We are a computational group specializing in applications of machine learning in medicine. Our ultimate goal is to identify risk factors and mechanisms affecting aging and contributing to the onset and progression of chronic diseases and cancer. We also develop predictive methods and tools that can directly improve health. We use probabilistic graphical models and other machine learning methods to integrate and mine high-dimensional, multi-modal biomedical data and to investigate biological processes pertinent to health and disease.
Representative Recent Publications
- K.L. Buschur, M. Chikina, P.V. Benos, “Causal network perturbations for instance-specific analysis of single cell and disease samples”, Bioinformatics (2019) 36:2515–2521. [Abstract] [Article] [PMC version]
- V.K. Raghu, W. Zhao, J. Pu, J.K. Leader, R. Wang, J. Herman, J.-M. Yuan, P.V. Benos*, D.O. Wilson, “Feasibility of lung cancer prediction from low-dose CT scan and smoking factors using causal models”, Thorax (2019) 74:643-649. [Abstract] [Article] [PMC version] *corresponding author
- A.J. Sedgewick, K. Buschur, I. Shi, J.D. Ramsey, V.K. Raghu, D.V. Manatakis, Y. Zhang, J. Bon, D. Chandra, C. Karoleski, F.C. Sciurba, P. Spirtes, C. Glymour, P.V. Benos, “Mixed Graphical Models for Integrative Causal Analysis with Application to Chronic Lung Disease Diagnosis and Prognosis”, Bioinformatics (2019) 35:1204-1212. [Abstract] [Article] [PMC version]
- C. Morse, T. Tabib, J. Sembrat, K.L. Buschur, H.T. Bittar, E. Valenzi, Y. Jiang, D.J. Kass, K. Gibson, W. Chen, A. Mora, P.V. Benos, M. Rojas, R. Lafyatis, “Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis”, European Respiratory Journal (2019) 54:1802441. [Abstract] [Article]
- J.E. McDonough, F. Ahangari1, Q. Li, S. Jain, S.E. Verleden, J. Herazo-Maya, M. Vukmirovic, G. Deluliis, A. Tzouvelekis, N. Tanabe, F. Chu, X. Yan, J. Verschakelen, R.J. Homer, D.V. Manatakis, J. Zhang, J. Ding, K. Maes, L. De Sadeleer, R. Vos, A. Neyrinck, P.V. Benos, Z. Bar-Joseph, D. Tantin, J.C. Hogg, B.M. Vanaudenaerde, W.A. Wuyts, N. Kaminski, “A dynamic regulatory model of gene expression changes in differentially affected regions of the human IPF lung”, JCI Insight (2019) 4:e131597. [Abstract] [Article]