R E S E A R C H

Robert Kincaid is a Senior Research Scientist in the Systems Biology Project in the Molecular Technology Laboratory at Agilent Laboratories. His main research interests are centered around user interface research to support interactive and visually-oriented data mining across combinations of widely disparate data. For in further details consult his CV/Resume.

From a computer science perspective these research interests group in roughly two categories:

1. Information Visualization and Visual Analytics - These are efforts to effectively visualize large multivariate datasets in ways that reveal insights in the data. Of course most of this data comes from Agilent life science instruments. Some examples include:

	Signal Lens: A Focus+Context approach for analyzing large time series of electronic signals. SignalLens enables a very compact visualization which supports ad hoc visual data mining of long electronic time series. A brief video demo was presented by Agilent CTO Darlene Solomon at the IEEE MTT-S International Microwave Symposium in 2009. This work has been accepted for presentation at the 2010 IEEE Information Visualization Conference.
	RFLP Decoder: This software was developed to support authenticating fish species; a problem important to the food industry and critical to complying with new regulations to protect endangered fish species from being overfished. This is now part of an Agilent product (Agilent DNA Fish ID Solution) and was published in the Journal of Visual Experiments. So you can see a complete demo of the lab protocol as well as the software.
	MassVis: This project supported a novel proteomics workflow developed by Kurt Dejgaard at McGill University. A cleverly designed scatter plot interface provides a highly interactive information browser for discovery of putative protein complexes. Pattern similarity matching is used to match ‘‘profiles’’ of similar proteins as a predictor of membership in a protein complex. Both supervised, interactive methods are provided as well as completely unsupervised complex prediction. This work was presented at the 2009 IEEE Symposium on Visual Analytics Science and Technology. The MassVis concept has been awarded US Patent 7,930,108.
	Line Graph Explorer: A scalable Focus+Context visualization designed specifically for large collections of line graphs. This work was done with the help of Heidi Lam at the University of British Columbia. Presented at AVI 2006, Venice Italy. You can also view a video demo (~100Mb!) LGE was also featured on Information Aesthetics. LGE is covered by two US Patents ( 7,825,929 and 7,750,908).
	VistaChrom: A visual environment for analyzing array-based comparative genomic hybridization data (aCGH). This was transferred as part of a new commercial aCGH platform and is now part of Agilent Genomic Workbench. See the recent publication in “Information Visualization” for details. Published in Information Visualization. [preprint]
	VistaClara: An exploratory heat map style visualization of gene expression data that combines additional meta-data to assist in finding meaningful patterns and biological insight. Published in SAC 2004 Proceedings.

2. Computational Data Analysis - This is primarily concerned with low-level analysis of data from microarrays, liquid chromatography, mass spectrometry, or more recently electropherograms from the Agilent 2100 Bioanalyzer. Here is an example from Mass Spectrometry:

Deconvolution of HDL Subfractions: Agilent has developed an assay for measuring HDL subfractions from human serum using the Agilent Bioanalyzer microfluidic platform. This required a novel and fully automatic algorithm to fit Gaussian peak shapes to the expected fractions. This enabled deconvoluting the overlapping peaks and permitted measurements of the HDL components. This algorithm was used to measure data from real clinical samples as published in Clinical Chemistry and Laboratory Medicine (see Muller et al. 2007 below).

Mass Hunter/ Mass Profiler: A visual environment for analyzing proteomic and metabolomic biomarkers using Mass Spectrometry. This software was announced and demonstrated at ASMS 2005 and released in late 2005. I contributed the plotting graphics and user interface improvements.

Recent Publications

A. Vailaya, P. Bluvas, R. Kincaid, A. Kuchinsky, M. Creech, A. Adler, An architecture for biological information extraction and representation, Proceedings of the 2004 ACM symposium on Applied computing (SACBIO 2004), ACM Press, Nicosia, Cyprus 2004.