Winter 2011: $19K awarded for team CIF application led by Dr. Adrian Chan: Clinical Engineering: "Engineering Health in Hospitals”.
Fall 2010: James Green becomes a Senior Member of the IEEE. * Robert Peace's CMBEC paper is accepted in extended form by the Journal of Medical and Biological Engineering.
Summer 2010: The Green Lab takes a well deserved beach day.
Spring 2010: Congratulations to Green Lab scholarship recipients: Robert Peace (NSERC PGS-M), Catalin Patulea (OGS), and Derrick Nhan (NSERC USRA)!
Spring 2009: Congratulations to undergraduate students Hanan Mahmoud and Robert Peace; for winning the Best Poster Award at the 2nd Annual Carleton Cell BE Programming Workshop for their poster: "Peptide Sequence Tag Identification Using the Cell BE".
Winter 2009: NSERC Discovery Grant renewed for 5 years to investigate "Real-time proteomics on heterogeneous multi-core processors". ** MITACS Training Grant of $10,000 awarded to run the 2nd Annual Carleton Cell BE Programming Workshop.
Fall 2008: Congratulations to graduate student Rémi Gagné for winning the Best Poster Award at the 2008 Health Canada Science Forum for his poster: "Guidelines for Chip-chip pre-processing and analysis". ** ORF grant of $114,628 awarded (to match CFI grant below). ** Cell BE equipment providing ~2.5 TERAFLOPS has arrived!
Spring 2008: Brian Earl and Davide Agnello awarded NSERC best research project for senior design project "Smart Rollator Usage Monitoring".
Winter 2008: Teaching Achievement Award of $15,0000 granted, partially to fund new biomedical engineering student projects to develop novel assistive devices for persons with disabilities.
Fall 2007: CFI grant of $114,628 awarded to fund development of novel mass spectrometry peptide identification strategies using Cell BE technology. See an article in Carleton Now.
Spring 2007: Amir Sadeghian and Ryan Chol-Ho Yim awarded NSERC best research project for senior design project "Eye Interact".
Summary
Protein structure prediction. Much like the shape of a tool suggests its intended purpose, knowledge of a protein's structure can provide substantial insight into its function. Therefore, computational prediction of protein structure based solely on protein sequence data is a challenge of fundamental importance to biomedical research. An effective solution promises significant advances in computational drug discovery and an increased understanding of complex disease processes such as cancer. We have recently developed a novel approach to determining the 1D secondary structure of proteins from protein sequence data which makes use of Parallel Cascade Identification (PCI), a powerful method of nonlinear system identification. We are currently working towards extending this method to the prediction of full 3D tertiary structure prediction.
Post-translational modification. While progress continues to be made on the prediction of structure from sequence, knowledge of a protein's structure may not be sufficient to discern its function. For example, most proteins undergo some form of post-translational modification (PTM) following initial synthesis which may have a profound impact on protein function. Our lab is therefore working to develop intelligent predictors of important PTM's such as sumoylation and phosphorylation. Iterative prediction of protein function and structure is a long term goal as well.
Bioinformatics web services. Please click here for a list of web services developed by our lab.
Areas of Research Interest
My research focus has been in the following areas:
Bioinformatics, proteomics, and prediction of protein structure, function, interaction, and post-translational modification
Machine intelligence, pattern classification, data mining
Development of novel assistive technology and devices
Applications of nonlinear system identification
I also have interest in: medical informatics, robotics, machine vision, and microprocessor applications
Current projects include:
Species-specific prediction of protein secondary structure
Hardware acceleration of bioinformatics algorithms using FPGA and IBM Cell BE technologies
Identification of thyroid response elements in genomic DNA (in collaboration with Health Canada)
Real-time processing of MS-MS and MALDI-ToF spectra
Identification of post-translational modifications in proteins, including sumoylation, glycosylation, and hydroxylation.
Reverse engineering of genetic networks using principles from DSP
Prediction of protein-protein interactions from sequence, and also the optimal ordering of wet-lab interaction pull-down experiments
Protein structure prediction.
Post-translational modification.
