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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

Overview of My Research

Brendan Mumey

Department of Computer Science

MSU

interest algorithms
Interest: Algorithms
  • In Computational Biology…
    • Epitope mapping
  • In Networking…
    • Optical networking (NSF supported)
    • Wireless networking
background antibody imprinting
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

slide5

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
Current Work
  • Improving algorithm to do multiple alignments
  • Refining substitution matrix based on PDB data
optical networking
Optical Networking

NSF Optical Network

current work1
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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