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The home page of Richard Boyce Ph.D, MS

Richard David Boyce

My name is Richard Boyce a postdoctoral associate at the University of Pittsburgh's Department of Biomedical Informatics. My primary research interest is biomedical knowledge representation and especially how to better support biomedical decision making when pertinent information is missing, inaccurate or uncertain.

You can download my CV by clicking on this link

We are living in an exciting era where an advance in the basic sciences can quickly lead to a dramatic improvement in outcomes for patients. Exciting new opportunities for individualized care are emerging as we discover the subtle variations in each person's genetic makeup that can influence their course during disease and their response to treatment. However, this is also an era when investigators and clinicians are being overwhelmed by the pace of scientific advance so that no one individual can stay abreast of all of the current knowledge in their field of study. My biomedical and health informatics training has given me insight into theories and methods for dealing with the great complexity of current biomedical research. These include methods for data visualization, knowledge representation (modeling), data sharing, and information retrieval.


Publications

Journal Publications

Boyce R, Collins C, Horn J, Kalet I. Computing with evidence part I: A drug-mechanism evidence taxonomy oriented toward confidence assignment. Journal of Biomedical Informatics. 2009. doi:10.1016/j.jbi.2009.05.001.

Boyce R, Collins C, Horn J, Kalet I. Computing with evidence part II: an evidential approach to predicting metabolic drug-drug interactions, Journal of Biomedical Informatics, 2009, doi:10.1016/j.jbi.2009.05.010

Boyce, R., Rose, T., Chilana. iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOPs) from multiply-aligned protein sequences. Nucleic Acids Research 2009 Web server edition. doi:10.1093/nar/gkp379.

J. P. Staheli, J. T. Ryan, A. G. Bruce, R. Boyce, and T. M. Rose. Consensus-degenerate hybrid oligonucleotide primers (CODEHOPs) for the detection of novel viruses in non-human primates. Methods, 49(1):32-41, 2009.

Boyce R., Collins C., Horn J., Kalet I., "Modeling Drug Mechanism Knowledge Using Evidence and Truth Maintenance," IEEE Transactions on Information Technology in Biomedicine. Volume 11(4) 2007, Page(s):386 - 397. Digital Object Identifier 10.1109/TITB.2007.890842. see the abstract on IEEEExplore

Conference Publications

Boyce R., Collins C., Horn J., Kalet I., "Qualitative Pharmacokinetic Modeling of Drugs," Proceedings of the 2005 America Medical Informatics Association conference. 71-75. PubMed ID: 16779004.

Boyce, R. Chase, R. "Conflation System MBP, Proceedings of the International Conference on Imaging Science, Systems, and Technology," CISST'03, v.1, 246 - 252, June, 2003.

Presentations

Boyce R., Karras B., Lober B., "Pre-processing to Improve the Classification of Chief Complaint Data," 2005 National Syndromic Surveillance Conference. click for a PDF version available online.

Rossini A., Boyce R., and Webster E. "The Statistical Reality Engine," Presented at Directions for Statistical Computing (DSC) 2005.

Boyce, R. "VRGL / StatVizVR - An Toolkit and an Environment for Statistical Visualization," Presented at the National Library of Medicine Training Directors' Meeting 2004

Boyce, R. "An Algorithm for Automatic Multi-Source Image Conflation Using Linear Features," Presented at SOURCE 2003, Central Washington University and the University of Washington Spring Research Conference, May 2002

Boyce, R. "The Synchronous Motor Project," 1994 McNair Scholars Program Journal, Summer Research Abstracts

Current Research Interests

  • Knowledge-based approaches to drug-drug interaction prediction and identification
  • integrating emerging genetic and genomic knowledge into drug therapy decision support
  • computational methods for simplifying biomedical knowledge-base development, curation, and use
  • applications of truth and belief maintenance systems to biomedical knowledge-representation

Current Projects

Knowledge-based Approaches to Drug Safety

The focus of this research is how to best represent drug mechanism knowledge for the purpose of predicting clinically relevant drug-drug interactions. My contributions include a novel qualitative model of drug-drug interactions and an evidence-centric knowledge collection system that links changes in assertions about drug properties to the set of predicted drug-drug interactions (Boyce 2009 Parts I and II, Boyce 2007). I am currently working on a project that uses these methods and observational study techniques to examine if the risk of experiencing falls increases for nursing home residents taking drug pairs that are predicted interact by metabolic inhibition. This project is supported by the University of Pittsburgh Institute on Aging.

iCODEHOP - the Interactive CODEHOPs design program

I designed and implemented a tool called iCODEHOP that assists in the design of degenerate PCR primers to detect novel proteins. The aim of the tool is to help researchers in many areas of clinical microbiology design effective DNA based diagnostics for infectious organisms with less effort. iCODEHOP, is a web application that links together several new and existing bioinformatics tools into a set of intuitive workflows. Users can quickly scan over an entire set of degenerate primers produced by the program to assess their relative quality and select individual degenerate primers for further analysis. The program predicts annealing temperatures for degenerate primer pools, displays phylogenetic information for the sequences covered by the primer, and allows the user to easily design new degenerate primers from sub-selections of their input sequences. The tool is currently hosted by the University of Washington's Center for Public Health Informatics and can be seen at the following URL: The interactive program for creating COnsensus DEgenerate Hybrid Oligonucleotide Primers

Previous Projects

Improving Signals used for Public Health Surveillance

An analogy for a target of Public Health Surveillance is that of a signal relaying community disease state. In practice, PH officials may monitor multiple syndromic and traditional signals to such as pharmacy orders, school absenteeism, water treatment plant turbidity logs, clinical diagnosis, surveys, and laboratory-test results. A syndromic signal differs from a more traditional PH surveillance signal (e.g case reports) in both the reliability and timeliness of the signal. As part of ongoing research on methods for using emergency department chief complaints as syndromic surveillance information signals, I developed an automated method for normalizing free-text chief complaints and investigated its its effect on the accuracy of chief complaint classification of a naive Bayesian classifier, COCO. (Boyce 2005)

Collaborative Statistical Visualization - enhancements to statistical consulting using the virtual world paradigm

The focus of my Master's degree was on building a platform that enables a statistician and a biomedical domain expert to collaboratively visualize multivariate bio-statistical data. We call the platform the Statistical Reality Engine (SRE), it is an environment for collaborative statistical visualization employing Virtual Reality. The system is designed so that many views can be rapidly prototyped and tested for usefulness. The SRE is an R package that provides a platform for experimentation with ideas for data visualization in Virtual Reality. How did we get a complex multi-threaded platform like OpenSG and VRJuggler to work with a interactive, single threaded, interpreter like R? The trick was to use Duncan Temple Lang's experimental REventLoop Package. The result is that VRJuggler's event loop replaces R's and provides an interactive R session to users using Readline.