Our ultimate goal is to investigate the molecular mechanisms of chronic diseases and cancer and develop predictive methods and tools that will improve health.  We develop computational methods to model biological processes and integrate and mine high-dimensional, multi-modal biomedical data.  We are very interested in the effect of gene regulatory networks and genotype in disease in combination with clinical data.


Indicative Recent Work

  1. D.A. Pociask, K.M. Robinson, K. Chen, K.J. McHugh, M.E. Clay, G.T. Huang, P.V. Benos, Y.M.W. Janssen-Heininger, J.K. Kolls, V. Anathy, J.F. Alcorn, “Epigenetic and Transcriptomic Regulation of Lung Repair during Recovery from Influenza Infection”, Am J Pathol, (2017), 187:851-863. Abstract (PubMed) and pdf. PMID: 28193481.  PMCID: PMC5397680
  2. A.J. Sedgewick, I. Shi, R.M. Donovan, P.V. Benos, “Learning mixed graphical models with separate sparsity parameters and stability-based model selection”, BMC Bioinformatics. (2016), 17 Suppl 5:175. Abstract (PubMed) and pdf.
  3. N. Olave, C.V. Lal, B. Halloran, K. Pandit, A.C. Cuna, O.M. Faye-Petersen, D.R. Kelly, T. Nicola, P.V. Benos, N. Kaminski, N. Ambalavanan, “Regulation of alveolar septation by microRNA-489″, Am J Physiol Lung Cell Mol Physiol, (2016), 10:L476-L487. Abstract (PubMed) and pdf.  PMID:26719145 [PubMed] PMCID:PMC4773841. Editor’s pick
  4. L.C. Villaruz(*), G.T. Huang(*), M. Romkes, J.M. Kirkwood, S.C. Buch, T. Nukui, K.T. Flaherty, S.J. Lee, M.A. Wilson, K.L. Nathanson, P.V. Benos, H.A. Tawbi, “MicroRNA expression profiling predicts clinical outcome of carboplatin/paclitaxel-based therapy in metastatic melanoma treated on the ECOG-ACRIN trial E2603″ Clinical Epigenetics, (2015), 7:58. Abstract (PubMed) and pdf.  PMID: 26052356 [PubMed] PMCID:PMC4457092.  (*) equal contribution
  5. Grace T. Huang, I. Tsamardinos, V. Raghu, N. Kaminski, P.V. Benos, “T-ReCS: Stable Selection of Dynamically Formed Groups of Features with Application to Prediction of Clinical Outcomes”, Pac Symp Biocomput, (2015), 20:431-442. Abstract (PubMed) and pdf.  PMID:25592602 [PubMed] PMCID:PMC4299881.