics. 15: 15-21. PMID 26884679 DOI: 10.4137/Cin.S32468  0.48
2016 Rettig EM, Talbot C, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig E, Wheelan S, Marchionni L, Considine M, Fakhry C, Papadopoulos N, et al. Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma. Cancer Prevention Research (Philadelphia, Pa.). PMID 26862087 DOI: 10.1158/1940-6207.Capr-15-0316  0.48
2015 Wang Z, Ling S, Rettig E, Sobel R, Tan M, Fertig EJ, Considine M, El-Naggar AK, Brait M, Fakhry C, Ha PK. Epigenetic screening of salivary gland mucoepidermoid carcinoma identifies hypomethylation of CLIC3 as a common alteration. Oral Oncology. PMID 26490796 DOI: 10.1016/J.Oraloncology.2015.09.010  0.48
2015 Izumchenko E, Chang X, Brait M, Fertig E, Kagohara LT, Bedi A, Marchionni L, Agrawal N, Ravi R, Jones S, Hoque MO, Westra WH, Sidransky D. Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA. Nature Communications. 6: 8258. PMID 26374070 DOI: 10.1038/Ncomms9258  0.48
2015 Fertig EJ, Lee E, Pandey NB, Popel AS. Analysis of gene expression of secreted factors associated with breast cancer metastases in breast cancer subtypes. Scientific Reports. 5: 12133. PMID 26173622 DOI: 10.1038/Srep12133  0.48
2015 Cheng H, Fertig EJ, Ozawa H, Hatakeyama H, Howard JD, Perez J, Considine M, Thakar M, Ranaweera R, Krigsfeld G, Chung CH. Decreased SMAD4 expression is associated with induction of epithelial-to-mesenchymal transition and cetuximab resistance in head and neck squamous cell carcinoma. Cancer Biology & Therapy. 1-7. PMID 26046389 DOI: 10.1080/15384047.2015.1056418  0.48
2015 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, et al. NF-κB and stat3 transcription factor signatures differentiate HPV-positive and HPV-negative head and neck squamous cell carcinoma. International Journal of Cancer. Journal International Du Cancer. PMID 25857630 DOI: 10.1002/Ijc.29558  0.48
2015 Gajula RP, Chettiar ST, Williams RD, Nugent K, Kato Y, Wang H, Malek R, Taparra K, Cades J, Annadanam A, Yoon AR, Fertig E, Firulli BA, Mazzacurati L, Burns TF, et al. Structure-function studies of the bHLH phosphorylation domain of TWIST1 in prostate cancer cells. Neoplasia (New York, N.Y.). 17: 16-31. PMID 25622896 DOI: 10.1016/J.Neo.2014.10.009  0.48
2015 Afsari B, Fertig EJ, Geman D, Marchionni L. switchBox: an R package for k-Top Scoring Pairs classifier development. Bioinformatics (Oxford, England). 31: 273-4. PMID 25262153 DOI: 10.1093/Bioinformatics/Btu622  0.48
2015 Considine M, Parker H, Wei Y, Xia X, Cope L, Ochs M, Fertig E. AGA: Interactive pipeline for reproducible genomics analyses F1000research. 4. DOI: 10.12688/f1000research.6030.1  0.48
2015 Kelton CJ, Lee W, Rusay M, Maxian O, Fertig EJ, Ochs MF. The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization Proceedings - 2015 Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2015. 1642-1649. DOI: 10.1109/BIBM.2015.7359922  0.48
2014 Fortin JP, Labbe A, Lemire M, Zanke BW, Hudson TJ, Fertig EJ, Greenwood CM, Hansen KD. Functional normalization of 450k methylation array data improves replication in large cancer studies. Genome Biology. 15: 503. PMID 25599564 DOI: 10.1186/S13059-014-0503-2  0.48
2014 Afsari B, Geman D, Fertig EJ. Learning dysregulated pathways in cancers from differential variability analysis. Cancer Informatics. 13: 61-7. PMID 25392694 DOI: 10.4137/Cin.S14066  0.48
2014 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. p16 protein expression and human papillomavirus status as prognostic biomarkers of nonoropharyngeal head and neck squamous cell carcinoma. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 32: 3930-8. PMID 25267748 DOI: 10.1200/Jco.2013.54.5228  0.48
2014 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. Loss of Trop2 causes ErbB3 activation through a neuregulin-1-dependent mechanism in the mesenchymal subtype of HNSCC. Oncotarget. 5: 9281-94. PMID 25238142 DOI: 10.18632/Oncotarget.2423  0.48
2014 Lee E, Fertig EJ, Jin K, Sukumar S, Pandey NB, Popel AS. Breast cancer cells condition lymphatic endothelial cells within pre-metastatic niches to promote metastasis. Nature Communications. 5: 4715. PMID 25178650 DOI: 10.1038/Ncomms5715  0.48
2014 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, et al. A 3'-UTR KRAS-variant is associated with cisplatin resistance in patients with recurrent and/or metastatic head and neck squamous cell carcinoma. Annals of Oncology : Official Journal of the European Society For Medical Oncology / Esmo. 25: 2230-6. PMID 25081901 DOI: 10.1093/Annonc/Mdu367  0.48
2014 Parker HS, Leek JT, Favorov AV, Considine M, Xia X, Chavan S, Chung CH, Fertig EJ. Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction. Bioinformatics (Oxford, England). 30: 2757-63. PMID 24907368 DOI: 10.1093/Bioinformatics/Btu375  0.48
2014 Guerrero-Preston R, Michailidi C, Marchionni L, Pickering CR, Frederick MJ, Myers JN, Yegnasubramanian S, Hadar T, Noordhuis MG, Zizkova V, Fertig E, Agrawal N, Westra W, Koch W, Califano J, et al. Key tumor suppressor genes inactivated by "greater promoter" methylation and somatic mutations in head and neck cancer. Epigenetics : Official Journal of the Dna Methylation Society. 9: 1031-46. PMID 24786473 DOI: 10.4161/Epi.29025  0.48
2014 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. Expression microarray analysis reveals alternative splicing of LAMA3 and DST genes in head and neck squamous cell carcinoma. Plos One. 9: e91263. PMID 24675808 DOI: 10.1371/Journal.Pone.0091263  0.48
2014 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, et al. Activation of the NOTCH pathway in head and neck cancer. Cancer Research. 74: 1091-104. PMID 24351288 DOI: 10.1158/0008-5472.Can-13-1259  0.48
2014 Fertig EJ, Stein-O'Brien G, Jaffe A, Colantuoni C. Pattern identification in time-course gene expression data with the CoGAPS matrix factorization. Methods in Molecular Biology (Clifton, N.J.). 1101: 87-112. PMID 24233779 DOI: 10.1007/978-1-62703-721-1_6  0.48
2014 Fortin JP, Fertig E, Hansen K. shinyMethyl: Interactive quality control of Illumina 450k DNA methylation arrays in R F1000research. 3. DOI: 10.12688/f1000research.4680.2  0.48
2013 Fertig EJ, Markovic A, Danilova LV, Gaykalova DA, Cope L, Chung CH, Ochs MF, Califano JA. Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis. Plos One. 8: e78127. PMID 24223768 DOI: 10.1371/Journal.Pone.0078127  0.48
2013 Taylor D, Fertig EJ, Restrepo JG. Dynamics in hybrid complex systems of switches and oscillators. Chaos (Woodbury, N.Y.). 23: 033142. PMID 24089978 DOI: 10.1063/1.4822017  0.48
2013 Gajula RP, Chettiar ST, Williams RD, Thiyagarajan S, Kato Y, Aziz K, Wang R, Gandhi N, Wild AT, Vesuna F, Ma J, Salih T, Cades J, Fertig E, Biswal S, et al. The twist box domain is required for Twist1-induced prostate cancer metastasis. Molecular Cancer Research : McR. 11: 1387-400. PMID 23982216 DOI: 10.1158/1541-7786.Mcr-13-0218-T  0.48
2013 Fertig EJ, Favorov AV, Ochs MF. Identifying context-specific transcription factor targets from prior knowledge and gene expression data. Ieee Transactions On Nanobioscience. 12: 142-9. PMID 23694699 DOI: 10.1109/Tnb.2013.2263390  0.48
2013 Bauman JE, Arias-Pulido H, Lee SJ, Fekrazad MH, Ozawa H, Fertig E, Howard J, Bishop J, Wang H, Olson GT, Spafford MJ, Jones DV, Chung CH. A phase II study of temsirolimus and erlotinib in patients with recurrent and/or metastatic, platinum-refractory head and neck squamous cell carcinoma. Oral Oncology. 49: 461-7. PMID 23384718 DOI: 10.1016/J.Oraloncology.2012.12.016  0.48
2012 Ochs MF, Fertig EJ. Matrix Factorization for Transcriptional Regulatory Network Inference. Ieee Symposium On Computational Intelligence in Bioinformatics and Computational Biology Proceedings Ieee Symposium On Computational Intelligence in Bioinformatics and Computational Biology. 2012: 387-396. PMID 25364782 DOI: 10.1109/CIBCB.2012.6217256  0.48
2012 Bedi A, Chang X, Noonan K, Pham V, Bedi R, Fertig EJ, Considine M, Califano JA, Borrello I, Chung CH, Sidransky D, Ravi R. Inhibition of TGF-β enhances the in vivo antitumor efficacy of EGF receptor-targeted therapy. Molecular Cancer Therapeutics. 11: 2429-39. PMID 22927667 DOI: 10.1158/1535-7163.Mct-12-0101-T  0.48
2012 Fertig EJ, Ren Q, Cheng H, Hatakeyama H, Dicker AP, Rodeck U, Considine M, Ochs MF, Chung CH. Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma. Bmc Genomics. 13: 160. PMID 22549044 DOI: 10.1186/1471-2164-13-160  0.48
2012 Francis MR, Fertig EJ. Quantifying the dynamics of coupled networks of switches and oscillators. Plos One. 7: e29497. PMID 22242172 DOI: 10.1371/Journal.Pone.0029497  0.48
2011 Fertig EJ, Danilova LV, Favorov AV, Ochs MF. Hybrid Modeling of Cell Signaling and Transcriptional Reprogramming and Its Application in C. elegans Development. Frontiers in Genetics. 2: 77. PMID 22303372 DOI: 10.3389/Fgene.2011.00077  0.48
2011 Li H, Liu JJ, Fertig E, Kalnay E, Kostelich E, Szunyogh I. Improved analyses and forecasts with AIRS temperature retrievals using the local ensemble transform Kalman filter Journal of Tropical Meteorology. 17: 43-49. DOI: 10.3969/J.Issn.1006-8775.2011.01.006  0.48
2011 Aravéquia JA, Szunyogh I, Fertig EJ, Kalnay E, Kuhl D, Kostelich EJ. Evaluation of a strategy for the assimilation of satellite radiance observations with the local ensemble transform Kalman filter Monthly Weather Review. 139: 1932-1951. DOI: 10.1175/2010Mwr3515.1  0.48
2010 Fertig EJ, Ding J, Favorov AV, Parmigiani G, Ochs MF. CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. Bioinformatics (Oxford, England). 26: 2792-3. PMID 20810601 DOI: 10.1093/Bioinformatics/Btq503  0.48
2010 Fertig B, Carruthers TJB, Dennison WC, Fertig EJ, Altabet MA. Eastern oyster (Crassostrea virginica) δ15N as a bioindicator of nitrogen sources: Observations and modeling Marine Pollution Bulletin. 60: 1288-1298. PMID 20381097 DOI: 10.1016/J.Marpolbul.2010.03.013  0.48
2009 Fertig EJ, Baek SJ, Hunt BR, Ott E, Szunyogh I, Aravéquia JA, Kalnay E, Li H, Liu J. Observation bias correction with an ensemble Kalman filter Tellus, Series a: Dynamic Meteorology and Oceanography. 61: 210-226. DOI: 10.1111/J.1600-0870.2008.00378.X  0.48
2008 Liu J, Fertig EJ, Li H, Kalnay E, Hunt BR, Kostelich EJ, Szunyogh I, Todling R. Comparison between Local Ensemble Transform Kalman Filter and PSAS in the NASA finite volume GCM - Perfect model experiments Nonlinear Processes in Geophysics. 15: 645-659. DOI: 10.5194/Npg-15-645-2008  0.48
2007 Fertig EJ, Hunt BR, Ott E, Szunyogh I. Assimilating non-local observations with a local ensemble Kalman filter Tellus, Series a: Dynamic Meteorology and Oceanography. 59: 719-730. DOI: 10.1111/J.1600-0870.2007.00260.X  0.48
2007 Fertig EJ, Harlim J, Hunt BR. A comparative study of 4D-VAR and a 4D Ensemble Kalman Filter: Perfect model simulations with Lorenz-96 Tellus, Series a: Dynamic Meteorology and Oceanography. 59: 96-100. DOI: 10.1111/J.1600-0870.2006.00205.X  0.48
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