Quantifying the Dynamics of Coupled Networks of Switches and Oscillators

by Francis, Matthew R., Fertig, Elana J.
Published 2012

shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R

by Fortin, Jean-Philippe, Fertig, Elana, Hansen, Kasper
Published 2014

Learning Dysregulated Pathways in Cancers from Differential Variability Analysis

by Afsari, Bahman, Geman, Donald, Fertig, Elana J
Published 2014

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

by Fertig, Elana J., Lee, Esak, Pandey, Niranjan B., Popel, Aleksander S.
Published 2015

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

by Fertig, Elana J., Danilova, Ludmila V., Favorov, Alexander V., Ochs, Michael F.
Published 2011

AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses

by Considine, Michael, Parker, Hilary, Wei, Yingying, Xia, Xaio, Cope, Leslie, Ochs, Michael, Fertig, Elana
Published 2015

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

by Lee, Esak, Fertig, Elana J., Jin, Kideok, Sukumar, Saraswati, Pandey, Niranjan B., Popel, Aleksander S.
Published 2014

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

by Fertig, Elana J, Ren, Qing, Cheng, Haixia, Hatakeyama, Hiromitsu, Dicker, Adam P, Rodeck, Ulrich, Considine, Michael, Ochs, Michael F, Chung, Christine H
Published 2012

Preferential Activation of the Hedgehog Pathway by Epigenetic Modulations in HPV Negative HNSCC Identified with Meta-Pathway Analysis

by Fertig, Elana J., Markovic, Ana, Danilova, Ludmila V., Gaykalova, Daria A., Cope, Leslie, Chung, Christine H., Ochs, Michael F., Califano, Joseph A.
Published 2013

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

by LING, SHIZHANG, RETTIG, ELENI M., TAN, MARIETTA, CHANG, XIAOFEI, WANG, ZHIMING, BRAIT, MARIANA, BISHOP, JUSTIN A., FERTIG, ELANA J., CONSIDINE, MICHAEL, WICK, MICHAEL J., HA, PATRICK K.
Published 2016

Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA

by Izumchenko, Evgeny, Chang, Xiaofei, Brait, Mariana, Fertig, Elana, Kagohara, Luciane T., Bedi, Atul, Marchionni, Luigi, Agrawal, Nishant, Ravi, Rajani, Jones, Sian, Hoque, Mohammad O., Westra, William H., Sidransky, David
Published 2015

Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination

by Stansfield, John C., Rusay, Matthew, Shan, Roger, Kelton, Conor, Gaykalova, Daria A., Fertig, Elana J., Califano, Joseph A., Ochs, Michael F.
Published 2016

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

by Fortin, Jean-Philippe, Labbe, Aurélie, Lemire, Mathieu, Zanke, Brent W, Hudson, Thomas J, Fertig, Elana J, Greenwood, Celia MT, Hansen, Kasper D
Published 2014

Expression Microarray Analysis Reveals Alternative Splicing of LAMA3 and DST Genes in Head and Neck Squamous Cell Carcinoma

by Li, Ryan, Ochs, Michael F., Ahn, Sun Mi, Hennessey, Patrick, Tan, Marietta, Soudry, Ethan, Gaykalova, Daria A., Uemura, Mamoru, Brait, Mariana, Shao, Chunbo, Westra, William, Bishop, Justin, Fertig, Elana J., Califano, Joseph A.
Published 2014

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

by Zhang, Kaihua, Jones, Lamont, Lim, Sora, Maher, Christopher A., Adkins, Douglas, Lewis, James, Kimple, Randall J., Fertig, Elana J., Chung, Christine H., Herrlich, Andreas, Ellis, Matthew J., Van Tine, Brian A., Michel, Loren S.
Published 2014

Key tumor suppressor genes inactivated by “greater promoter” methylation and somatic mutations in head and neck cancer

by Guerrero-Preston, Rafael, Michailidi, Christina, Marchionni, Luigi, Pickering, Curtis R, Frederick, Mitchell J, Myers, Jeffrey N, Yegnasubramanian, Srinivasan, Hadar, Tal, Noordhuis, Maartje G, Zizkova, Veronika, Fertig, Elana, Agrawal, Nishant, Westra, William, Koch, Wayne, Califano, Joseph, Velculescu, Victor E, Sidransky, David
Published 2014

Structure-Function Studies of the bHLH Phosphorylation Domain of TWIST1 in Prostate Cancer Cells12

by Gajula, Rajendra P., Chettiar, Sivarajan T., Williams, Russell D., Nugent, Katriana, Kato, Yoshinori, Wang, Hailun, Malek, Reem, Taparra, Kekoa, Cades, Jessica, Annadanam, Anvesh, Yoon, A-Rum, Fertig, Elana, Firulli, Beth A., Mazzacurati, Lucia, Burns, Timothy F., Firulli, Anthony B., An, Steven S., Tran, Phuoc T.
Published 2015

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

by Hill, Steven M., Heiser, Laura M., Cokelaer, Thomas, Unger, Michael, Nesser, Nicole K., Carlin, Daniel E., Zhang, Yang, Sokolov, Artem, Paull, Evan O., Wong, Chris K., Graim, Kiley, Bivol, Adrian, Wang, Haizhou, Zhu, Fan, Afsari, Bahman, Danilova, Ludmila V., Favorov, Alexander V., Lee, Wai Shing, Taylor, Dane, Hu, Chenyue W., Long, Byron L., Noren, David P., Bisberg, Alexander J., Mills, Gordon B., Gray, Joe W., Kellen, Michael, Norman, Thea, Friend, Stephen, Qutub, Amina A., Fertig, Elana J., Guan, Yuanfang, Song, Mingzhou, Stuart, Joshua M., Spellman, Paul T., Koeppl, Heinz, Stolovitzky, Gustavo, Saez-Rodriguez, Julio, Mukherjee, Sach
Published 2016