Graduate Research Assistant
Bioinformatics
B.S. Applied Mathematics
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. |
| E-mail: | etal@uga.edu |
Lab website: http://esbg.bmb.uga.edu/
My lab is investigating the structural and functional impact of variations in the amino acid sequences of protein kinases. In particular, we've studied how certain point mutations in EGFR, a receptor tyrosine kinase, 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.
Separately, but using some approaches applied in our cancer work, I have investigated patterns of evolutionary divergence in the kinomes of several protozoan parasite species.
For Google Summer of Code 2009, under the mentorship of National Evolutionary Synthesis Center (NESCent), I added support for the emerging PhyloXML format Biopython. Since then I've expanded the module and reorganized some existing code into a more general framework for phylogenetics, called Bio.Phylo.
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.
| ID | Title | Topics |
|---|---|---|
| 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 |