Aydin Tozeren

Summary

Affiliation: Drexel University
Country: USA

Publications

  1. ncbi Pathway-specific differences between tumor cell lines and normal and tumor tissue cells
    Adam Ertel
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Bossone 714, Drexel University, 3143 Chestnut Street, Philadelphia, PA 19104, USA
    Mol Cancer 5:55. 2006
  2. ncbi Automated detection of regions of interest for tissue microarray experiments: an image texture analysis
    Bilge Karacali
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania 19104 2875, USA
    BMC Med Imaging 7:2. 2007
  3. ncbi Automated recognition of cell phenotypes in histology images based on membrane- and nuclei-targeting biomarkers
    Bilge Karacali
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
    BMC Med Imaging 7:7. 2007
  4. ncbi Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality
    Adam Ertel
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
    BMC Genomics 9:628. 2008
  5. ncbi Switch-like genes populate cell communication pathways and are enriched for extracellular proteins
    Adam Ertel
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
    BMC Genomics 9:3. 2008
  6. ncbi Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets
    Michael Gormley
    School of Biomedical Engineering, Drexel University, Philadelphia, PA, USA
    BMC Bioinformatics 8:415. 2007
  7. ncbi Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types
    Noor B Dawany
    Center for Integrated Bioinformatics, Drexel University, Bossone Research Building 711, 3102 Market Street, Philadelphia, PA 19104, USA
    BMC Bioinformatics 11:483. 2010
  8. ncbi Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification
    Michael Gormley
    School of Biomedical Engineering, Drexel University, Philadelphia, PA, USA
    BMC Bioinformatics 9:486. 2008
  9. ncbi Host sequence motifs shared by HIV predict response to antiretroviral therapy
    William Dampier
    Center for Integrated Bioinformatics, Drexel University, Bossone Research Center 711, 3120 Market Street, Philadelphia, PA 19104, USA
    BMC Med Genomics 2:47. 2009
  10. ncbi Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs
    Perry Evans
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Drexel University, Bossone 714, 3120 Market Street, Philadelphia, PA 19104, USA
    BMC Med Genomics 2:27. 2009

Research Grants

  1. GPBA Short Laboratory Courses in High Throughput Biology
    Aydin Tozeren; Fiscal Year: 2006

Collaborators

Detail Information

Publications18

  1. ncbi Pathway-specific differences between tumor cell lines and normal and tumor tissue cells
    Adam Ertel
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Bossone 714, Drexel University, 3143 Chestnut Street, Philadelphia, PA 19104, USA
    Mol Cancer 5:55. 2006
    ..The aim of the study was to identify significant alterations in pathway usage in cell lines in comparison with normal and tumor tissue...
  2. ncbi Automated detection of regions of interest for tissue microarray experiments: an image texture analysis
    Bilge Karacali
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania 19104 2875, USA
    BMC Med Imaging 7:2. 2007
    ..However, standard procedures for sampling tissue for molecular profiling have not yet been established...
  3. ncbi Automated recognition of cell phenotypes in histology images based on membrane- and nuclei-targeting biomarkers
    Bilge Karacali
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
    BMC Med Imaging 7:7. 2007
    ..In this study, we present an automated image analysis protocol for detailed morphological protein marker profiling of tumoroid cross section images...
  4. ncbi Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality
    Adam Ertel
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
    BMC Genomics 9:628. 2008
    ....
  5. ncbi Switch-like genes populate cell communication pathways and are enriched for extracellular proteins
    Adam Ertel
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
    BMC Genomics 9:3. 2008
    ..Two-component normal mixtures were fit to the data to identify bimodal genes and their potential roles in cell signaling and disease progression...
  6. ncbi Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets
    Michael Gormley
    School of Biomedical Engineering, Drexel University, Philadelphia, PA, USA
    BMC Bioinformatics 8:415. 2007
    ..We also determined the relevance of expression profiles on test arrays from independent datasets, measured on either the same or different microarray platforms...
  7. ncbi Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types
    Noor B Dawany
    Center for Integrated Bioinformatics, Drexel University, Bossone Research Building 711, 3102 Market Street, Philadelphia, PA 19104, USA
    BMC Bioinformatics 11:483. 2010
    ....
  8. ncbi Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification
    Michael Gormley
    School of Biomedical Engineering, Drexel University, Philadelphia, PA, USA
    BMC Bioinformatics 9:486. 2008
    ..It is of interest to determine the prediction potential of bimodal genes for class discovery in large-scale datasets...
  9. ncbi Host sequence motifs shared by HIV predict response to antiretroviral therapy
    William Dampier
    Center for Integrated Bioinformatics, Drexel University, Bossone Research Center 711, 3120 Market Street, Philadelphia, PA 19104, USA
    BMC Med Genomics 2:47. 2009
    ..Some of these predictive motifs overlap with known HIV-1 resistance sites. These motifs are well established in bioinformatics databases and hence do not require identification via in vitro mutation experiments...
  10. ncbi Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs
    Perry Evans
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Drexel University, Bossone 714, 3120 Market Street, Philadelphia, PA 19104, USA
    BMC Med Genomics 2:27. 2009
    ..Nevertheless, our study validates the role of linear binding motifs shared by virus and host proteins as an important part of the crosstalk between virus and host...
  11. ncbi Origins and evolution of cell phenotypes in breast tumors
    Aydin Tozeren
    School of Biomedical Engineering, Science, and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
    J Theor Biol 233:43-54. 2005
    ..The model developed provides realistic simulations for standard breast cancer therapies and can be used in the optimization studies of chemotherapy, radiotherapy, hormone therapy and emerging individualized therapies for cancer...
  12. ncbi Sequence- and interactome-based prediction of viral protein hotspots targeting host proteins: a case study for HIV Nef
    Mahdi Sarmady
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 6:e20735. 2011
    ..Scanning of HIV Nef motifs on multiple alignments of hepatitis C protein NS5A produces results consistent with literature, indicating the potential value of the hotspot discovery in advancing our understanding of virus-host crosstalk...
  13. ncbi Attenuation of Forkhead signaling by the retinal determination factor DACH1
    Jie Zhou
    Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Proc Natl Acad Sci U S A 107:6864-9. 2010
    ..Attenuation of FOX function by the cell fate determination pathway has broad implications given the diverse role of FOX proteins in cellular biology and tumorigenesis...
  14. ncbi Large-scale integration of microarray data reveals genes and pathways common to multiple cancer types
    Noor B Dawany
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, USA
    Int J Cancer 128:2881-91. 2011
    ..Our results point to the value of integrating microarray data in the study of combination drug therapies targeting metastasis...
  15. ncbi Signaling perturbations induced by invading H. pylori proteins in the host epithelial cells: a mathematical modeling approach
    William Dampier
    Center for Integrated Bioinformatics, Bossone 714, School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
    J Theor Biol 248:130-44. 2007
    ..pylori infected stomach epithelium. The quantitative model presented in this study lays the foundation for investigating the affects of single nucleotide polymorphisms (SNPs) on the efficiency of drug treatment...
  16. ncbi HIV protein sequence hotspots for crosstalk with host hub proteins
    Mahdi Sarmady
    Center for Integrated Bioinformatics, Drexel University, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 6:e23293. 2011
    ..The hotspot map produced in this study is the first global portrayal of HIV motifs involved in altering the host protein network at highly connected hub nodes...
  17. ncbi Modular composition predicts kinase/substrate interactions
    Yichuan Liu
    Center for Integrated Bioinformatics, Drexel University, Philadelphia, PA 19104, USA
    BMC Bioinformatics 11:349. 2010
    ..We identified statistically enriched pairs of strings of domains (signature pairs) in kinase-substrate couples presented in the 2006 version of the PTM database...
  18. ncbi Heterogeneous breast tumoroids: An in vitro assay for investigating cellular heterogeneity and drug delivery
    Alexandra P Vamvakidou
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, USA
    J Biomol Screen 12:13-20. 2007
    ..The fact that one can form a large number of 1-mm tumoroids in 1 coculture attests to the potential use of this system at high-throughput investigations of cancer drug development and drug delivery into the tumor...

Research Grants1

  1. GPBA Short Laboratory Courses in High Throughput Biology
    Aydin Tozeren; Fiscal Year: 2006
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