Ph.D. Candidate, Institute of Bioinformatics
Graduate Research Assistant, Department of Biochemistry and Molecular Biology
I work in Dr. Kannan's Evolutionary Systems Biology Group (ESBG). I joined the Institute of Bioinformatics Ph.D. program at UGA in Fall 2008.
|Office:||A318 Life Sciences Bldg.|
Lab website: http://esbg.bmb.uga.edu/
My lab investigates the processes of evolution and functional diversification in protein kinases, an enzyme superfamily that controls cell signal transduction. In particular, we've studied how certain point mutations in EGFR, a receptor tyrosine kinase and known oncogene, can drive the development of cancer in human cells. I am currently following up these initial studies by developing a larger-scale method for identifying such oncogenic variations in newly sequenced protein kinase genes.
Using some of the same approaches applied in our cancer work, I am investigating patterns of evolutionary divergence in the “kinomes” of the Apicomplexa, a phylum of parasitic protozoa that include the pathogens that cause widespread diseases such as malaria and cryptosporidiosis (see ISMB 2012 poster). We have reviewed specifically the topic of protein kinase evolution in the malaria parasite Plasmodium falciparum.
I actively contribute to Biopython, chiefly as maintainer of the Bio.Phylo module for working with phylogenetic tree data. This project originated in Google Summer of Code 2009 under the mentorship of National Evolutionary Synthesis Center (NESCent) to support the emerging phyloXML format, and has grown and picked up new contributors since then. I also help maintain the structural biology module, Bio.PDB.
If you'd like to generate a personal UGA MyWeb page like this one for yourself, try this handy web form. I wrote it for IOB students to use in Fall 2008.
|BINF 8210||Computational Methods in Bioinformatics||Sequence comparison and analysis, functional site prediction, structure prediction and analysis, biological data analysis|
|BINF 8211||Advanced Methods for Biological Data Analyses||Gene finding, genomic rearrangements, microarray data analyses, protein function inference, protein-protein interaction prediction, pathway and network prediction, data mining tools|
|BINF 6040||Essential Biology for Quantitative Scientists||Core concepts in molecular biology|
|BINF 8990||Bioinformatics Colloquium||Weekly seminars by students and established researchers (alternating each week)|
|CHEM 8330||Molecular Modeling||Homology modeling (MOE), MD simulation and refinement (Amber), ligand docking (AutoDock); analysis of model quality and simulation results|
|CSCI 6470||Algorithms||Analysis techniques, design techniques (divide-and-conquer, dynamic programming, greedy, and branch-and-bound), sorting, basic graph algorithms, NP-completeness, approximation algorithms|
|CSCI 6490||Algorithms for Computational Biology||Classical sequence comparison, multiple sequence alignment, DNA sequence assembly, DNA physical mapping, genome rearrangement, evolutionary tree construction, protein folding|
|FORS 8980||Functional Genomics||Genomics technologies: gene discovery, transposable elements, ESTs, transcriptomics & microarray analysis, next-generation sequencing (NGS), alternative splicing, gene family evolution, RNA silencing & interference, forward & reverse genetics, proteomics & mass spectrometry, metabolomics, gene correlation networks, ecological genomics|
|GENE 8150||Fundamentals of Evolutionary Genetics||Population genetics, evolutionary ecology, quantitative genetics, molecular evolution; analysis and visualization with R|
|GENE 8940||Applied Genome Analysis||Genome sequence assembly, automated annotation, large-scale expression studies, proteomics, SNP and comparative genome analysis|
|GRSC 8550||Responsible Conduct of Research||Codes of ethics for professional organizations, intellectual property, human and animal testing, development of personal professionalism and ethics|
|STAT 6320||Statistical Analysis II||Linear regression; multiple regression; associated estimation and inference methods; model building, selection, and diagnostics; analysis of variance; the analysis of covariance; design of experiments; SAS|
|STAT 6630||Statistical Methods in Bioinformatics I||Analysis of single DNA sequences, sequences alignment, BLAST searches, and related topics; simulations with R|
|STAT 6640||Statistical Methods in Bioinformatics II||Sequence comparisons, DNA database searches, evolutionary models, phylogenetic tree construction and related topics|