Elana J. Fertig, Ph.D. - Publications

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

44/149 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
Low-probability matches
2021 Stein-O'Brien GL, Clark BS, Sherman T, Zibetti C, Hu Q, Sealfon R, Liu S, Qian J, Colantuoni C, Blackshaw S, Goff LA, Fertig EJ. Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species. Cell Systems. 12: 203. PMID 33600760 DOI: 10.1016/j.cels.2021.01.005  0.01
2021 Ajina R, Malchiodi ZX, Fitzgerald AA, Zuo A, Wang S, Moussa M, Cooper CJ, Shen Y, Johnson QR, Parks JM, Smith JC, Catalfamo M, Fertig EJ, Jablonski SA, Weiner LM. Antitumor T-cell Immunity Contributes to Pancreatic Cancer Immune Resistance. Cancer Immunology Research. PMID 33509790 DOI: 10.1158/2326-6066.CIR-20-0272  0.01
2021 Humtsoe JO, Kim HS, Leonard B, Ling S, Keam B, Marchionni L, Afsari B, Considine M, Favorov AV, Fertig EJ, Kang H, Ha PK. Newly identified members of fibroblast growth factor receptor 1 splice variants engage in crosstalk with the AXL/AKT axis in salivary adenoid cystic carcinoma. Cancer Research. PMID 33408119 DOI: 10.1158/0008-5472.CAN-20-1780  0.01
2020 Ho WJ, Sharma G, Zhu Q, Stein-O'Brien G, Durham J, Anders R, Popovic A, Mo G, Kamel I, Weiss M, Jaffee E, Fertig EJ, Yarchoan M. Integrated immunological analysis of a successful conversion of locally advanced hepatocellular carcinoma to resectability with neoadjuvant therapy. Journal For Immunotherapy of Cancer. 8. PMID 33219090 DOI: 10.1136/jitc-2020-000932  0.01
2020 Mi H, Gong C, Sulam J, Fertig EJ, Szalay AS, Jaffee EM, Stearns V, Emens LA, Cimino-Mathews AM, Popel AS. Digital Pathology Analysis Quantifies Spatial Heterogeneity of CD3, CD4, CD8, CD20, and FoxP3 Immune Markers in Triple-Negative Breast Cancer. Frontiers in Physiology. 11: 583333. PMID 33192595 DOI: 10.3389/fphys.2020.583333  0.01
2020 Sherman TD, Gao T, Fertig EJ. CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures. Bmc Bioinformatics. 21: 453. PMID 33054706 DOI: 10.1186/s12859-020-03796-9  0.01
2020 Lopatina T, Favaro E, Danilova L, Fertig EJ, Favorov AV, Kagohara LT, Martone T, Bussolati B, Romagnoli R, Albera R, Pecorari G, Brizzi MF, Camussi G, Gaykalova DA. Extracellular Vesicles Released by Tumor Endothelial Cells Spread Immunosuppressive and Transforming Signals Through Various Recipient Cells. Frontiers in Cell and Developmental Biology. 8: 698. PMID 33015029 DOI: 10.3389/Fcell.2020.00698  0.01
2020 Fertig EJ. A Mentee's Baby Registry: Supporting New Academic Parents in 2020. Cell Systems. PMID 33007226 DOI: 10.1016/j.cels.2020.09.002  0.01
2020 Ren S, Gaykalova DA, Guo T, Favorov AV, Fertig EJ, Tamayo P, Callejas-Valera JL, Allevato M, Gilardi M, Santos J, Fukusumi T, Sakai A, Ando M, Sadat S, Liu C, et al. HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers. Oncogene. PMID 32848210 DOI: 10.1038/S41388-020-01431-8  0.01
2020 Kagohara LT, Zamuner F, Davis-Marcisak EF, Sharma G, Considine M, Allen J, Yegnasubramanian S, Gaykalova DA, Fertig EJ. Correction: Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines. British Journal of Cancer. PMID 32694696 DOI: 10.1038/s41416-020-0998-0  0.01
2020 Wu AA, Bever KM, Ho WJ, Fertig EJ, Niu N, Zheng L, Parkinson RM, Durham JN, Onners BL, Ferguson A, Wilt C, Ko AH, Wang-Gillam A, Laheru DA, Anders RA, et al. A Phase 2 Study of Allogeneic GM-CSF Transfected Pancreatic Tumor Vaccine (GVAX) with Ipilimumab as Maintenance Treatment for Metastatic Pancreatic Cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 32591464 DOI: 10.1158/1078-0432.Ccr-20-1025  0.01
2020 Sakai A, Ando M, Fukusumi T, Ren S, Liu C, Qualliotine J, Haft S, Sadat S, Saito Y, Guo TW, Xu G, Sasik R, Fisch KM, Gutkind JS, Fertig EJ, et al. Aberrant expression of CPSF1 promotes head and neck squamous cell carcinoma via regulating alternative splicing. Plos One. 15: e0233380. PMID 32437477 DOI: 10.1371/Journal.Pone.0233380  0.01
2020 Chu NJ, Anders RA, Fertig EJ, Cao M, Hopkins AC, Keenan BP, Popovic A, Armstrong TD, Jaffee EM, Zimmerman JW. Inhibition of miR-21 regulates mutant KRAS effector pathways and intercepts pancreatic ductal adenocarcinoma development. Cancer Prevention Research (Philadelphia, Pa.). PMID 32409593 DOI: 10.1158/1940-6207.Capr-20-0053  0.01
2020 Erbe R, Kessler MD, Favorov AV, Easwaran H, Gaykalova DA, Fertig EJ. Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets. Nucleic Acids Research. PMID 32392348 DOI: 10.1093/Nar/Gkaa349  0.01
2020 Lu Y, Shiau F, Yi W, Lu S, Wu Q, Pearson JD, Kallman A, Zhong S, Hoang T, Zuo Z, Zhao F, Zhang M, Tsai N, Zhuo Y, He S, ... ... Fertig EJ, et al. Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development. Developmental Cell. PMID 32386599 DOI: 10.1016/J.Devcel.2020.04.009  0.01
2020 Micali N, Kim SK, Diaz-Bustamante M, Stein-O'Brien G, Seo S, Shin JH, Rash BG, Ma S, Wang Y, Olivares NA, Arellano JI, Maynard KR, Fertig EJ, Cross AJ, Bürli RW, et al. Variation of Human Neural Stem Cells Generating Organizer States In Vitro before Committing to Cortical Excitatory or Inhibitory Neuronal Fates. Cell Reports. 31: 107599. PMID 32375049 DOI: 10.1016/J.Celrep.2020.107599  0.01
2020 Kagohara LT, Zamuner F, Davis-Marcisak EF, Sharma G, Considine M, Allen J, Yegnasubramanian S, Gaykalova DA, Fertig EJ. Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines. British Journal of Cancer. PMID 32362655 DOI: 10.1038/S41416-020-0851-5  0.01
2020 Ho WJ, Danilova L, Lim SJ, Verma R, Xavier S, Leatherman JM, Sztein MB, Fertig EJ, Wang H, Jaffee E, Yarchoan M. Viral status, immune microenvironment and immunological response to checkpoint inhibitors in hepatocellular carcinoma. Journal For Immunotherapy of Cancer. 8. PMID 32303615 DOI: 10.1136/Jitc-2019-000394  0.01
2020 Tsujikawa T, Crocenzi T, Durham JN, Sugar EA, Wu AA, Onners B, Nauroth JM, Anders RA, Fertig EJ, Laheru DA, Reiss K, Vonderheide RH, Ko AH, Tempero MA, Fisher GA, et al. Evaluation of Cyclophosphamide/GVAX Pancreas Followed by Listeria-mesothelin (CRS-207) With or Without Nivolumab in Patients with Pancreatic Cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 32273276 DOI: 10.1158/1078-0432.Ccr-19-3978  0.01
2020 Malone MK, Smrekar K, Park S, Blakely B, Walter A, Nasta N, Park J, Considine M, Danilova LV, Pandey NB, Fertig EJ, Popel AS, Jin K. Cytokines secreted by stromal cells in TNBC microenvironment as potential targets for cancer therapy. Cancer Biology & Therapy. 1-10. PMID 32213106 DOI: 10.1080/15384047.2020.1739484  0.01
2020 Sharma G, Colantuoni C, Goff LA, Fertig EJ, Stein-O'Brien G. projectR: An R/Bioconductor package for transfer learning via PCA, NMF, correlation, and clustering. Bioinformatics (Oxford, England). PMID 32167521 DOI: 10.1093/Bioinformatics/Btaa183  0.01
2020 Guo T, Zambo KDA, Zamuner FT, Ou T, Hopkins C, Kelley DZ, Wulf HA, Danilova L, Considine M, Sidransky D, Favorov A, Florea L, Fertig E, Gaykalova DA, Winkler E, et al. Chromatin structure regulates Cancer Specific Alternative Splicing Events in Primary HPV related Oropharyngeal squamous cell carcinoma. Epigenetics. PMID 32164487 DOI: 10.1080/15592294.2020.1741757  0.01
2020 Roussos Torres ET, Sidiropoulos DN, Davis-Marcisak E, Kagohara LT, Connolly RM, Stearns V, Jaffee EM, Fertig EJ. Characterization of the immune tumor microenvironment of HER2-positive breast cancer following treatment with entinostat and immune checkpoint inhibition. Journal of Clinical Oncology. 38: e15061-e15061. DOI: 10.1200/Jco.2020.38.15_Suppl.E15061  0.01
2019 Jafarnejad M, Sové RJ, Danilova L, Mirando AC, Zhang Y, Yarchoan M, Tran PT, Pandey NB, Fertig EJ, Popel AS. Mechanistically detailed systems biology modeling of the HGF/Met pathway in hepatocellular carcinoma. Npj Systems Biology and Applications. 5: 29. PMID 32801315 DOI: 10.1038/s41540-019-0107-2  0.01
2019 Ho WJ, Yarchoan M, Charmsaz S, Munday RM, Danilova L, Sztein MB, Fertig EJ, Jaffee EM. Multi-panel mass cytometry reveals anti-PD1 therapy-mediated B and T cell compartment remodeling in tumor-draining lymph nodes. Jci Insight. PMID 31855578 DOI: 10.1172/Jci.Insight.132286  0.01
2019 Flam EL, Danilova L, Kelley DZ, Stavrovskaya E, Guo T, Considine M, Qian J, Califano JA, Favorov A, Fertig EJ, Gaykalova DA. Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer. Scientific Reports. 9: 15034. PMID 31636280 DOI: 10.1038/S41598-019-51018-X  0.01
2019 Jafarnejad M, Sové RJ, Danilova L, Mirando AC, Zhang Y, Yarchoan M, Tran PT, Pandey NB, Fertig EJ, Popel AS. Mechanistically detailed systems biology modeling of the HGF/Met pathway in hepatocellular carcinoma. Npj Systems Biology and Applications. 5: 29. PMID 31452933 DOI: 10.1038/s41540-019-0107-2  0.01
2019 Espinosa-Cotton M, Fertig EJ, Stabile LP, Gaither-Davis A, Bauman JE, Schmitz S, Gibson-Corley KN, Cheng Y, Jensen IJ, Badovinac VP, Laux D, Simons AL. A preliminary analysis of interleukin-1 ligands as potential predictive biomarkers of response to cetuximab. Biomarker Research. 7: 14. PMID 31346466 DOI: 10.1186/S40364-019-0164-0  0.01
2019 Davis-Marcisak EF, Sherman TD, Orugunta P, Stein-O'Brien GL, Puram SV, Roussos Torres ET, Hopkins AC, Jaffee EM, Favorov AV, Afsari B, Goff LA, Fertig EJ. Differential variation analysis enables detection of tumor heterogeneity using single-cell RNA-sequencing data. Cancer Research. PMID 31337651 DOI: 10.1158/0008-5472.Can-18-3882  0.01
2019 Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, ... ... Fertig EJ, et al. Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nature Communications. 10: 2415. PMID 31142745 DOI: 10.1038/S41467-019-10557-7  0.01
2019 Clark BS, Stein-O'Brien GL, Shiau F, Cannon GH, Davis-Marcisak E, Sherman T, Santiago CP, Hoang TV, Rajaii F, James-Esposito RE, Gronostajski RM, Fertig EJ, Goff LA, Blackshaw S. Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification. Neuron. PMID 31128945 DOI: 10.1016/J.Neuron.2019.04.010  0.01
2019 Hughes RM, Simons BW, Khan H, Miller R, Kugler V, Torquato S, Theodros D, Haffner MC, Lotan TL, Huang J, Davicioni E, An SS, Riddle RC, Thorek DL, Garraway IP, ... Fertig EJ, et al. Asporin Restricts Mesenchymal Stromal Cell Differentiation, Alters the Tumor Microenvironment, and Drives Metastatic Progression. Cancer Research. PMID 31123087 DOI: 10.1158/0008-5472.Can-18-2931  0.01
2019 Stein-O'Brien GL, Clark BS, Sherman T, Zibetti C, Hu Q, Sealfon R, Liu S, Qian J, Colantuoni C, Blackshaw S, Goff LA, Fertig EJ. Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species. Cell Systems. 8: 395-411.e8. PMID 31121116 DOI: 10.1016/J.Cels.2019.04.004  0.01
2019 Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, ... ... Fertig EJ, et al. Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nature Communications. 10: 2188. PMID 31097695 DOI: 10.1038/S41467-019-09937-W  0.01
2019 Danilova L, Ho WJ, Zhu Q, Vithayathil TT, De Jesus-Acosta A, Azad NS, Laheru DA, Fertig EJ, Anders R, Jaffee EM, Yarchoan M. Programmed cell death ligand-1 (PD-L1) and CD8 expression profiling identify an immunologic subtype of pancreatic ductal adenocarcinomas with favorable survival. Cancer Immunology Research. PMID 31043417 DOI: 10.1158/2326-6066.Cir-18-0822  0.01
2019 Sherman TD, Kagohara LT, Cao R, Cheng R, Satriano M, Considine M, Krigsfeld G, Ranaweera R, Tang Y, Jablonski SA, Stein-O'Brien G, Gaykalova DA, Weiner LM, Chung CH, Fertig EJ. CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer. Plos Computational Biology. 14: e1006935. PMID 31002670 DOI: 10.1371/Journal.Pcbi.1006935  0.01
2019 Tao Y, Kang B, Petkovich DA, Bhandari YR, In J, Stein-O'Brien G, Kong X, Xie W, Zachos N, Maegawa S, Vaidya H, Brown S, Chiu Yen RW, Shao X, Thakor J, ... ... Fertig E, et al. Aging-like Spontaneous Epigenetic Silencing Facilitates Wnt Activation, Stemness, and Braf-Induced Tumorigenesis. Cancer Cell. 35: 315-328.e6. PMID 30753828 DOI: 10.1016/J.Ccell.2019.01.005  0.01
2018 Aldeghaither DS, Zahavi DJ, Murray JC, Fertig EJ, Graham GT, Zhang Y, O'Connell A, Ma J, Jablonski SA, Weiner LM. A Mechanism of Resistance to Antibody-Targeted Immune Attack. Cancer Immunology Research. PMID 30563830 DOI: 10.1158/2326-6066.Cir-18-0266  0.01
2018 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. Enter the Matrix: Factorization Uncovers Knowledge from Omics. Trends in Genetics : Tig. PMID 30143323 DOI: 10.1016/J.Tig.2018.07.003  0.01
2018 Kelley DZ, Flam EL, Guo T, Danilova LV, Zamuner F, Bohrson C, Considine M, Windsor EJ, Bishop JA, Zhang C, Koch WM, Sidransky D, Westra WH, Chung CH, Califano JA, ... ... Fertig EJ, et al. Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma. Translational Research : the Journal of Laboratory and Clinical Medicine. PMID 30118659 DOI: 10.1016/J.Trsl.2018.07.007  0.01
2018 Ren S, Gaykalova D, Wang J, Guo T, Danilova L, Favorov A, Fertig E, Bishop J, Khan Z, Flam E, Wysocki PT, DeJong P, Ando M, Liu C, Sakai A, et al. Discovery and development of differentially methylated regions in human papillomavirus related oropharyngeal squamous cell carcinoma. International Journal of Cancer. PMID 30070359 DOI: 10.1002/Ijc.31778  0.01
2018 Ye IC, Fertig EJ, DiGiacomo JW, Considine M, Godet I, Gilkes DM. Molecular Portrait of Hypoxia in Breast Cancer: A Prognostic Signature and Novel HIF-regulated Genes. Molecular Cancer Research : McR. PMID 30037853 DOI: 10.1158/1541-7786.Mcr-18-0345  0.01
2018 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, et al. Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance. Genome Medicine. 10: 37. PMID 29792227 DOI: 10.1186/S13073-018-0545-2  0.01
2018 Dinalankara W, Ke Q, Xu Y, Ji L, Pagane N, Lien A, Matam T, Fertig EJ, Price ND, Younes L, Marchionni L, Geman D. Digitizing omics profiles by divergence from a baseline. Proceedings of the National Academy of Sciences of the United States of America. PMID 29666255 DOI: 10.1073/Pnas.1721628115  0.01
2018 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, et al. Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer. Bioinformatics (Oxford, England). PMID 29342249 DOI: 10.1093/Bioinformatics/Bty004  0.01
2017 Finegersh A, Kulich S, Guo T, Favorov AV, Fertig EJ, Danilova LV, Gaykalova DA, Califano JA, Duvvuri U. DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma. Scientific Reports. 7: 15173. PMID 29123240 DOI: 10.1038/S41598-017-15634-9  0.01
2017 Stavrovskaya ED, Niranjan T, Fertig EJ, Wheelan SJ, Favorov AV, Mironov AA. StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data. Bioinformatics (Oxford, England). 33: 3158-3165. PMID 29028265 DOI: 10.1093/Bioinformatics/Btx379  0.01
2017 Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Wick HC, Danilova LV, Easwaran H, Favorov AV, Qian J, Gaykalova DA, Fertig EJ. Epigenetic regulation of gene expression in cancer: techniques, resources and analysis. Briefings in Functional Genomics. PMID 28968850 DOI: 10.1093/Bfgp/Elx018  0.01
2017 Kelley DZ, Flam E, Izumchenko E, Danilova L, Wulf HA, Guo T, Singman DA, Afsari B, Skaist A, Considine M, Stavrovskaya E, Bishop JA, Westra WH, Khan Z, Koch WM, ... ... Fertig EJ, et al. 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. Cancer Research. PMID 28947419 DOI: 10.1158/0008-5472.Can-17-0833  0.01
2017 Shuptrine CW, Ajina R, Fertig EJ, Jablonski SA, Kim Lyerly H, Hartman ZC, Weiner LM. An unbiased in vivo functional genomics screening approach in mice identifies novel tumor cell-based regulators of immune rejection. Cancer Immunology, Immunotherapy : Cii. PMID 28770278 DOI: 10.1007/S00262-017-2047-2  0.01
2017 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, et al. A novel functional splice variant of AKT3 defined by analysis of alternative splice expression in HPV-positive oropharyngeal cancers. Cancer Research. PMID 28733453 DOI: 10.1158/0008-5472.Can-16-3106  0.01
2017 Gandy LM, Gumm J, Blackford AL, Fertig EJ, Diaz LA. A Software Application for Mining and Presenting Relevant Cancer Clinical Trials per Cancer Mutation. Cancer Informatics. 16: 1176935117711940. PMID 28690394 DOI: 10.1177/1176935117711940  0.01
2017 Ozawa H, Ranaweera R, Izumchenko E, Makarev E, Zhavoronkov A, Fertig EJ, Howard JD, Markovic A, Bedi A, Ravi R, Perez J, Le QT, Kong CS, Jordan RCK, Wang H, et al. SMAD4 loss is associated with cetuximab resistance and induction of MAPK/JNK activation in head and neck cancer cells. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 28522603 DOI: 10.1158/1078-0432.Ccr-16-1686  0.01
2017 Gandy LM, Gumm J, Fertig B, Thessen A, Kennish MJ, Chavan S, Marchionni L, Xia X, Shankrit S, Fertig EJ. Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques. Plos One. 12: e0175860. PMID 28437440 DOI: 10.1371/Journal.Pone.0175860  0.01
2017 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, et al. PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. Bioinformatics (Oxford, England). PMID 28174896 DOI: 10.1093/Bioinformatics/Btx058  0.01
2017 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, et al. Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC. Oncotarget. PMID 28146432 DOI: 10.18632/Oncotarget.14856  0.01
2017 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. Comparative mutational landscape analysis of patient-derived tumour xenografts. British Journal of Cancer. PMID 28118322 DOI: 10.1038/Bjc.2016.450  0.01
2017 Aldeghaither DS, Murray JC, Roth SM, Fertig EJ, Tang S, Jablonski SA, Weiner LM. Induction of tumor cell-based ADCC resistance to create new tumor cell survival and therapy resistance mechanisms. Journal of Clinical Oncology. 35: 130-130. DOI: 10.1200/Jco.2017.35.7_Suppl.130  0.01
2016 Archer TC, Fertig EJ, Gosline SJ, Hafner M, Hughes SK, Joughin BA, Meyer AS, Piccolo SR, Shajahan-Haq AN. Systems Approaches to Cancer Biology. Cancer Research. PMID 27864348 DOI: 10.1158/0008-5472.Can-16-1580  0.01
2016 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, et al. CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network. Oncotarget. PMID 27650546 DOI: 10.18632/Oncotarget.12075  0.01
2015 Considine M, Parker H, Wei Y, Xia X, Cope L, Ochs M, Fertig E. AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses. F1000research. 4: 28. PMID 26535111 DOI: 10.12688/F1000Research.6030.2  0.01
2013 JD H, H C, J P, E R, EJ F, M C, MF O, RJ S, J W, CH C. miRNA array analysis determines miR-205 is overexpressed in head and neck squamous cell carcinoma and enhances cellular proliferation Journal of Cancer Research & Therapy. 1: 153-162. DOI: 10.14312/2052-4994.2013-24  0.01
2012 Fertig EJ, Slebos R, Chung CH. Application of genomic and proteomic technologies in biomarker discovery. American Society of Clinical Oncology Educational Book / Asco. American Society of Clinical Oncology. Meeting. 377-82. PMID 24451767 DOI: 10.14694/EdBook_AM.2012.32.377  0.01
2012 Bauman JE, Arias-Pulido H, Lee S, Considine M, Fekrazad MH, Howard J, Bishop JA, Olson GT, Jones DV, Fertig EJ, Chung CH. Phase II study of temsirolimus and erlotinib in patients (pts) with recurrent/metastatic (R/M), platinum-refractory head and neck squamous cell carcinoma (HNSCC). Journal of Clinical Oncology. 30: 5549-5549. DOI: 10.1200/Jco.2012.30.15_Suppl.5549  0.01
2020 Guo T, Zambo KDA, Zamuner FT, Ou T, Hopkins C, Kelley DZ, Wulf HA, Danilova LV, Considine M, Sidransky D, Favorov AV, Florea L, Fertig EJ, Gaykalova DA. Abstract A25: Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma Clinical Cancer Research. 26. DOI: 10.1158/1557-3265.Aacrahns19-A25  0
2020 Torres ETR, Kagohara LT, Davis E, Rafie C, Christmas B, Zhu Q, Wang C, Lim D, Anders R, Fertig E, Chung V, Lorusso P, Brufsky A, Jaffee EM, Stearns V, et al. Abstract P5-04-06: Reprogramming the suppressive tumor microenvironment of breast cancer Cancer Research. DOI: 10.1158/1538-7445.Sabcs19-P5-04-06  0
2020 Zimmerman JW, Burkhart RA, Chu NJ, Fertig EJ, Jaffee EM. Abstract 5716: miR-21 inhibition regulates mutant KRAS effector pathways and intercepts development of pancreatic ductal adenocarcinoma Tumor Biology. DOI: 10.1158/1538-7445.Am2020-5716  0
2020 Ho WJ, Lin J, Danilova L, Phyo Z, Charmsaz S, Mohan A, Armstrong T, Park BH, Fertig EJ, Zhang Z, Jaffee EM. Abstract 3398: PTPN22 is a systemic target for augmenting antitumor immunity Tumor Biology. DOI: 10.1158/1538-7445.Am2020-3398  0
2020 Sidiropoulos DN, Davis-Marcisak E, Rafie C, Kagohara LT, Sharma G, Connolly RM, Stearns V, Yegnasubramanian S, Jaffee EM, Fertig EJ, Torres ETR. Abstract 1555: Single cell level treatment-specific characterization of HER2+ breast cancers treated with immune checkpoint inhibitors and entinostat Tumor Biology. DOI: 10.1158/1538-7445.Am2020-1555  0
2019 Zamuner FT, Vorontsov I, Flam E, Mukhina V, Danilova L, Ou T, Stavrovskaya E, Guo T, Windsor E, Kelley DZ, Parfenov M, Considine M, Fertig EJ, Favorov A, Gaykalova DA. Abstract 5206: Role of super-enhancers in HPV+ head and neck squamous cell carcinoma Cancer Research. 79: 5206-5206. DOI: 10.1158/1538-7445.Sabcs18-5206  0
2019 Davis-Marcisak EF, Orugunta P, Stein-O'Brien G, Puram SV, Torres ER, Hopkins A, Jaffee EM, Favorov AV, Afsari B, Goff LA, Fertig EJ. Abstract 4697: Expression variation analysis for tumor heterogeneity in single-cell RNA-sequencing data Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-4697  0
2019 Ajina R, Zuo A, Moussa M, Cooper SJ, Shen Y, Johnson QR, Parks JM, Smith JC, Fertig E, Catalfamo M, Jablonski SA, Weiner LM. Abstract 4584: Malignant pancreatic cancer cells respond to immune selection pressure to foster immunosuppression Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-4584  0
2019 Ho WJ, Danilova L, Zhu Q, Vithayathil T, Jesus-Acosta AD, Azad N, Laheru D, Fertig E, Anders R, Jaffee E, Yarchoan M. Abstract 3993: Programmed cell death ligand-1 (PD-L1) and CD8 expression profiling identifies an immunologic subtype of pancreatic ductal adenocarcinomas with favorable survival Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-3993  0
2019 Afsari B, Cope L, Gaykalova DA, Geman D, Puram S, Goff LA, Favorov A, Fertig EJ. Abstract 3399: Uncovering hidden sources of transcriptional dysregulation arising from inter- and intra-tumor heterogeneity Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-3399  0
2019 Kagohara LT, Zamuner F, Considine M, Stein-O'Brien G, Sherman T, Gaykalova DA, Fertig EJ. Abstract 3024: Transcriptional and epigenetic regulation of resistance markers in cetuximab sensitive HNSCC cells Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-3024  0
2019 Torres ETR, Rafie C, Davis E, Kagohara LT, Fertig EJ, Jaffee EM. Abstract 5027: Sequencing the tumor microenvironment and myeloid derived suppressor cells to understand response to immunotherapy in primary HER2 positive breast cancer Cancer Research. 79: 5027-5027. DOI: 10.1158/1538-7445.Am2019-5027  0
2018 Espinosa-Cotton MM, Dahl RA, Fertig E, Jensen I, McLaren AJ, Miller K, Rodman SN, Schmitz S, Simons AL. Abstract 5734: Interleukin-1 signaling is required for HNSCC tumor response to cetuximab Immunology. DOI: 10.1158/1538-7445.Am2018-5734  0
2018 Ren S, Gaykalova DA, Guo TW, Favorov AV, Fertig EJ, Khan Z, DeJong PM, Ando M, Liu C, Sakai A, Fukusumi T, Haft S, Sadat S, Gutkind JS, Koch WM, et al. Abstract 3320: Discovery and development of DNA methylation biomarkers in human papillomavirus related oropharyngeal squamous cell carcinoma Cancer Research. 78: 3320-3320. DOI: 10.1158/1538-7445.Am2018-3320  0
2017 Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, et al. A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. Cell Systems. PMID 28988802 DOI: 10.1016/J.Cels.2017.09.004  0
2017 Leonard B, Humtsoe JO, Kim H, Ling S, Marchionni L, Fertig EJ, Considine M, Ha P. Abstract 64: Abnormal splicing events in adenoid cystic carcinoma Clinical Cancer Research. 23: 64-64. DOI: 10.1158/1557-3265.Aacrahns17-64  0
2017 Kagohara LT, Stein-O'Brien G, Li S, Thakar M, Ranaweera R, Considine M, Califano JA, Chung CH, Gaykalova D, Fertig EJ. Abstract 86: Time course analysis of gene expression and epigenetic interactions in acquired cetuximab resistance in head and neck squamous cell carcinoma Cancer Research. 77: 86-86. DOI: 10.1158/1538-7445.Am2017-86  0
2017 Aldeghaither DS, Murray JC, Roth SM, Fertig EJ, Tang S, Jablonski SA, Weiner LM. Abstract 633: Induction of ADCC resistance profoundly alters tumor cell phenotype and stress response Cancer Research. 77: 633-633. DOI: 10.1158/1538-7445.Am2017-633  0
2017 Kelley DZ, Flam EL, Guo T, Bohrson C, Considine M, Danilova LV, Bishop JA, Zhang C, Koch WM, Sidransky D, Westra W, Wheelan S, Florea L, Fertig EJ, Califano JA, et al. Abstract 4474: Functional characterization of alternatively splicedGSNin head and neck cancer Cancer Research. 77: 4474-4474. DOI: 10.1158/1538-7445.Am2017-4474  0
2017 Afsari B, Guo T, Considine M, Kelley D, Flam E, Florea L, Ha P, Geman D, Ochs MF, Califano JA, Gaykalova DA, Favorov AV, Fertig EJ. Abstract 3577: Splice expression variation analysis (SEVA) for differential gene isoform usage in cancer Cancer Research. 77: 3577-3577. DOI: 10.1158/1538-7445.Am2017-3577  0
2017 Kelley DZ, Flam EL, Wulf HA, Guo T, Izumchenko E, Singman DA, Danilova LV, Stavrovskaya ED, Considine M, Bishop JA, Westra WH, Khan Z, Koch WM, Sidransky D, Wheelan S, ... ... Fertig EJ, et al. Abstract 2424: The in-parallel whole-genome ChIP-Seq analysis of primary tissues, patient derived xenografts, and cancer cell lines from HPV-relative HNSCC samples Cancer Research. 77: 2424-2424. DOI: 10.1158/1538-7445.Am2017-2424  0
2016 Rettig EM, Talbot CC, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig E, Wheelan S, Marchionni L, Considine M, Ling S, Fakhry C, et al. Correction: Whole-genome sequencing of salivary gland adenoid cystic carcinoma (Cancer Prevention Research (2016) 9 (265-274) DOI: 10.1158/1940-6207.CAPR-15-0316) Cancer Prevention Research. 11. PMID 28642227 DOI: 10.1158/1940-6207.Capr-17-0178  0
2016 Shuptrine CW, Fertig EJ, Salcie-Gautreaux M, Weiner LM. Abstract A142: An in vivo functional genomics screen identifies molecular determinants of adaptive immune rejection Cancer Immunology Research. 4. DOI: 10.1158/2326-6074.Cricimteatiaacr15-A142  0
2016 Fertig EJ, Ozawa H, Thakar M, Howard J, Krigsfeld G, Favorov AV, Gaykalova DA, Ochs MF, Chung CH. Abstract 777: The CoGAPS matrix factorization algorithm infers feedback mechanisms from therapeutic inhibition of EGFR that increases expression of growth factor receptors Cancer Research. 76: 777-777. DOI: 10.1158/1538-7445.Am2016-777  0
2016 Brait M, Izumchenko E, Kagohara L, Long S, Wysocki P, Faherty B, Fertig E, Khor T, Bruckheimer E, Baia G, Ciznadija D, Sloma I, Ben-Zvi I, Paz K, Sidransky D. Abstract 3640: Validation of qBiomarker as an accurate and efficient mutation detection method in a comprehensive analysis of patient-derived tumor xenografts Cancer Research. 76: 3640-3640. DOI: 10.1158/1538-7445.Am2016-3640  0
2016 Gaykalova DA, Kelley D, Guo T, Bohrson C, Tiscareno I, Zizkova V, Considine M, Danilova L, Flam E, Bishop J, Ahn J, Merritt S, Goldsmith M, Zhang C, Koch W, ... ... Fertig E, et al. Abstract 2880: The discovery of novel GSN alternative splicing in head and neck squamous cell carcinoma Cancer Research. 76: 2880-2880. DOI: 10.1158/1538-7445.Am2016-2880  0
2015 Michailidi C, Noordhuis M, Hadar T, Marchioni L, Fertig E, Agrawal N, Westra W, Koch W, Califano J, Velculescu V, Sidransky D, Guerrero-Preston R. Abstract B1-62: Bumphunting analysis identifies PAX5 promoter methylation and p53 somatic mutations in genomic instability pathways linked to very poor survival in head and neck cancer Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-62  0
2015 Guo T, Gaykalova D, Considine M, Bishop JA, Westra WH, Khan Z, Fertig E, Califano JA. Abstract 4807: Discovery of novel alternative splicing events in human papillomavirus-related oropharyngeal squamous cell carcinoma Cancer Research. 75: 4807-4807. DOI: 10.1158/1538-7445.Am2015-4807  0
2014 Fortin JP, Fertig E, Hansen K. shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R. F1000research. 3: 175. PMID 25285208 DOI: 10.12688/F1000Research.4680.2  0
2014 Considine M, Parker HS, Wei Y, Xia XX, Cope L, Ochs MF, Fertig EJ. Abstract LB-317: Interactive pipeline for reproducible genomics analyses Cancer Research. 74. DOI: 10.1158/1538-7445.Am2014-Lb-317  0
2014 Afsari B, Fertig EJ, Younes L, Geman D, Marchionni L. Abstract 5342: Hardwiring mechanism into predicting cancer phenotypes by computational learning Cancer Research. 74: 5342-5342. DOI: 10.1158/1538-7445.Am2014-5342  0
2014 Loyo M, Kagohara LT, Sun W, Tan M, Fertig E, Ochs M, Izumchenko E, Brait M, Califano J, Sidransky D. Abstract 527: Analysis of the interaction between microRNAs and Notch pathway members in HNSCC (head and neck squamous cell carcinoma) Cancer Research. 74: 527-527. DOI: 10.1158/1538-7445.Am2014-527  0
2014 Gaykalova DA, Manola J, Ozawa H, Morton K, Bishop J, Considine M, Sharma R, Zhang C, Fertig E, Tan M, Hennessey P, Ahn J, Koch W, Khan Z, Chung CH, et al. Abstract 3409: Transcription factor signature of head and neck squamous cell carcinoma Cancer Research. 74: 3409-3409. DOI: 10.1158/1538-7445.Am2014-3409  0
2014 Guerrero-Preston R, Michailidi C, Marchionni L, Pickering C, Frederick M, Myers J, Yegnasubramanian S, Hadar T, Noordhuis M, Fertig E, Agrawal N, Westra W, Koch W, Califano J, Velculescu V, et al. Abstract 2482: Key tumor suppressor genes inactivated by promoter methylation and somatic mutations in head and neck cancer Cancer Research. 74: 2482-2482. DOI: 10.1158/1538-7445.Am2014-2482  0
2014 Ozawa H, Cheng H, Fertig EJ, Howard JD, Markovic A, Hughes R, Perez J, Quon H, Chung CH. Abstract 2474: Smad4 loss induces cetuximab resistance and increased metastatic potential in head and neck squamous cell carcinoma Cancer Research. 74: 2474-2474. DOI: 10.1158/1538-7445.Am2014-2474  0
2013 Gajula R, Chettiar S, Williams R, Thiyagarajan S, Aziz K, Gandhi N, Wild A, Salih T, Kato Y, Cades J, Fertig E, Chung C, Herman J, Hales R, Rudin C, et al. Abstract B45: The Twist box domain is required for Twist1-induced metastasis of prostate cancer cells Cancer Research. 73. DOI: 10.1158/1538-7445.Tim2013-B45  0
2013 Howard JD, Cheng H, Ratner E, Fertig EJ, Perez J, Quon H, Considine M, Ochs M, Weidhaas J, Chung CH. Abstract 3100: MicroRNA profiling reveals miR-205 upregulation is associated with head and neck squamous cell carcinoma and modulates E2F1 signaling. Cancer Research. 73: 3100-3100. DOI: 10.1158/1538-7445.Am2013-3100  0
2013 Fertig EJ, Markovic A, Danilova LV, Gaykalova DA, Cope L, Chung CH, Califano JA, Ochs MF. Abstract 2901: An integrated matrix factorization algorithm for DNA methylation and gene expression identi es HNSCC clinical subtypes and GLI1 signaling speci c to HPV-negative HNSCC. Cancer Research. 73: 2901-2901. DOI: 10.1158/1538-7445.Am2013-2901  0
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. Abstract 1493: The Twist box is required for Twist1-induced prostate cancer metastasis. Cancer Research. 73: 1493-1493. DOI: 10.1158/1538-7445.Am2013-1493  0
2012 Cheng H, Fertig E, Ozawa H, Hatakeyama H, Considine M, Perez J, Ochs M, Chung CH. Abstract 1889: Smad4 inactivation correlates with EMT and cetuximab resistance in head and neck squamous cell carcinoma Cancer Research. 72: 1889-1889. DOI: 10.1158/1538-7445.Am2012-1889  0
2011 Fertig E, Ding J, Favorov A, Parmigiani G, Ochs M. Inferring Coordinated Gene Activity in Pattern Sets F1000research. 2. DOI: 10.7490/F1000Research.798.1  0
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