P. Takis Benos, Ph.D.

  • Professor
  • Department of Computational and Systems Biology

Education & Training

  • Ph.D. in Molecular Biology from University of Crete , 1997
  • BSc, Mathematics, University of Crete, 1991

Research Interest Summary

studying gene regulatory interactions and gene networks in disease using computational algorithms.

Research Categories

Research Interests

The ultimate goal of Dr. Benos’ laboratory is to help understand the molecular mechanisms and factors that facilitate a disease phenotype. They develop computational and statistical models to study gene expression regulation in a systems' biology framework. They analyze high-throughput expression data for protein coding and microRNA (miRNA) genes together with genome-wide DNA and RNA association data (ChIP-seq and CLIP-seq), and epigenetic data in order to identify biologically important and disease relevant gene (sub)networks. 

The main focus of Dr. Benos’ laboratory is on gene expression regulation, both at the transcriptional, post-transcriptional, and epigenetic level. Computational and mathematical methods are used to model cis-regulatory sites and modules, and miRNA targets; to find associations between the in vivo DNA binding affinity of transcription factors, the status of the chromatin and the expression level of their target genes; and to identify gene subneworks, and related polymorphisms or epigenetic marks that are critically associated to clinical phenotypes of terminal diseases, like pulmonary fibrosis and cancer. Dr. Benos’ laboratory continues to develop innovative computational methods to solve currently important biological and biomedical problems.

Representative Publications

GT Huang, KI Cunningham, PV Benos, CS Chennubhotla, “Spectral clustering strategies for heterogeneous disease expression data”, Pac Symp Biocomput (2013), 2013:212-223. PMID: 23424126

GT Huang, C. Athanassiou, PV Benos, “mirConnX: Condition-specific mRNA-microRNA network integrator.” Nucl Acids Res, (2011), 39:W416-423. PMID: 21558324

KV Pandit*, D Corcoran*, …, PV 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
* equal contribution; ‡ corresponding authors

DL Corcoran*, KV Pandit*, B Gordon, A Bhattacharjee, N Kaminski‡, PV Benos‡, “Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data”, PLoS ONE (2009), 4: e5279. PMID: 19390574

R Brower-Sinning, DM Carter, CJ Crevar, E Ghedin, TM Ross, PV Benos, “The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus”, Genome Biol (2009), 10:R18. PMID: 19216739

P Mao, K Joshi, J Li, SH Kim, P Li, L Santana-Santos, S Luthra, UR Chandran, PV Benos, L Smith, M Wang, B Hu, SY Cheng, RW Sobol, I Nakano, “Mesenchymal glioma stem cells are maintained by activated glycolytic metabolism involving aldehyde dehydrogenase 1A3”, Proc Natl Acad Sci USA, (2013), accepted. PMID: 23650391.

C. Coronnello, R. Hartmaier, A. Arora, L. Huleihel, K.V. Pandit, A.S. Bais, M. Butterworth, N. Kaminski, G.D. Stormo, S. Oesterreich, P.V. Benos, “Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density”, PLoS Comput Biol, (2012), 8:e1002830, PMID: 23284279

A.S. Bais, N. Kaminski, P.V. Benos, “Finding subtypes of transcription factor motif pairs with distinct regulatory roles”, Nucl Acids Res, (2011), 39:e76. PMID: 21486752

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

S. Mahony, D.L. Corcoran, E. Feingold, P.V. Benos, “Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome”, Genome Biol (2007) 8:R84. PMID: 17506886