Overview of my research
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Overview of My Research PowerPoint PPT Presentation


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Overview of My Research. Brendan Mumey Department of Computer Science MSU. Interest: Algorithms. In Computational Biology… Epitope mapping In Networking… Optical networking (NSF supported) Wireless networking. Background: Antibody Imprinting .

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Overview of My Research

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Overview of My Research

Brendan Mumey

Department of Computer Science

MSU


Interest: Algorithms

  • In Computational Biology…

    • Epitope mapping

  • In Networking…

    • Optical networking (NSF supported)

    • Wireless networking


Background: Antibody Imprinting

  • Step 1: Find an antibody that binds the protein:

    Step 2: Probe the antibody with a random peptide library of short peptide sequences:

protein

target

antibody

probes

antibody


15%

85%

Validation case: Antibody 9D7 epitope on IL-10


  • The grey squares are the alignment of a random set of peptides

  • The gold triangles are the genuine epitope

  • The large yellow triangles are key residues mediating binding of antibody to antigen


Current Work

  • Improving algorithm to do multiple alignments

  • Refining substitution matrix based on PDB data


Optical Networking

NSF Optical Network


Routing and Wavelength Assignment


Markov based RWA results


Current Work

  • Extending some ideas from Multicommodity Flow for improved algorithms

  • New software simulation system (RAPTOR) for testing RWA algorithms with physical impairments modeled


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