Aydin Tozeren, PhD

Professor Emeritus
School of Biomedical Engineering, Science and Health Systems

Bio

Dr. Aydin Tozeren, Emeritus Professor of Biomedical Engineering at Drexel University and former Co-Director of the Greater Philadelphia Bioinformatics Alliance, received his PhD from Columbia University. He brings decades of experience in analysis of high-density data sets for deducing molecular signatures of complex diseases. Previously, he held academic and research positions at Columbia University, the National Institutes of Health and the Catholic University of America. He is published in the areas of bioinformatics, human and bacterial genomes, pathogenic cell circuits in bacteria, cell adhesion and signaling, molecular basis of muscle contraction, and biomechanics. His former doctoral students are making an important impact in advancing bioinformatics research in leading Philadelphia Medical Institutions.

Education

PhD, Bioengineering, Columbia University, 1974
MS, Engineering Mechanics, Columbia University, 1972
BS, Orta Dogu Technical University, 1971

Research Interests

Bioinformatics and biomarkers, bacterial gene circuits; Markov chains for sequence analysis.

Publications

Books:

New Biology for Engineers and Computer Scientists (April 2003), Aydin Tozeren and SW Byers, Prentice Hall, NJ.

Human Body Dynamics: Classical Mechanics & Human Movement (1999), Aydin Tozeren, Springer-Verlag, New York, NY.

Recent Peer-Reviewed Publications:

Pancreatic cancer survival analysis defines a signature that predicts outcome. Raman P, Maddipati R, Lim KH, Tozeren A. PLoS One. 2018 Aug 9;13(8):e0201751. doi: 10.1371/journal.pone.0201751. eCollection 2018.

Cyclin D1-mediated microRNA expression signature predicts breast cancer outcome. Wang G, Gormley M, Qiao J, Zhao Q, Wang M, Di Sante G, Deng S, Dong L, Pestell T, Ju X, Casimiro MC, Addya S, Ertel A, Tozeren A, Li Q, Yu Z, Pestell RG. Theranostics. 2018 Mar 11;8(8):2251-2263. doi: 10.7150/thno.23877. eCollection 2018.

FXYD5 is a Marker for Poor Prognosis and a Potential Driver for Metastasis in Ovarian Carcinomas. Raman P, Purwin T, Pestell R, Tozeren A. Cancer Inform. 2015 Oct 12;14:113-9. doi: 10.4137/CIN.S30565. eCollection 2015.

Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity--a large-scale system analysis of decoded bacterial genomes. Shestov M, Ontañón S, Tozeren A. BMC Genomics. 2015 Oct 13;16:773. doi: 10.1186/s12864-015-1957-7.

Kinase-independent role of cyclin D1 in chromosomal instability and mammary tumorigenesis. Casimiro MC, Di Sante G, Crosariol M, Loro E, Dampier W, Ertel A, Yu Z, Saria EA, Papanikolaou A, Li Z, Wang C, Addya S, Lisanti MP, Fortina P, Cardiff RD, Tozeren A, Knudsen ES, Arnold A, Pestell RG. Oncotarget. 2015 Apr 20;6(11):8525-38.

A community computational challenge to predict the activity of pairs of compounds. Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y; NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A; NCI-DREAM Community. Nat Biotechnol. 2014 Dec;32(12):1213-22. doi: 10.1038/nbt.3052. Epub 2014 Nov 17.

A community effort to assess and improve drug sensitivity prediction algorithms. Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G. Nat Biotechnol. 2014 Dec;32(12):1202-12. doi: 10.1038/nbt.2877. Epub 2014 Jun 1.

Cyclin D1 induction of Dicer governs microRNA processing and expression in breast cancer. Yu Z, Wang L, Wang C, Ju X, Wang M, Chen K, Loro E, Li Z, Zhang Y, Wu K, Casimiro MC, Gormley M, Ertel A, Fortina P, Chen Y, Tozeren A, Liu Z, Pestell RG. Nat Commun. 2013;4:2812. doi: 10.1038/ncomms3812.

Dachshund binds p53 to block the growth of lung adenocarcinoma cells. Chen K, Wu K, Cai S, Zhang W, Zhou J, Wang J, Ertel A, Li Z, Rui H, Quong A, Lisanti MP, Tozeren A, Tanes C, Addya S, Gormley M, Wang C, McMahon SB, Pestell RG. Cancer Res. 2013 Jun 1;73(11):3262-74. doi: 10.1158/0008-5472.CAN-12-3191. Epub 2013 Mar 14.

Bioinformatics analysis reveals transcriptome and microRNA signatures and drug repositioning targets for IBD and other autoimmune diseases. Clark PM, Dawany N, Dampier W, Byers SW, Pestell RG, Tozeren A. Inflamm Bowel Dis. 2012 Dec;18(12):2315-33. doi: 10.1002/ibd.22958. Epub 2012 Apr 5.

Identification of common biological pathways and drug targets across multiple respiratory viruses based on human host gene expression analysis. Smith SB, Dampier W, Tozeren A, Brown JR, Magid-Slav M. PLoS One. 2012;7(3):e33174. doi: 10.1371/journal.pone.0033174. Epub 2012 Mar 14.

ChIP sequencing of cyclin D1 reveals a transcriptional role in chromosomal instability in mice. Casimiro MC, Crosariol M, Loro E, Ertel A, Yu Z, Dampier W, Saria EA, Papanikolaou A, Stanek TJ, Li Z, Wang C, Fortina P, Addya S, Tozeren A, Knudsen ES, Arnold A, Pestell RG. J Clin Invest. 2012 Mar;122(3):833-43. doi: 10.1172/JCI60256. Epub 2012 Feb 6. Erratum in: J Clin Invest. 2013 May 1;123(5):2332.

HIV protein sequence hotspots for crosstalk with host hub proteins. Sarmady M, Dampier W, Tozeren A. PLoS One. 2011;6(8):e23293. doi: 10.1371/journal.pone.0023293. Epub 2011 Aug 15.

Sequence- and interactome-based prediction of viral protein hotspots targeting host proteins: a case study for HIV Nef. Sarmady M, Dampier W, Tozeren A. PLoS One. 2011;6(6):e20735. doi: 10.1371/journal.pone.0020735. Epub 2011 Jun 28.

Large-scale integration of microarray data reveals genes and pathways common to multiple cancer types. Dawany NB, Dampier WN, Tozeren A. Int J Cancer. 2011 Jun 15;128(12):2881-91. doi: 10.1002/ijc.25854. Epub 2011 Apr 11.

Domain altering SNPs in the human proteome and their impact on signaling pathways. Liu Y, Tozeren A. PLoS One. 2010 Sep 23;5(9):e12890. doi: 10.1371/journal.pone.0012890.

Evans P, Sacan A, Ungar L, Tozeren A. Sequence alignment reveals possible MAPK docking motifs on HIV proteins. PLoS One. 2010 Jan 28;5(1):e8942.

Dampier W, Evans P, Ungar L, Tozeren A. Host sequence motifs shared by HIV predict response to antiretroviral therapy. BMC Med Genomics. 2009 Jul 23;2:47.

Evans P, Dampier W, Ungar L, Tozeren A. Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs. BMC Med Genomics. 2009 May 18;2:27.

Gormley M, Tozeren A. Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification. BMC Bioinformatics. 2008 Nov 17;9:486.

Dampier W, Tozeren A. Signaling perturbations induced by invading H. pylori proteins in the host epithelial cells: a mathematical modeling approach. J Theor Biol. 2007 Sep 7;248(1):130-44.

Zhou J, Wang C, Wang Z, Dampier W, Wu K, Casimiro MC, Chepelev I, Popov VM, Quong A, Tozeren A, Zhao K, Lisanti MP, Pestell RG: Attenuation of Forkhead signaling by the retinal determination factor DACH. PNAS. 2010 02746.

Liu Y, Tozeren A: Modular composition predicts kinase/substrate interactions. BMC Bioinformatics. 2010, In press.

Ertel A, Tozeren A. Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality. BMC Genomics. 2008 Dec 23;9:628.

Ertel A, Tozeren A. Switch-like genes populate cell communication pathways and are enriched for extracellular proteins. BMC Genomics. 2008 Jan 4;9:3.

Gormley M, Dampier W, Ertel A, Karacali B, Tozeren A. Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets. BMC Bioinformatics. 2007; 8: 415.

Avvisato CL, Yang X, Shah S, Hoxter B, Li W, Gaynor R, Pestell R, Tozeren A, Byers SW. Mechanical force modulates global gene expression and beta-catenin signaling in colon cancer cells. J Cell Sci. 2007; 120: 2672-82.

Vamvakidou AP, Mondrinos MJ, Petushi SP, Garcia FU, Lelkes PI, Tozeren A. Heterogeneous breast tumoroids: An in vitro assay for investigating cellular heterogeneity and drug delivery. J Biomolecular Screening. 2007;12, 13-20.

Ertel A, Verghese A, Byers SW, Ochs M, Tozeren A. Pathway-specific differences between tumor cell lines and normal and tumor tissue cells. Mol Cancer. 2006;5(1):55.

Petushi S, Garcia FU, Haber MM, Katsinis C, Tozeren A. Large-scale computations on histology images reveal grade-differentiating parameters for breast cancer. BMC Med Imaging. 2006 Oct 27;6:14.

Tozeren A, Coward CW, Petushi SP. Origins and evolution of cell phenotypes in breast tumors. J Theor Biol. 2005 Mar 7;233(1):43-54.