Todd Stokes, PhD

todd.stokes@bme.gatech.edu

Education

  • Doctor of Philosophy, Bioengineering, Georgia Institute of Technology, Atlanta, GA May 2009

    • Dissertation Title: Development of a Visualization and Information Management Platform in Translational Biomedical Informatics
    Advisor and Thesis Committee Chair: May D. Wang, Ph.D. (Dept. of Biomedical Engineering)
    Awards: Ti:GER Graduate Research Fellowship, National Science Foundation (2006)

  • Bachelor of Science, Computer Engineering, Georgia Institute of Technology, Atlanta, GA May 2000

    • Honors: National Merit Scholarship (1995)
    Dean’s Scholarship, Georgia Tech (1995)
    Governor’s Scholarship, State of Georgia (1995)
    Georgia Engineering Foundation Scholarship (1995)

Research Interests and Projects

  • Cancer Biomedical Informatics Grid (caBIG) Project Manager for the Center for Cancer Nanotechnology Excellence (CCNE):
    •  Oral presentation at the first annual CCNE symposium. Adopted caNanoLab information management system for nanotechnology. Organized workshops for bioinformaticians and clinicians to gain support for caBIG. Prepared the caCORRECT Grid Services for Silver-level Compatibility Review. Our team was the first non-funded (volunteer) development team to submit tools for Silver-level review.

  • caCORRECT (Chip Artifact Correction for Microarrays):
    • Web-based microarray statistical error analysis & visualization software for improving biomarker search and laboratory protocols.
    • Presented at American Association for Cancer Research (AACR) conference in Washington D.C.
    • Best Poster Award at the Center for Cancer Nanotechnology Excellence Symposium 2006.
    • Presented at the 2006 caBIG Annual Meeting in Washington D.C.

  • ArrayWiki Community Repository for Array-based Biological Data:
    • A Wiki to support collaboration on microarray quality and microarray data analysis issues. More than 2000 experiments were automatically imported from a large public repository and analyzed by caCORRECT. Additional visualization and compression techniques were employed to improve data usability and scalability.
    • Presented at Biomedical Engineering Society (BMES) conference in Hollywood, California.
    • Presented at International Multi-Symposiums on Computer and Computational Sciences (IMSCCS) conference in Iowa City, IA.
    • Presented at the 2008 caBIG Annual Meeting in Washington D.C.

  • Food and Drug Administration (FDA) Microarray Quality Control (MAQC) Project Team:
    • Analyzed large clinical microarray datasets as part of a multi-national collaboration. Contributed to four papers: a comprehensive study of the KNN classifier, a study on the effects of artifacts on microarray analysis, a standard operation procedure (SOP) for statistical performance metrics, and figures for the overview paper. All were submitted to Nature Biotechnology in March 2009.
  • Advised many graduate and undergraduate students, and served as Resource Manager for three years, overseeing student assistants, acquiring, installing and supporting 30+ PCs and servers, source code repositories, an internal lab status reporting system, an internal Wiki for policies and documentation, the lab web site, and visualization demo systems.

Publications

JOURNAL PUBLICATIONS
  1. 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.
  2. Stokes TH, Torrance JT, Li H, Wang MD. “ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses.” BMC Bioinformatics, 9(Suppl 6):S18, 2008
  3. 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. 21 Nov. 2008.
  4. Phan JH, Moffitt RA, Stokes TH, Liu J, Young AN, Nie S, Wang MD. “Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment.” Trends in Biotechnology. 30 April 2009.

Publications Under Review:

  1. The MAQC Consortium (currently 159 authors led by Leming Shi). “The MAQC-II Project: A comprehensive study of common practices for the development and validation of microarray-based predictive models.” Nature Biotechnology. (Under review for MAQC Phase II Special Issue, June)
  2. Parry RM*, Jones W*, Stokes TH*, Phan JH, Moffitt RA, Fang H, Shi L, Oberthuer A, Fischer M, Tong W, Wang MD. “K-nearest neighbors (KNN) models for microarray gene-expression analysis and reliable clinical outcome prediction.” Nature Biotechnology. (Under review for MAQC Phase II Special Issue, June)
  3. Osunkoya AO, Yin-Goen Q, Phan JH, Moffitt RA, Stokes TH, Wang MD, Young AN. “Diagnostic biomarkers for renal cell carcinoma: identification with novel bioinformatics systems for microarray data analysis.” Human Pathology. (Accepted).

CONFERENCE PUBLICATIONS

  1. Stokes TH, Wang MD. “SimpleVisGrid: Grid Services for Visualization of Diverse Biomedical Knowledge and Molecular Systems Data.” (submitted to IEEE EMBS 2009).
  2. Ahrens MA, Stokes TH, Wang, MD. Enhancing Molecular Marker Data Quality Service for Clinical Translation through Review in caBIG™. (submitted to AMIA 2009).
  3. Stokes TH, Torrance JT, Goasduff NL, Li H, and Wang MD. “Arraywiki: Liberating Microarray Data from Non-Collaborative Public Repositories.” International Multi-Symposiums on Computer and Computational Sciences, IMSCCS, Iowa City, IA, 2007, pp. 92-99.
  4. Phan JH, Moffitt RA, Stokes TH, and Wang MD. “Evolving Biological Behavior in Gene-Based Cellular Simulations," in IEEE 7th International Symposium on BioInformatics and BioEngineering, BIBE, Boston, MA, 2007. pp. 509-516.
  5. Stokes TH, Han RX, Moffitt RA, and Wang MD. “Extending Microarray Quality Control and Analysis Algorithms to Illumina Chip Platform.” 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, France, 2007, pp. 4637-4640.
  6. Torrance JT, Moffitt RA, Stokes TH, and Wang MD. “Can We Trust Biomarkers? Visualization and Quantification of Outlier Probes in High Density Oligonucleotide Microarrays.” IEEE/NIH Life Science Systems and Applications Workshop, LSSA, Boston, MA, 2007, pp. 196-199.
  7. Stokes TH, Phan JH, Quo CF, Nie S, and Wang MD, “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.
  8. Stokes TH, Phan JH, Feng WM, Tuteja G, and Wang MD, “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.
  9. Henning P, Stiles D, Stokes TH, Wang J, Wheeler D, Sidorov I, Tan P, Cam M and Wang MD, “ChipQC: Microarray Artifact Visualization Tool.” Int'l Conf. on Intelligent Systems for Molecular Biology, 2005 Jun 25-29.
  10. Moffitt RA, Stokes TH, Phan JH, and Wang MD, “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.

Current and previous students

  • Martin Ahrens
  • Sovandy Hang
  • Henry Li
  • Nolwenn Le Goasduff
  • Pierre LaRochelle
  • Kathy Pham
  • Randy Xiao Han
  • Aditya Desai
  • Kinjal Shah
  • Adeel Yusuf
  • Nitin Kumar
  • Jasreet Hundal
  • Malcolm Thomas

Experience

  • Ph.D. Student and Technology Provider for the Ti:GER program, Georgia Tech School of Management Aug. 2006 – May 2008

    • Technological Innovation: Generating Economic Results (Ti:GER) Program (funded by NSF): Teams were composed of one Ph.D. student, one MBA student, and two J.D. students from Emory Law School specializing in contract law and patent law. Over two years, we developed a technology roadmap, marketing plans, a commercialization plan, and ultimately a business plan for the Georgia Tech Business Plan Competition in 2008.

    OmniBioSuite (proposed commercialization venture): a cancer patient status report that could accurately update life expectancy and help patients weigh potential outcomes from various treatment options based on each successive laboratory test result..

  • Graduate Research Assistant, Georgia Tech Research Institute, Atlanta, GA Aug. 2004 – Dec. 2004

    • Supervisors: George A. Wright, Ph.D. (Electronic Systems Laboratory) Philip West, Ph.D. (Electronic Systems Laboratory)
    Contributed interfaces for Realistic Operational Communications Scenarios (ROCS) for simulating and analyzing network traffic for US Marines battlefield communications (Python).

  • Senior Systems Engineer, Home Depot, Inc., Atlanta, GA June 2000 – Aug. 2004

    • Contact Center Web Services Implementation and Support: Developed distributed, web-hosted applications for a 500-user Call Center for the Southeast region including rollout and support to smaller Call Centers in Southwest, Midwest, and West Coast.

    Document Management (Technical Lead) and Product Lookup: These systems supported the installed services products. Home Depot manages the ordering and customer experience for independent contractors and business partners. Designed and implemented through entire software lifecycle with a 4-tier architecture, including: Visual Basic web browser management application for client-side presentation, Java Servlet web user interfaces using distributed software patterns and enterprise identity management system with distributed sessions, XML web services to deliver enterprise data from the IBM mainframe, third party applet/server classes for image viewing, transforming, and annotation, third party enterprise fax servers and Computer Telephony Interface software.

    Installed Sales and Landscape Supply Performance Reporting (Technical Lead): Delivered 100% accurate and clean PDF print reports for executives and managers. Java Servlets using Optio DCS for report formatting. COBOL Batch Architecture for data collation using multi-threaded logic modules.

    Recognition Awards for Entrepreneurial Spirit and Problem Solving. Developed and delivered training classes in mainframe web service development. Sun Certifications as Java Programmer and J2EE Enterprise Architect.

  • Undergraduate Teaching Assistant, Georgia Institute of Technology, Atlanta, GA Jan. 2000 – May 2000

    • Faculty Supervisor: Richard M. Bass, Ph.D.( Dept. of Electrical and Computer Engineering)
    Created HTML/Perl interactive online quizzes and problem solution animations in Macromedia Flash for Introduction to Analog Circuits.

  • Undergraduate Co-op Researcher, Georgia Tech Research Institute, Atlanta, GA Jan. 1997 – Aug. 1999

    • Supervisors: John J. Landgren, Ph.D. (Electronic Systems Laboratory) Thomas G. Pratt, Ph.D. (Electronic Systems Laboratory)
    Contributed to scenario builder for analyzing network traffic for US Marines battlefield communications (Visual Basic). Designed and implemented system unit tests with LoadRunner. Refactored antenna pattern data analysis and visualization programs from Fortran to Matlab. Developed 3D animation of jets using electronic countermeasures with empirical equations driving missile flight.