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Robert Kincaid
Address
519 Spindrift Way
Half Moon Bay CA 94019
[email protected]
http://rkincaid.net
Phone
650 224 1289
Education
1982 Ph.D. Theoretical Chemistry, Cornell University, Ithaca NY
1979 M.S. Theoretical Chemistry, Cornell University, Ithaca NY
1976 B.S. Chemistry, Texas Christian University, Fort Worth TX
Professional
Affiliations and Activities
Senior Member of the Association for Computing Machinery
Senior Member of IEEE & Member of IEEE Computer Society
Member of International Society for Computational Biology
Member of Sigma Xi
Poster co-chair, 2012-2013 IEEE BioVis, Industry Liaison, 2011 IEEE BioVis
Program Committee 2011-2013 IEEE InfoVis & IEEE BioVis
Co-chair for Student Volunteers, 2004 IEEE Visualization
Paper Reviewer for:
IEEE Transactions on Visualization and Computer Graphics
IEEE BioVis Symposium
IEEE Visualization Conference
IEEE Information Visualization Conference
IEEE Symposium on Visual Analytics Science and Technology
EuroVis/IEEE-VGTC Symposium on Visualization
ACM Symposium on Applied Computing
Proteomics, Bioinformatics, Pacific Symposium on Biocomputing
Experience
Agilent Laboratories
May 2013 - Present
Section Manager, Computational Biology and Informatics
Agilent Laboratories / Molecular Technologies Lab, Santa Clara CA
Leads cross-functional distributed team of computer scientists, mathematicians and
computational biologist conducting research in support of data analysis of life science instrument
data.
Agilent Laboratories
April 2000 – May 2013
Senior Research Scientist Computational Biology and Computer Science
Agilent Laboratories / Molecular Technologies Lab, Santa Clara CA
Main research interests are Information Visualization and Visual Analytics that support
interactive and visually-oriented data mining across widely disparate data (either separately or in
joint analyses; particularly how various “omics” data can be combined with other
complementary measurements such as clinical attributes and phenotypes.
More recently I have investigated using emerging user interface technologies in laboratory work
flows such as applying augmented reality to guide manual processes, using portable devices,
natural user interfaces, etc. Most of my more recent publications describe the work publically
accessible, but the more interesting aspects are still company confidential.
Signal Lens
RFLP Decoder
Signal Lens: Designed and coded a novel research prototype which provides a very compact
visualization which supports ad hoc visual data mining of long electronic time series. This work
was presentation at the 2010 IEEE Information Visualization Conference and received a "Paper
Honorable Mention" award and was published in the IEEE Transactions on Visualization and
Computer Graphics. Additionally, a brief video demo was presented by Agilent CTO Darlene
Solomon at the IEEE MTT-S International Microwave Symposium in 2009 and received press
coverage. This research inspired an ongoing effort within Agilent to rethink the traditional
visualization paradigms of electronic test and measurement equipment using advanced concepts
from the fields of Information Visualization and Visual analytics.
RFLP Decoder: Designed and coded software and algorithms 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 overfishing. This software was released commercially as
a critical component of the “Agilent DNA Fish ID Solution” and published in the Journal of
Visual Experiments.
MassVis
MassVis: Designed and coded a visual analysis research platform to support 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
also been awarded US patent 7,930,108.
Line Graph Explorer
VistaChrom
Line Graph Explorer: Designed visualization and supervised a summer intern to code a
research prototype providing a scalable Focus+Context visualization designed specifically for
large collections of line graphs. Some features from this prototype were transferred to the
Agilent product “DNA Analytics”. A detailed description of the prototype was publish at the
ACM Workshop on Advanced Visual Interfaces (AVI ’06, Venice Italy). Line Graph Explorer
was also awarded two US patents (7,750,908 & 7,825,929).
VistaChrom: Designed and wrote a visual analytics environment for analyzing microarraybased comparative genomic hybridization data (aCGH). This was transferred as part of a new
microarray-based CGH platform and is now known commercially as DNA Analytics (formerly
CGH Analytics). Currently over 1000 scientific papers (largely in cancer genomics) cite the
CGH or DNA Analytics platforms and frequently use screen shots from the application for
publication figures. A detailed discussion of the application design and methodology was
published in the journal “Information Visualization”.
Mass Hunter/Profiler: Designed and coded the visualization components for a new Agilent
platform for analyzing proteomic and metabalomic biomarkers based using Mass Spectrometry.
This software was announced and demonstrated at ASMS and released commercially in 2005.
VistaClara
Hewlett-Packard &
Agilent Technologies
June 1997 April 2000
VistaClara: Designed and coded an exploratory heat map style visualization of gene expression
data that combines additional meta-data to assist in finding meaningful patterns in the data.
Published in SAC 2004 Proceedings. Portions of VistaClara were incorporated into the Agilent
product “Synapsia” and a refactored version of VistaClara was provided as a free plug-in to the
open source network analysis platform “Cytoscape”.
Technical Lead, Bioinformatics
Bioscience Products/Chemical Applications Group, Santa Clara CA
Responsible for the design and implementation of the data storage subsystem for a next
generation Microarray system.
Responsible for design and development of Microarray probe design software used internally for
the design and manufacturing of DNA Microarrays. This work led to inventorship in several
microarray-related patents.
Successfully led a cross-functional integration effort with third party software from Rosetta
Inpharmatics including design of XML schemas to enable data exchange between both systems.
This work was critical to allow Agilent DNA Microarray scanners to seamlessly interoperate
with Rosetta’s software.
Responsible for specifying, installing and maintaining an HP NetServer running NT Server, MS
SQL Server, Sybase 11 and Oracle 8. This system operated as the central data storage system for
the new Micro-Array system.
Engineering lead of a small team responsible for on-going software support (enhancements and
bug fixes) the 241 N- And C-Terminal Protein Sequencer.
Other Work
Senior MS-Windows Developer.
First Floor
1996 - 1997
Responsible for graphical user interfaces (design and implementation). Designed and developed
a notification add-on for the SmartBookmarks/InfoPilot line which interfaces to FirstFloor
ActiveX/OLE automation interfaces as well as MAPI. Developed Java applets to provide CDF
navigation capabilities to Netscape Netcaster Channels.
Oracle
Spring 1996
Senior Software Engineer Distributed Solutions Group, Workgroup Solutions Division.
Delivered ocx-based components for database import/export/load as part of a remote database
administration console (Enterprise Manager). This relied on an OLE2.0 distributed computing
model. Developed prototype for web software management utilizing Java with CORBA and
CORBA-like ORB's. This development included rich sophisticated UI comparable to traditional
standalone MFC-based applications, but was completely platform independent and accessible via
Web browsers.
Xerox
1985-1995
Principal Software Scientist
1995 - Implemented Windows, Macintosh and Motif-based file upload functionality to World
Wide Web servers. This involved direct low-level connectivity to remote Web servers including
proxy services via the Windows Sockets API, Unix sockets and MacTCP. This file upload
functionality was officially adopted in HTML 3.0. This is in support of a new Web-based service
that also requires a sophisticated database back-end to maintain and handle customer job
requests.
1994 - Responsible for overall software architecture of a new Microsoft At Work-based multifunction fax device. Specifically responsible for implementing the low level printer driver
(DMA-based) as well as a "paper user interface" (i.e. Optical Mark Recognition) based on PARC
developed "DataGlyph" technology.
1993 - Responsible for developing and prototyping new product concepts based on PARC
technology, as well as providing overall technical leadership to the Tools and Utilities line of
business. Developed new collaborative network-based applications based on PARC research in
work group collaboration. Implemented and prototyped next generation of UI products from
XSoft including TabWorks (was bundled on most Compaq computers).
1991-1992 - Lead developer and team leader of Rooms for Windows, the first highly successful
and visible Windows-based product from the XSoft division of Xerox. Significant contributions
were made to the actual development as well as a broad range of technical program management
roles.
1990-1991 - Manager of "Operating Environments and Toolkit Support" responsible for
coupling Xerox proprietary environment with SunOS and X11 via interoperability tools and
environments.
1988-1990 - Team leader and key contributor to the X-Environment Window project (X server
provided within the ViewPoint/GlobalView environment). Personally implemented direct lowlevel modifications to Sun Microsystems' X11/NeWS server code. Significant contributor to the
Companion 386 project (PC/Viewpoint interoperability via a tethered PC environment).
Involved heavy use of DOS and assembler development, including DOS device driver
development.
1985-1987 - Lead developer and Team Leader of a large (~15 developers) engineering group
responsible for developing a C-based PC word processor (Writer II/III shipped ~1986).
Good Software
1984-1985
PharmAssist
1983-1984
Contributed to development of C-based PC word processor
Contributed to development of UCSD Pascal-based in-store pharmacy automation system.
Publications
Orit Shaer, Consuelo Valdes, Sirui Liu, Kara Lu, Casey Grote, Veronica Lin, Linda Ding, Nicole
Francisco, Kimberly Chang, Wendy Xu, Nahum Seifelassie, Robert Kincaid, Designing RealityBased Interfaces for Experiential Bio-Design, Personal and Ubiquitous Computing (Special
Edition on Educational Interfaces, Software, and Technology) in press.
Melanie Tory, Robert Kincaid, Comparing Physical, Overlay, and Touch Screen Parameter
Controls, ACM Interactive Tabletops and Surfaces 2013 Conference (ITS), 2013 (accepted).
Orit Shaer, Consuelo Valdes, Sirui Liu, Kara Lu, Traci Haddock, Swapnil Bhatia, Douglas
Densmore, Robert Kincaid, MoClo Planner: Interactive Visualization for Modular Cloning
Bio-Design, Accepted IEEE Symposium on Biological Data Visualization (BioVis), 2013
(accepted).
Wendy Xu, Kimberly Chang, Nicole Francisco, Consuelo Valdes, Robert Kincaid, and Orit
Shaer, From Wet Lab Bench to Tangible Virtual Experiment: SynFlo. ACM Internation
Conference on Tangible, Embedded and Embodied Interaction (TEI’13).
Sirui Liu, Kara Lu, Nahum Seifeselassie, Casey Grote, Nicole Francisco, Veronica Lin, Linda
Ding, Consuelo Valdes, Robert Kincaid, and Orit Shaer, MoClo planner: supporting
innovation in bio-design through multi-touch interaction. ACM international conference on
Interactive tabletops and surfaces (ITS '12) 307-310.
Kimberly Chang, Wendy Xu, Nicole Francisco, Consuelo Valdes, Robert Kincaid, and Orit
Shaer, SynFlo: an interactive installation introducing synthetic biology concepts, ACM
international conference on Interactive tabletops and surfaces (ITS '12) 303-306.
Robert Kincaid, Tactile Guides for Touch Screen Controls (BCS HCI 2012) 339-344.
Ankit Singh, Alex Endert, Lauren Bradel, Christopher Andrews, Chris North and Robert Kincaid,
Using Large Displays for Live Visual History of Cyber-security Analytic Process, in
International Symposium on Visualization for Cyber Security (VizSec)2011: Carnegie Mellon
University.
Steffen Mueller, Harini Ravi, Natalia Novoradovskaya, Robert Kincaid and Yang-Lee Chee,
Enhanced fish species identification by PCR-RFLP using the 2100 Bioanalyzer system.
International Food Research Journal, 2011. 18(3): p. 1154-1158.
R. Kincaid, SignalLens: Focus plus Context Applied to Electronic Time Series. IEEE
Transactions on Visualization and Computer Graphics, 2010. 16(6): p. 900-907.
R Formosa, H Ravi, S Happe, D Huffman, N Novoradovskaya, R Kincaid and S Garrett, DNAbased Fish Species Identification Protocol. Journal of Visualized Experiments, 2010(38).
R Kincaid and K Dejgaard. MassVis: Visual analysis of protein complexes using mass
spectrometry. in IEEE Symposium on Visual Analytics Science and Technology. 2009. IEEE.
O. Mueller, E. Chang, D. Deng, T. Franz, D. Jing, R. Kincaid, Y. Konigshofer, M. Kratzmeier,
M. McNulty, H. Qian, J. Schneider, H. Schulte, U. Seedorf, X. D. Tian, M. Van Cleve, D. Yang
and G. Assmann, PROCAM Study: risk prediction for myocardial infarction using
microfluidic high-density lipoprotein (HDL) sub-fractionation is independent of HDL
cholesterol. Clinical Chemistry and Laboratory Medicine, 2008. 46(4): p. 490-498.
R. Kincaid, A. Kuchinsky and M. Creech, VistaClara: An expression browser plug-in for
Cytoscape. Bioinformatics, 2008. 24(18): p. 2112-2114.
A. Barsky, T. Munzner, J. Gardy and R. Kincaid, Cerebral: Visualizing Multiple Experimental
Conditions on a Graph with Biological Context. IEEE Transactions on Visualization and
Computer Graphics, 2008. 14(6): p. 1253-1260.
H. Lam, T. Munzner and R. Kincaid, Overview use in multiple visual information resolution
interfaces. IEEE Transactions on Visualization and Computer Graphics, 2007. 13(6): p. 12781285.
D. X. F. Deng, A. Tsalenko, A. Vailaya, A. Ben-Dor, R. Kundu, I. Estay, R. Tabibiazar, R.
Kincaid, Z. Yakhini, L. Bruhn and T. Quertermous, Differences in vascular bed disease
susceptibility reflect differences in gene expression response to atherogenic stimuli.
Circulation Research, 2006. 98(2): p. 200-208.
A. Vailaya, A. Kuchinsky, R. Kincaid, A. Adler, R. Tabibiazar, R. Wagner and T. Quertermous.
Ontology-based statistical analysis of microarray data. in 8th Annual Bio-Ontologies
Meeting. 2005.
A. Vailaya, P. Bluvas, R. Kincaid, A. Kuchinsky, M. Creech and A. Adler, An architecture for
biological information extraction and representation. Bioinformatics, 2005. 21(4): p. 430-438.
J. Y. King, R. Ferrara, R. Tabibiazar, J. M. Spin, M. M. Chen, A. Kuchinsky, A. Vailaya, R.
Kincaid, A. Tsalenko, D. X. F. Deng, A. Connolly, P. Zhang, E. Yang, C. Watt, Z. Yakhini, A.
Ben-Dor, A. Adler, L. Bruhn, P. Tsao, T. Quertermous and E. A. Ashley, Pathway analysis of
coronary atherosclerosis. Physiological Genomics, 2005. 23(1): p. 103-118.
R Kincaid, A Ben-Dor and Z Yakhini, Exploratory visualization of array-based comparative
genomic hybridization. Information Visualization, 2005. 4(3): p. 176-190.
Aditya Vailaya, Peter Bluvas, Robert Kincaid, Allan Kuchinsky, Michael Creech and Annette
Adler, An architecture for biological information extraction and representation, in
Proceedings of the 2004 ACM Symposium on Applied Computing, 2004, ACM: Nicosia,
Cyprus. p. 103-110.
R Kincaid. VistaClara: an interactive visualization for exploratory analysis of DNA
microarrays. in ACM Symposium on Applied Computing. 2004. ACM.
M. T. Barrett, A. Scheffer, A. Ben-Dor, N. Sampas, D. Lipson, R. Kincaid, P. Tsang, B. Curry,
K. Baird, P. S. Meltzer, Z. Yakhini, L. Bruhn and S. Laderman, Comparative genomic
hybridization using oligonucleotide microarrays and total genomic DNA. Proceedings of the
National Academy of Sciences of the United States of America, 2004. 101(51): p. 17765-17770.
G Delenstarr, H Cattell, C Chen, AN Dorsel, RH Kincaid, K Nguyen, NM Sampas, S Schidel,
KW Shannon and A Tu. Estimation of the confidence limits of oligonucleotide-array-based
measurements of differential expression. in SPIE. 2001.
D. Huckaby, R. Pitis, R. Kincaid and C. Hamilton, Inclusion-exclusion calculation of the
dipole-dipole energy of hexagonal ice and of cubic ice. The Journal of Chemical Physics, 1993.
98: p. 8105.
RH Kincaid and DA Huckaby, Harmonic surface entropy of noble gas crystals: Cell cluster
method. The Journal of Chemical Physics, 1983. 78: p. 2598.
RH Kincaid and HA Scheraga, Revised empirical potential for conformational,
intermolecular, and solvation studies. 7. Testing of parameters by application to liquid
methane. The Journal of Physical Chemistry, 1982. 86(5): p. 838-841.
RH Kincaid and HA Scheraga, Revised empirical potential for conformational,
intermolecular, and solvation studies. 6. Testing of parameters by application to liquid
ammonia. The Journal of Physical Chemistry, 1982. 86(5): p. 833-838.
RH Kincaid and HA Scheraga, Acceleration of convergence in Monte Carlo simulations of
aqueous solutions using the metropolis algorithm. Hydrophobic hydration of methane.
Journal of Computational Chemistry, 1982. 3(4): p. 525-547.
RH Kincaid and DA Huckaby, Cell cluster calculations of the surface entropy of harmonic
fcc crystals. The Journal of Chemical Physics, 1982. 76: p. 3836.
RL Kincaid and DA Huckaby, Two methods for calculating the effect of vacancy defects on
the free energy of harmonic solids. The Journal of Chemical Physics, 1976. 65: p. 2353.
Issued
Patents
Pat. No.
8,340,389
8,131,471
7,930,108
7,894,998
7,879,541
7,825,929
7,750,908
7,588,889
7,519,605
7,344,831
7,224,362
7,155,453
6,950,756
6,920,448
6,461,816
6,251,588
Title
Cellular- or Sub-Cellular-Based Visualization Information Using Virtual Stains
Methods and system for simultaneous visualization and manipulation of multiple data types
Exploratory Visualization of Protein Complexes by Molecular Weight
Method for identifying suitable nucleic acid probe sequences for use in nucleic acid arrays
Apparatus and methods of detecting features on a microarray
Systems, tools and methods for focus and context viewing of large collections of graphs
Focus plus context viewing and manipulation of large collections of graphs
Chemical arrays and methods of using the same
Systems, methods and computer readable media for performing a domain-specific metasearch,
and visualizing search results therefrom
Methods for controlling cross-hybridization in analysis of nucleic acid sequences
Systems and methods for providing visualization and network diagrams
Biotechnology information naming system
Rearrangement of microarray scan images to form virtual arrays
Domain specific knowledge-based metasearch system and methods of using
Methods for controlling cross-hybridization in analysis of nucleic acid sequences
Method for evaluating oligonucleotide probe sequences