Ferhat Ay
Ferhat Ay, Ph.D.
Computer and Information Science and Engineering
University Of Florida
Office: E403
Bioinformatics Lab
University of Florida
Gainesville, FL 32611-6120
Phone: 1-352-3281017
e-mail: fay@cise.ufl.edu
News

I am going to be in Seattle, WA starting from 09/2011.

I have been awarded the Computing Innovation Fellowship for post-doctoral research with Dr. William Stafford Noble at the department of Genome Sciences in University of Washington (UW)

CV

Education:
  • Ph.D. Computer and Information Science and Engineering ~ University of Florida, Summer 2011.
  • B.S. Computer Engineering ~ Middle East Technical University, TURKEY, Spring 2007
  • B.Sc. Mathematics ~ Middle East Technical University, TURKEY, Spring 2007

  • Journal Papers:
    1. Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

      The modENCODE Consortium, Sushmita Roy*, Jason Ernst*, Peter V. Kharchenko*, Pouya Kheradpour*, Nicolas Negre*, Matthew L. Eaton*, Jane M. Landolin*, Christopher A. Bristow*, Lijia Ma*, Michael F. Lin*, Stefan Washietl*, Bradley I. Arshinoff*, Ferhat Ay*, Patrick E. Meyer*, Nicolas Robine*, Nicole L. Washington*, Luisa Di Stefano*, et. al., Susan E. Celniker, Steven Henikoff, Gary H. Karpen, Eric C. Lai, David M. MacAlpine, Lincoln D. Stein, Kevin P. White and Manolis Kellis
      * = equal contributors, co-first authors

      Abstract
      Science, 330(6012):1787-1797, 2010 (PDF)
    2. SubMAP: Aligning metabolic pathways with subnetwork mappings

      Ferhat Ay, Manolis Kellis, Tamer Kahveci

      Abstract
      Journal of Computational Biology (JCB), 18(3):1-17, 2011. (PDF)

    3. Scalable steady state analysis of boolean biological regulatory networks

      Ferhat Ay, Fei Xu, Tamer Kahveci

      Abstract
      PLoS ONE 4(12): e7992, 2009. doi:10.1371/journal.pone.0007992 (PDF)


    4. A fast and accurate algorithm for comparative analysis of metabolic pathways

      Ferhat Ay, Tamer Kahveci, Valerie de Crecy-Lagard

      Abstract
      Journal of Bioinformatics and Computational Biology (JBCB) 2009 Jun;7(3):389-428. (PDF)




    Conference Papers:
    5. A novel framework for large scale metabolic network alignments by compression *HONORARY BEST PAPER

      Michael Dang, Ferhat Ay, Tamer Kahveci

      Abstract
      Accepted (as a regular paper) to ACM BCB 2011 - Presentation (PPT)
      Proceedings of 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011;2:274-83. (PDF)

    6. SubMAP: Aligning metabolic pathways with subnetwork mappings
    7. Finding steady states of large scale regulatory networks through partitioning

      Ferhat Ay, Günhan Gülsoy, Tamer Kahveci

      Abstract
      Accepted to GENSIPS 2010 - Presentation (PPT)
      Proceedings of the IEEE International Workshop on Genomic Signal Processing and Statistics 2010; 1-4. (PDF)
    8. Functional similarities of reaction sets in metabolic pathways

      Ferhat Ay, Tamer Kahveci

      Abstract
      Accepted to ACM BCB 2010 - Presentation (PPT)
      Proceedings of 1st ACM International Conference On Bioinformatics and Computational Biology 2010;1:102-11. (PDF)

    9. Finding dynamic modules of biological regulatory networks

      Ferhat Ay, Thang N. Dinh, My T. Thai, Tamer Kahveci

      Abstract
      Accepted to IEEE BIBE 2010 - Presentation (PPT)
      Proceedings of 10th International Conference on Bioinformatics and Bioengineering 2010;136-43. (PDF)

    10. Scalable steady state analysis of boolean biological regulatory networks
    11. Consistent alignment of metabolic pathways without abstraction *BEST PAPER AWARD

      Ferhat Ay, Tamer Kahveci, Valerie de Crecy-Lagard

      Abstract
      Accepted to CSB 2008 - Presentation (PPT)
      Proceedings of 7th Annual Conference on Computational Systems Bioinformatics 2008;7:237-48. (PDF)


    Recent Awards:

    Workshop Papers and Posters:
    Links:

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