Single-cell multi-omics; Bioinformatics and pattern detection algorithm development; Therapeutic resistance in cancer; Transcriptional regulation in cancer ...read more
Lab Website: Fertig Lab
Hill SM, Heiser L, 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, 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; HPN-DREAM Consortium. Inferring causal molecular networks: empirical assessment through a community-based effort. Nature methods. Nat Methods. 2016;13(4):310-318. PMID: 26901648. PMCID in progress. I lead the winning team, Stochastic Chaos, for the HPN-DREAM Breast Cancer Network Inference Challenge, Subchallenge 2a, predicting phospho-protein trajectories of measurements of cancer cells in response to targeted therapeutics.
Fertig EJ, Favorov AV, Ochs MF. Identifying context-specific transcription factor targets from prior knowledge and gene expression data. IEEE Tran Nanobioscience. 2013;12(3):142-9. PMID: 23694699, PMCID: PMC3759534. Winner of IEEE BIBM 2012 Best Paper Award.
Fertig EJ, Ren Q, Cheng H, Hatakeyama H, Dicker AP, Rodeck U, Considine M, Ochs MF, Chung CH. Gene expression signatures modulated by EGFR activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma. BMC Genomics. 2012;13:160. PMID: 22549044, PMCID: PMC3460736. Featured in a commentary in BMC Medicine.
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. 2013;8(11):e78127. PMID: 24223768, PMCID: PMC3817178
Fertig EJ, Harlim J, Hunt BR. A comparative study of 4D-VAR and 4D-LETKF: Perfect model simulations with Lorenz-96. Tellus A. 2007;59(1):96-100. Not NCI Funded, No PMID or PMCID.
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