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Ronald C. Taylor, Ph.D.

Expertise

Ronald C. Taylor
Ronald C. Taylor

Dr. Ronald. C. Taylor is a research scientist with extensive experience in reconstruction of biological networks and genome-wide models, analysis of high throughput gene expression and protein abundance data, analysis of bacterial communities, metabolic modeling of bacteria, algorithm development for inference of regulatory networks from gene expression data (focused on information-theoretic approaches), metatranscriptomic analysis, high performance computing techniques (e.g., Hadoop, HBase platforms on Linux clusters) for large scale data analysis and construction of data warehouses, automated reasoning and machine learning techniques as applied to analysis of metabolic and signaling pathways and genomic data, biological database design, development of biological data transfer standards, and construction of bioinformatics software in general.

Education

  • Ph.D., Bioinformatics, George Mason University, 2003
  • M.S., Biology, Case Western Reserve University, 1991
  • M.S., Computer Science, Case Western Reserve University, 1985
  • B.S., Physics, Case Western Reserve University, 1979

Professional Affiliations

  • Secretary 2000-2006, Treasurer 2006-present, Functional Genomics Data (FGED) Society
  • Member, International Society for Computational Biology, 1997-present

Honors and Awards

  • Outstanding Mentor Award, US Department of Energy, Office of Science, 2006
  • Navachat Tongvichat Bioinformatics Memorial Scholarship, George Mason University, 2001
  • NIH Employee Sustained Superior Performance Award, 1992, 1993, 1998, 1999
  • NIH Division of Computer Research and Technology web site award, 1996
  • Argonne National Laboratory (Department of Energy) Graduate Assistantship, 1989-1991
  • Presidential Scholar, Case Western Reserve University, 1975-1979
  • National Merit Scholar, 1975-1979

Patents

  • National Cancer Institute Invention Report "BRB ArrayTools - a desktop software package for the analysis of DNA microarray data" Inventors: R Simon, A Peng, L McShane, M Radmacher, R Taylor, and M Abramson. (2001)
  • International Application No. PCT/US99/20942: New Invention: "Identification of Novel Viral Targets Containing Frameshifting Signals That Are Targets for Anti-viral Therapies" Inventors: JD Dinman, R Taylor, and SW Peltz. Filed: September 13, 1999. (1999)

Selected Publications

Perkins, E.; Chipman, J. K.; Edwards, S.; Tanwir, H.; Falciani, F.; Taylor, R. C.; Van Aggelen, G.; Vulpe, C.;  Antczak, P.; and Loguinov, A. (2011). "Reverse Engineering Adverse Outcome Pathways." Environmental Toxicology and Chemistry, 30(1):22-38.

Taylor, R. C. (2010). "An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics." BMC Bioinformatics, 11(Suppl12):S1, http://www.biomedcentral.com/1471-2105/11/S12/S1.

Taylor, R.C.; Singhal, M.; Weller, J.; Khoshnevis, S.; Shi, L.; and McDermott, J. (2009) "A Network Inference Workflow Applied to Virulence-related Processes in Salmonella typhimurium." Annals of the New York Academy of Sciences, vol. 1158, pp. 143-158. PubMed, New York, NY.

Taylor, R.C.; Singhal, M.; Daly, D. S.; Gilmore, J.; Cannon, W. R.; Domico, K.; White, A. M.; Auberry, D. L.; Auberry, K. J.; Hooker, B.; Hurst, G.; McDermott, J.; McDonald, W. H.; Pelletier, D.; Schmoyer, D.; and Wiley, H. S. (2009) "An analysis pipeline for the inference of protein-protein interaction networks." International Journal of Data Mining and Bioinformatics. 3(4) (Sp. Iss. SI):409-430.

Taylor R.C.; Acquaah-Mensah, G.; Singhal, M.; Malhotra, D.; and Biswal, S. (2008) "Network Inference Algorithms Elucidate Nrf2 Regulation of Mouse Lung Oxidative Stress." PLoS Comput Biol 4(8): e1000166. doi:10.1371/journal.pcbi.1000166.

Taylor, R.C., Shah, A., Treatman, C., Blevins, M. (2006). "SEBINI: Software Environment for BIological Network Inference." Bioinformatics 22(21):2706-2708.

Contact Information

Systems Biology at PNNL

Research & Capabilities

Resources