User:Tstokes
From ArrayWiki
Todd Stokes, founder of ArrayWIki, and cofounder of caCORRECT
Here is my CV:
Todd Hamilton Stokes
Department of Biomedical Engineering
Georgia Institute of Technology and Emory University
313 Ferst Drive, Rm. 4238, Atlanta, GA 30332-0535
todd [dot] stokes [at] bme [dot] gatech [dot] edu
Education
Ph.D. in Bioengineering (complete in May 2009)
Georgia Institute of Technology, Atlanta, GA
Advisor: May D. Wang
Topic: Information Visualization and Knowledge Management
Title: Development of an Information Management and Visualization Platform for Translational Biomedical Informatics
Minor: Bioinformatics
B.S. in Computer Engineering (May 2000)
Georgia Institute of Technology, Atlanta, GA
High Honors
Certificate in Economics
Research and Work Experience
Graduate Research Assistant and Lab Resource Manager in the Biomedical Engineering Department with May Wang (2004-present)
Working in the area of bioinformatics including imaging, visualization, biomarker selection, and quality control.
Developed a business plan for omniBioSuite as part of the National Science Foundation Ti:GER Commercialization Fellowship
Senior System Engineer in Home Depot, Inc. Information Systems Department (2000-2004)
Contact Center Web Service Implementation and Support: developed distributed, web-hosted applications for a 500-user call center for the southeast region including rollout and support to call centers in southwest, midwest, and west coast.
Student Programmer in the Electronic Systems Laboratory at Georgia Tech Research Institute (Summer 2000)
Network control simulation software and electronic countermeasures data processing.
Teaching Experience
Teaching Practicum (Spring 2007)
Biomedical Image Processing taught by May D. Wang
Developed and presented introductory lectures. Led tutorial in Matlab. Designed evaluation instrument for Matlab skills used to balance project teams. Mentored Project Based Learning teams.
Teaching Assistant in Electrical & Computer Engineering Georgia Tech (Spring 2000)
Introduction to Analog Circuit Design (two semesters)
Designed online quizzes and animated circuit solutions using Macromedia Flash (now Adobe).
Publications
Journal Papers (Refereed)
Stokes TH, Moffitt RA, Phan JH, and Wang MD, “chip artifact CORRECTion (ca-CORRECT): a bioinformatics system for quality assurance of genomics and proteomics array data," Annals of Biomedical Engineering, vol. 35, pp. 1068-1080, 2007.
Stokes TH, Torrance JH, Li H, Wang MD, “ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses.” Accepted for publication in BMC Bioinformatics, February, 2007.
Merrill AH Jr, Stokes TH, Momin A, Park H, Portz BJ, Kelly S, Wang E, Sullards MC, Wang MD. “Sphingolipidomics: a valuable tool for understanding the roles of sphingolipids in biology and disease.” Journal of Lipids Research. 2008.
Phan JH, Moffitt RA, Stokes TH, Liu J, Young AN, Nie S, Wang MD. “Biomarkers, Nanotechnology, and Personalized Medicine.” Trends in Biotechnology. 2009.
Conference Proceedings
T. H. Stokes, J. T. Torrance, N. L. Goasduff, H. Li, and M. D. Wang, “Arraywiki: Liberating Microarray Data from Non-Collaborative Public Repositories.” International Multi-Symposiums on Computer and Computational Sciences (IMSCCS '07), 2007 Aug 13-15; pp. 92-99.
J. H. Phan, R. A. Moffitt, T. H. Stokes, and M. D. Wang, “Evolving Biological Behavior in Gene-Based Cellular Simulations," in IEEE 7th International Symposium on BioInformatics and BioEngineering, BIBE, Boston, MA, 2007. pp. 509-516.
T. H. Stokes, R. X. Han, R. A. Moffitt, and M. D. Wang, “Extending Microarray Quality Control and Analysis Algorithms to Illumina Chip Platform.” International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS '07), 2007 Aug 23-26; pp. 4637-4640.
J. T. Torrance, R. A. Moffitt, T. H. Stokes, and M. D. Wang, “Can We Trust Biomarkers? Visualization and Quantification of Outlier Probes in High Density Oligonucleotide Microarrays.” IEEE/NIH Life Science Systems and Applications Workshop (LSSA '07), 2007 Nov 8-9; pp. 196-199.
T. H. Stokes, J. H. Phan, C. F. Quo, S. Nie, and M. D. Wang, “Bio-Nano-Informatics: An Integrated Information Management System for Personalized Oncology," in 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, New York City, NY, 2006, pp. 3325-3328.
T. H. Stokes, J. H. Phan, W. M. Feng, G. Tuteja, and M. D. Wang, “GAVis: a Tool for Visualization and Control of Genetic Algorithms for -omic Data Analysis," in 27th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, Shanghai, China, 2005, pp. 2855-2858.
P. Henning, D. Stiles, T. H. Stokes, G. Wang, D. Wheeler, I. Sidorov, P. Tan, M. Cam and M. D. Wang, “ChipQC: Microarray Artifact Visualization Tool.” Int'l Conf. on Intelligent Systems for Molecular Biology, 2005 Jun 25-29.
R. A. Moffitt, T. H. Stokes, J. H. Phan and M. D. Wang, “Simple Outlier Removal Improves the Results of Support Vector Machines as a Biomarker Selection Tool.” Int'l Conf. on Intelligent Systems for Molecular Biology, 2005 Jun 25-29.
Professional Activities
Students Mentored
Gabe Wardi and Michelle Lightfoot (2005). Senior Design Team. Transforming an infant stomach model taken from low-res CT scans into a more detailed model using Visible Human Project.
Kathy Pham (2006). Using Google API to implement spell check on web-based status reports. SVG animated Game of Life simulation. Meta-tags for status report reviewer assignments.
Randy Xiao Han (2006-2007). Matlab processing of Illumina microarrays to conform the bead layout to a regular grid pattern.
Pierre LaRochelle (2006-2007). Google Calendar for the Intralab. Web-based surveys implemented in Ruby.
Henry Li (2006-2007). Star Rating system for status reports. ArrayWiki GEO data imports.
Kinjal Shah (2007). Gene Ontology Mining Tool using GraphViz for SVG visualization.
Talks
Graduate Coursework
Information Theory (ECE) Principles of Management for Engineers (MGT)
