Robert Kincaid

Publications

• Enhanced fish species identification by PCR-RFLP using the 2100 Bioanalyzer system

  Steffen Mueller, Harini Ravi, Natalia Novoradovskaya, Robert Kincaid, Yang-Lee Chee

  International Food Research Journal. 01/2011; 18:1154-1158.

• Using Large Displays for Live Visual History of Cyber-security Analytic Process

  A. Singh, A. Endert, L. Bradel, C. Andrews, C. North, R. Kincaid

  ACM VizSec 2011; 01/2011

• DNA-based fish species identification protocol.

  Rachel Formosa, Harini Ravi, Scott Happe, Danielle Huffman, Natalia Novoradovskaya, Robert Kincaid, Steve Garrett

  Journal of visualized experiments : JoVE. 01/2010;

  We have developed a fast, simple, and accurate DNA-based screening method to identify the fish species present in fresh and processed seafood samples. This versatile method employs PCR amplification of genomic DNA extracted from fish samples, followed by restriction fragment length polymorphism (RFL... [more] We have developed a fast, simple, and accurate DNA-based screening method to identify the fish species present in fresh and processed seafood samples. This versatile method employs PCR amplification of genomic DNA extracted from fish samples, followed by restriction fragment length polymorphism (RFLP) analysis to generate fragment patterns that can be resolved on the Agilent 2100 Bioanalyzer and matched to the correct species using RFLP pattern matching software. The fish identification method uses a simple, reliable, spin column- based protocol to isolate DNA from fish samples. The samples are treated with proteinase K to release the nucleic acids into solution. DNA is then isolated by suspending the sample in binding buffer and loading onto a micro- spin cup containing a silica- based fiber matrix. The nucleic acids in the sample bind to the fiber matrix. The immobilized nucleic acids are washed to remove contaminants, and total DNA is recovered in a final volume of 100 mul. The isolated DNA is ready for PCR amplification with the provided primers that bind to sequences found in all fish genomes. The PCR products are then digested with three different restriction enzymes and resolved on the Agilent 2100 Bioanalyzer. The fragment lengths produced in the digestion reactions can be used to determine the species of fish from which the DNA sample was prepared, using the RFLP pattern matching software containing a database of experimentally- derived RFLP patterns from commercially relevant fish species.

• MassVis: Visual analysis of protein complexes using mass spectrometry

  R Kincaid, K Dejgaard

  IEEE Symposium on Visual Analytics Science and Technology; 01/2009
• 4.93

  Impact points

  VistaClara: an expression browser plug-in for Cytoscape.

  Robert Kincaid, Allan Kuchinsky, Michael Creech

  Bioinformatics (Oxford, England). 10/2008; 24(18):2112-4.

  SUMMARY: VistaClara is a plug-in for Cytoscape which provides a more flexible means to visualize gene and protein expression within a network context. An extended attribute browser is provided in the form of a graphical and interactive permutation matrix that resembles the heat map displays popular ... [more] SUMMARY: VistaClara is a plug-in for Cytoscape which provides a more flexible means to visualize gene and protein expression within a network context. An extended attribute browser is provided in the form of a graphical and interactive permutation matrix that resembles the heat map displays popular in gene-expression analysis. This extended browser permits a variety of display options and interactions not currently available in Cytoscape. AVAILABILITY: http://chianti.ucsd.edu/cyto_web/plugins/index.php.
• 1.89

  Impact points

  PROCAM Study: risk prediction for myocardial infarction using microfluidic high-density lipoprotein (HDL) subfractionation is independent of HDL cholesterol.

  Odilo Mueller, Elaine Chang, David Deng, Torsten Franz, Debra Jing, Robert Kincaid, Yves Konigshofer, Martin Kratzmeier, Michael McNulty, Hao Qian, Juergen Schneider, Helmut Schulte, Udo Seedorf, Xioadan Tian, Mark Van-Cleve, Dorothy Yang, Gerd Assmann

  Clinical chemistry and laboratory medicine : CCLM / FESCC. 01/2008; 46(4):490-8.

  BACKGROUND: High-density lipoprotein (HDL) subfractions are among the new emerging risk factors for atherosclerosis. In particular, HDL 2b has been shown to be linked to cardiovascular risk. This study uses a novel microfluidics-based method to establish HDL 2b clinical utility using samples from th... [more] BACKGROUND: High-density lipoprotein (HDL) subfractions are among the new emerging risk factors for atherosclerosis. In particular, HDL 2b has been shown to be linked to cardiovascular risk. This study uses a novel microfluidics-based method to establish HDL 2b clinical utility using samples from the Prospective Cardiovascular Muenster (PROCAM) Study. METHODS: Method performance was established by measuring accuracy, precision, linearity and inter-site precision. Serum samples from 503 individuals collected in the context of the PROCAM study were analyzed by electrophoresis on a microfluidics system. Of these, 251 were male survivors of myocardial infarction (cases), while 252 individuals were matched healthy controls. HDL cholesterol, HDL 2b concentration and HDL 2b percentage were analyzed. RESULTS: This novel method showed satisfactory assay performance with an inter-site coefficient of variance of <10% for HDL 2b percentage. Parallel patient testing on 52 samples between two sites resulted in a correlation coefficient of r=0.95. Significant differences were observed in the HDL 2b subfraction between cases and controls independent of other risk factors. Including HDL 2b percentage in logistic regression reduced the number of false positives from 64 to 39 and the number of false negative cases from 48 to 45, in the context of this study. CONCLUSIONS: The novel method showed satisfactory assay performance in addition to drastically reduced analysis times and improved ease of use as compared to other methods. Clinical utility of HDL 2b was demonstrated supporting the findings of previous studies.
• 9.21

  Impact points

  Differences in vascular bed disease susceptibility reflect differences in gene expression response to atherogenic stimuli.

  David Xing-Fei Deng, Anya Tsalenko, Aditya Vailaya, Amir Ben-Dor, Ramendra Kundu, Ivette Estay, Raymond Tabibiazar, Robert Kincaid, Zohar Yakhini, Laurakay Bruhn, Thomas Quertermous

  Circulation research. 03/2006; 98(2):200-8.

  Atherosclerosis occurs predominantly in arteries and only rarely in veins. The goal of this study was to test whether differences in the molecular responses of venous and arterial endothelial cells (ECs) to atherosclerotic stimuli might contribute to vascular bed differences in susceptibility to ath... [more] Atherosclerosis occurs predominantly in arteries and only rarely in veins. The goal of this study was to test whether differences in the molecular responses of venous and arterial endothelial cells (ECs) to atherosclerotic stimuli might contribute to vascular bed differences in susceptibility to atherosclerosis. We compared gene expression profiles of primary cultured ECs from human saphenous vein (SVEC) and coronary artery (CAEC) exposed to atherogenic stimuli. In addition to identifying differentially expressed genes, we applied statistical analysis of gene ontology and pathway annotation terms to identify signaling differences related to cell type and stimulus. Differential gene expression of untreated venous and arterial endothelial cells yielded 285 genes more highly expressed in untreated SVEC (P<0.005 and fold change >1.5). These genes represented various atherosclerosis-related pathways including responses to proliferation, oxidoreductase activity, antiinflammatory responses, cell growth, and hemostasis functions. Moreover, stimulation with oxidized LDL induced dramatically greater gene expression responses in CAEC compared with SVEC, relating to adhesion, proliferation, and apoptosis pathways. In contrast, interleukin 1beta and tumor necrosis factor alpha activated similar gene expression responses in both CAEC and SVEC. The differences in functional response and gene expression were further validated by an in vitro proliferation assay and in vivo immunostaining of alphabeta-crystallin protein. Our results strongly suggest that different inherent gene expression programs in arterial versus venous endothelial cells contribute to differences in atherosclerotic disease susceptibility.

• Line graph explorer: scalable display of line graphs using Focus+Context.

  Robert Kincaid, Heidi Lam

  Proceedings of the working conference on Advanced visual interfaces, AVI 2006, Venezia, Italy, May 23-26, 2006; 01/2006
• 3.93

  Impact points

  Pathway analysis of coronary atherosclerosis.

  Jennifer Y King, Rossella Ferrara, Raymond Tabibiazar, Joshua M Spin, Mary M Chen, Allan Kuchinsky, Aditya Vailaya, Robert Kincaid, Anya Tsalenko, David Xing-Fei Deng, [......], Peng Zhang, Eugene Yang, Clifton Watt, Zohar Yakhini, Amir Ben-Dor, Annette Adler, Laurakay Bruhn, Philip Tsao, Thomas Quertermous, Euan A Ashley

  Physiological genomics. 10/2005; 23(1):103-18.

  Large-scale gene expression studies provide significant insight into genes differentially regulated in disease processes such as cancer. However, these investigations offer limited understanding of multisystem, multicellular diseases such as atherosclerosis. A systems biology approach that accounts ... [more] Large-scale gene expression studies provide significant insight into genes differentially regulated in disease processes such as cancer. However, these investigations offer limited understanding of multisystem, multicellular diseases such as atherosclerosis. A systems biology approach that accounts for gene interactions, incorporates nontranscriptionally regulated genes, and integrates prior knowledge offers many advantages. We performed a comprehensive gene level assessment of coronary atherosclerosis using 51 coronary artery segments isolated from the explanted hearts of 22 cardiac transplant patients. After histological grading of vascular segments according to American Heart Association guidelines, isolated RNA was hybridized onto a customized 22-K oligonucleotide microarray, and significance analysis of microarrays and gene ontology analyses were performed to identify significant gene expression profiles. Our studies revealed that loss of differentiated smooth muscle cell gene expression is the primary expression signature of disease progression in atherosclerosis. Furthermore, we provide insight into the severe form of coronary artery disease associated with diabetes, reporting an overabundance of immune and inflammatory signals in diabetics. We present a novel approach to pathway development based on connectivity, determined by language parsing of the published literature, and ranking, determined by the significance of differentially regulated genes in the network. In doing this, we identify highly connected "nexus" genes that are attractive candidates for therapeutic targeting and followup studies. Our use of pathway techniques to study atherosclerosis as an integrated network of gene interactions expands on traditional microarray analysis methods and emphasizes the significant advantages of a systems-based approach to analyzing complex disease.
• 4.93

  Impact points

  An architecture for biological information extraction and representation.

  Aditya Vailaya, Peter Bluvas, Robert Kincaid, Allan Kuchinsky, Michael Creech, Annette Adler

  Bioinformatics (Oxford, England). 03/2005; 21(4):430-8.

  Motivations: Technological advances in biomedical research are generating a plethora of heterogeneous data at a high rate. There is a critical need for extraction, integration and management tools for information discovery and synthesis from these heterogeneous data. RESULTS: In this paper, we prese... [more] Motivations: Technological advances in biomedical research are generating a plethora of heterogeneous data at a high rate. There is a critical need for extraction, integration and management tools for information discovery and synthesis from these heterogeneous data. RESULTS: In this paper, we present a general architecture, called ALFA, for information extraction and representation from diverse biological data. The ALFA architecture consists of: (i) a networked, hierarchical, hyper-graph object model for representing information from heterogeneous data sources in a standardized, structured format; and (ii) a suite of integrated, interactive software tools for information extraction and representation from diverse biological data sources. As part of our research efforts to explore this space, we have currently prototyped the ALFA object model and a set of interactive software tools for searching, filtering, and extracting information from scientific text. In particular, we describe BioFerret, a meta-search tool for searching and filtering relevant information from the web, and ALFA Text Viewer, an interactive tool for user-guided extraction, disambiguation, and representation of information from scientific text. We further demonstrate the potential of our tools in integrating the extracted information with experimental data and diagrammatic biological models via the common underlying ALFA representation. CONTACT: aditya_vailaya@agilent.com.

• Exploratory visualization of array-based comparative genomic hybridization.

  Robert Kincaid, Amir Ben-Dor, Zohar Yakhini

  Information Visualization. 01/2005; 4:176-190.
• 9.43

  Impact points

  Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA.

  Michael T Barrett, Alicia Scheffer, Amir Ben-Dor, Nick Sampas, Doron Lipson, Robert Kincaid, Peter Tsang, Bo Curry, Kristin Baird, Paul S Meltzer, Zohar Yakhini, Laurakay Bruhn, Stephen Laderman

  Proceedings of the National Academy of Sciences of the United States of America. 01/2005; 101(51):17765-70.

  Array-based comparative genomic hybridization (CGH) measures copy-number variations at multiple loci simultaneously, providing an important tool for studying cancer and developmental disorders and for developing diagnostic and therapeutic targets. Arrays for CGH based on PCR products representing as... [more] Array-based comparative genomic hybridization (CGH) measures copy-number variations at multiple loci simultaneously, providing an important tool for studying cancer and developmental disorders and for developing diagnostic and therapeutic targets. Arrays for CGH based on PCR products representing assemblies of BAC or cDNA clones typically require maintenance, propagation, replication, and verification of large clone sets. Furthermore, it is difficult to control the specificity of the hybridization to the complex sequences that are present in each feature of such arrays. To develop a more robust and flexible platform, we created probe-design methods and assay protocols that make oligonucleotide microarrays synthesized in situ by inkjet technology compatible with array-based comparative genomic hybridization applications employing samples of total genomic DNA. Hybridization of a series of cell lines with variable numbers of X chromosomes to arrays designed for CGH measurements gave median ratios for X-chromosome probes within 6% of the theoretical values (0.5 for XY/XX, 1.0 for XX/XX, 1.4 for XXX/XX, 2.1 for XXXX/XX, and 2.6 for XXXXX/XX). Furthermore, these arrays detected and mapped regions of single-copy losses, homozygous deletions, and amplicons of various sizes in different model systems, including diploid cells with a chromosomal breakpoint that has been mapped and sequenced to a precise nucleotide and tumor cell lines with highly variable regions of gains and losses. Our results demonstrate that oligonucleotide arrays designed for CGH provide a robust and precise platform for detecting chromosomal alterations throughout a genome with high sensitivity even when using full-complexity genomic samples.

• VistaClara: an interactive visualization for exploratory analysis of DNA microarrays

  R Kincaid

  ACM Symposium on Applied Computing; 01/2004

• Estimation of the confidence limits of oligonucleotide-array-based measurements of differential expression

  G Delenstarr, H Cattell, C Chen, AN Dorsel, RH Kincaid, K Nguyen, NM Sampas, S Schidel, KW Shannon, A Tu

  SPIE; 01/2001

• Inclusion-exclusion calculation of the dipole-dipole energy of hexagonal ice and of cubic ice

  D. Huckaby, R. Pitis, R. Kincaid, C. Hamilton

  The Journal of Chemical Physics. 01/1993; 98:8105.

• Harmonic surface entropy of noble gas crystals: Cell cluster method

  RH Kincaid, DA Huckaby

  The Journal of Chemical Physics. 01/1983; 78:2598.

• Cell cluster calculations of the surface entropy of harmonic fcc crystals

  RH Kincaid, DA Huckaby

  The Journal of Chemical Physics. 01/1982; 76:3836.

• Revised empirical potential for conformational, intermolecular, and solvation studies. 7. Testing of parameters by application to liquid methane

  RH Kincaid, HA Scheraga

  The Journal of Physical Chemistry. 01/1982; 86(5):838-841.

• Revised empirical potential for conformational, intermolecular, and solvation studies. 6. Testing of parameters by application to liquid ammonia

  RH Kincaid, HA Scheraga

  The Journal of Physical Chemistry. 01/1982; 86(5):833-838.

• Acceleration of convergence in Monte Carlo simulations of aqueous solutions using the metropolis algorithm. Hydrophobic hydration of methane

  RH Kincaid, HA Scheraga

  Journal of Computational Chemistry. 01/1982; 3(4):525-547.