Systems Biology and Computational Biology

Understanding the molecular basis of diseases from a network perspective is a research focus of Panayiotis (Takis) Benos, PhD, and Madhavi Ganapathiraju, PhD.

Dr. Benos is an associate professor in the Department of Computational and Systems Biologyand co-director of the Joint CMU-Pitt PhD Program in Computational Biology.  In particular, Dr. Benos’ group is developing algorithms to infer regulatory gene modules of proteins and non-coding RNA genes (microRNAs) that are critically associated with lung diseases, such as idiopathic pulmonary fibrosis (IPF), and tissue and organ development.

Dr. Ganapathiraju is an assistant professor in the Department of Biomedical Informatics, Intelligent Systems Program, the Joint CMU-Pitt PhD Program in Computational Biologyand the Molecular and Cellular Cancer Biology Program which fall under various schools and institutes in University of Pittsburgh.  The research work in her group is on developing algorithms for computational systems biology through data intensive pattern mining from biological data. Primary focus is on the discovery and mining of protein-protein interactions (intra-species and host-virus interactomes).

Sample of related publications

K.V. Pandit, D. Corcoran, H. Yousef, M. Yarlagadda, A. Tzouvelekis, K.F. Gibson, K. Konishi, S.A. Yousem, M. Singh, D. Handley, T. Richards, M. Selman, S.C. Watkins, A. Pardo, A. Ben-Yehudah, D. Bouros, O. Eickelberg, P. Ray, P.V. Benos, N. Kaminski, “Inhibition and role of let-7d in idiopathic pulmonary fibrosis”, Am J Respir Crit Care Med, (2010), 182:220-229.  PMID: 20395557

D.L. Corcoran, K.V. Pandit, B. Gordon, A. Bhattacharjee, N. Kaminski,P.V. Benos, “Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data”, PLoS One (2009), 4:e5279.  PMID: 19390574

A.B. Tchagang, K.V. Bui, T. McGinnis, P.V. Benos, “Extracting Biologically Significant Patterns from Short Time Series Gene Expression Data”, BMC Bioinformatics (2009), 10:255.  PMID: 19695084

T.P. Mohamed, J.G. Carbonell, M. Ganapathiraju, "Active Learning for Human Protein-Protein Interaction Prediction", BMC Bioinformatics (2010), 11:S1. PMID: 20122232 

H.U. Osmanbeyoglu, J.A. Wehner, J.G. Carbonell, M. Ganapathiraju, "Active machine learning for transmembrane helix prediction", BMC Bioinformatics (2010), 11:S1. PMID: 20122233