MATTHEW LEE SETTLES
EDUCATION
Fall, 2008 PhD (expected) Bioinformatics and
Computational Biology
· 4.0 GPA,
· University of Idaho, Moscow, Idaho
· Dissertation Topic: Meta-analysis of Microarray
Gene Expression Data.
· Supervisor: Terence Soule, PhD and Barrie
Robison, PhD
2005 M.S. Computer Science
· University of Idaho, Moscow, Idaho
· Specialization: Population Based Stochastic
Optimization
· Thesis Title: Breeding Swarms: A Hybrid GA\PSO
for Real Parameter Optimization.
· Supervisor: Terence Soule, PhD
2002 B.S. Electrical Engineering (magna cum laude), 3.7
GPA
· University of Portland, Portland, Oregon
· Computer Engineering Track
2000 Associates in Arts (honors)
· Engineering Transfer Program, Clark College,
Vancouver, Washington
EXPERIENCE
8/2008-current Research Associate, Dr. Michael Skinner
Labratory, School of Molecular Biology,
Washington State University, Pullman,WA
8/2008-current Research Associate, Dr. Holly Neigbergs,
Department of Animal Sciences,
Washington State University, Pullman,WA
8/2008-current Manager, Bioinformatics Core,
Washington State University, Pullman,WA
8/2005-7/2007 Research Assistant, Fish Physiology and
Genomics Research Group
University of Idaho, Moscow, Idaho.
· Working on an NSF funded study of metabolism and
physiology using salmonid and
zebrafish models.
· This work includes supporting a diverse team of
biologists by the design and analysis
of microarray experiments.
8/2002-5/2005 Research Assistant, Neural Fuzzy Systems
Research Group
University of Idaho, Moscow, Idaho.
· Worked on an Idaho EPSCoR funded study of neural
fuzzy networks.
· This work included the study and design of new
algorithms to evolve and train recurrent
neural networks.
1/1996-2/2002 Engineering Technician
S.E.H. America, Vancouver, Washington.
· Supported an engineering group by designing and
creating computer application tools
designed to automate common tasks and to transition from
paper systems to electronic
systems.
· Applications were created using such tools as:
Visual Basic, SQL Server, Oracle Server,
Access, Excel and Word.
· Contributed to the success of audits, customer
tours, ISO 9000 and ISO 14000 audits.
GRANTS, HONORS AND AWARDS
April, 2008 United States Department of Agriculture
(USDA) Travel award, $2000 to attend and
present a poster to the ISAFG (International Symposium on
Animal Functional Genomics)
conference in Edinburgh, UK, April 7-9, 2008.
September, 2006 Microarray Gene Expression Data Society
Travel award, $800 to attend and present a
poster to the MGED9 conference in Seattle, Washington,
Sept 7-10, 2006.
June, 2006 Graduate and Professional Student Association
(GPSA) Graduate Student TravelAward,
$400 to attend the GECCO 2006 conference in Seattle,
Washington, July 8-12, 2006.
May, 2006 Graduate and Professional Student Association
(GPSA) 2006 Service to the University
Award for co-writing an accepted student fee proposal to
use student fee moneys to
establish a Student Research and Scholarship Grant
Program at the University of Idaho.
April, 2006 Cowrote an accepted proposal to establish a
Student Research and Scholarship Grant
Program at the University of Idaho. $5.00/student
(approximately $100,000 in year 1)
of student fee moneys will be used to establish and
administer a Grant Program available
to all students at the University of Idaho. Grant money
will be used to support
undergraduate and graduate student research and travel in
the sciences and arts.
July, 2005 GECCO 2005 Graduate Student Travel Grant, $300
to attend and give a presentation at
the GECCO 2005 conference in Washington, D.C., June
25-29, 2006.
COMMITTEE INVOLVEMENT
3/2007 University of Idaho Strategic Action Plan -
Invited member of a student panel on
interdisciplinary
research.
8/2006-5/2007 University of Idaho Student Grant Program -
College of Graduate Studies representative
and Committee Chair.
8/2005-5/2007 University of Idaho Graduate and
Professional Student Association - Senator.
TEACHING EXPERIENCE
Spring, 2007 Instructor, BCB404: Special Topics:
Bioinformatics Using R and Bioconductor
University of Idaho, Moscow, Idaho.
· Developed curriculum, lab materials and taught
the course.
Fall, 2005 Guest Lecturer, CS472/572: Evolutionary
Computation
University of Idaho, Moscow, Idaho.
· Three week guest lecturer on Particle Swarm
Optimization, Breeding Swarm Optimization,
Multi-objective Optimization and Constraint
Handling.
PRESENTATIONS AND INVITED LECTURES
August, 2006 IBEST Bioinformatics Workshop 2006,
organizer and instructor on microarray analysis
using R/Bioconductor, University of Idaho, Moscow,
ID.
March, 2006 Microarray Data Analysis for the Biologist,
Bioinformatics Seminar, University of Idaho
Aquaculture Research Institute, Hagerman, ID.
RESEARCH INTERESTS
Bioinformatics, Computational Biology, Microarray
Analysis, Gene Networks, Breeding Swarm
Optimization,
Particle Swarm Optimizers, Genetic Algorithms, Genetic
Programming, Machine Learning, Artificial
Neural Networks.
M.S. THESIS ABSTRACT
Genetic Algorithms and Particles Swarm Optimization are
both population based stochastic search algorithms
that have proven to be successful in solving very
difficult problems. However, both models have
strengths and weaknesses. Previous researchers have
suggested that a hybrid of the GA and PSO models
could lead to further advances. In this thesis we present
a novel hybrid algorithm, Breeding Swarms,
combining
the strengths of GAs with those of PSO. The Breeding
Swarms algorithm improves search results
for real valued problems by controlling the amount of
diversity in the population. We performed
experiments
on optimizing standard benchmark functions and recurrent
neural networks. Results show that the
Breeding Swarm algorithm produces significantly better
results than either GA or PSO, scales well to large
problems and is more consistent over different problem
domains.
PHD DISSERTATION ABSTRACT
Understanding the interactions between components of a
biological system, or "systems biology", is an
issue
that requires complex modeling methods. Most of these
methods require more data than is currently
generated in the typical experiment, or will be generated
in the near future. Combining data sets from
different sources and analysis from currently available
data is one way of addressing this problem. The
development of algorithms and methods that facilitate the
integration of different sources and perspectives
of biological data is needed for continued advancement in
modeling systems level interactions. Gene
expression microarrays are a high-throughput technique to
profiling genome wide transcription that is
producing
input data for many modern systems level approaches.
Methods that allow for the integration of
information from different sources and analysis of
microarray data is the focus of this research.
REFEREED PUBLICATIONS
Robert E Drew, Kenneth J. Rodnick, Matthew L Settles,
Jurij Wacyk, Erin J Churchill, Madison S. Powell,
Ronald W Hardy, Gordon K Murdoch, Rodney A. Hill, and
Barrie D Robison Effect of Starvation on Gene
Expression in Multiple Tissues of Zebrafish. Physiol.
Genomics (Accepted August 26, 2008)
Coram, T., Settles, M., Wang, M, Chen, X, Surveying
expression level polymorphism and single-feature
polymorphism in near-isogenic wheat lines differing for
the Yr5 stripe rust resistance locus. TAG Theoretical
and
Applied Genetics, Volume 117, Number 3, August,
2008.
Barrie D. Robison, Robert E. Drew, Gordon K. Murdoch,
Madison Powell, Kenneth J. Rodnick, Matt
Settles, David Stone, Erin Churchill, Rodney A. Hill,
Madhusudhan R. Papasani, Solange S. Lewis, Ronald
W. Hardy, Sexual dimorphism in hepatic gene expression
and the response to dietary carbohydrate manipulation
in
the zebrafish (Danio rerio), Comparative Biochemistry and
Physiology Part D: Genomics and ProteomicsVolume
3, Issue 2, , June 2008, Pages 141-154.
Coram, T., Settles, M., Chen, X, Transcriptome analysis
of high-temperature adult-plant resistance
conditioned
by Yr39 during the wheat-Puccinia striiformis f. sp.
tritici interactio. Molecular Plant Pathology,
Volume
9, Number 4, July, 2008.
Settles, M., Soule, T. Choosing an Algorithm: An
Experimental Comparison of the Genetic Algorithm
and
Binary Particle Swarm. Proceedings of the 17th IMACS
World Congress on Scientific Computation, Applied
Mathematics and Simulation. Paris, France, 11-15 July
2005.
Settles, M., Soule, T. Breeding Swarms: A GA/PSO Hybrid.
In Proceeding of the Genetic and Evolutionary
Computation Conference (GECCO-2005). Washington D.C.,
25-29 June 2005. ASME Press
Settles, M., Nathan, P., Soule, T. Breeding Swarms: A New
Approach to Recurrent Neural Network Training.
In Proceeding of the Genetic and Evolutionary Computation
Conference (GECCO-2005). Washington
D.C., 25-29 June 2005. ASME Press.
Settles, M., Soule, T. A Hybrid GA/PSO to Evolve
Artificial Recurrent Neural Networks. C. Dagli and
et
al., eds. In Intelligent Engineering Systems Through
Artificial Neural Networks (ANNIE-2003), vol. 13,
pages 51-56, St. Louis, Missouri, 2-5 Nov. 2003. ASME
Press.
Settles, M., and Rylander, B. Neural network learning
using particle swarm optimizers. Zemliak, A. and
Mastorakis, N., eds. In Advances in Information Science
and Soft Computing, pages 224-226. Cancun,
Mexico, June 2002. WSEAS Press.
PUBLISHED ABSTRACTS/REFEREED POSTERS
Matt Settles, et al., Whole Genome Association Study of
Johne’s Disease. International Symposium on
Animal
Functional Genomics (ISAFG), Edinburgh, UK, April 7-9,
2008. Poster
Sam S. Hunter, Matt Settles, James Foster, Deborah L.
Stenkamp, Barrie Robison Generating gene
coexpression
networks from zebrafish microarray data. Northwest
Regional Developmental Biology Conference,
Friday Harbor Laboratories, San Juan Island, Washington,
March 14-17, 2007. Poster
Settles, M., Soule, T. Feature Selection of Microarray
Data Using Particle Swarm Optimization. Poster,
MGED9, Seattle, WA, Sept. 7-9, 2006. Published
Abstract/Poster
Drew, R., Settles, M., Rodnick, K., Wyzac, J., Robison,
B. Effects of Starvation on Zebrafish. Poster,
MGED9, Seattle, WA, Sept. 7-9, 2006. Published
Abstract/Poster
Settles, M., Rodebaugh, B., Soule, T. Comparison of
Genetic Algorithm and Particle Swarm Optimizer
When Evolving a Recurrent Neural Network. In Proceedings
of the Genetic and Evolutionary Computation
Conference (GECCO-2003), vol. 2723, pages 148-149.
Chicago, Illinois, 12-15 July 2003. Springer Press.
Poster
MANUSCRIPTS IN REVIEW
Coram, T., Settles, M., Chen, X. Large-scale analysis of
antisense transcription in wheat using the
Affymetrix
GeneChip Wheat Genome Array. Submitted to BMC Plant
Biology, Sept. 2008.
MANUSCRIPTS IN PREPARATION
Settles, M., Soule, T. Breeding Swarms: A PSO/GA for Real
Parameter Optimization. To be submitted to IEEE
Transactions on Evolutionary Computation.
Settles, M., Soule, T., Robison, B. The Effects of Single
Feature Polymorphisms on Gene Expression
Summarization.
To be submitted Bioinformatics.
Settles, M., Soule, T., Murdock, G., Robison, B. On
Normalizing Microarrays from Multiple Tissue Types
To be submitted BMC Bioinformatics.
Settles, M., Zanella, R., Neigbergs, H. Whole Genome
Association Analysis of Johne’s Disease in 4 US
dairys using
the Illumina BovineSNP50 50k SNP chip. To be submitted to
Journal of Animal Genomics.
Settles, M., Lucker, B., Guerrero-Bosagna, C., Skinner,
M. Comparison of IP/Input and IP/IP for Methylation
Analysis using Nimblegen Tiling Arrays. To be submitted
to Genomics.
Guerrero-Bosagna, C., Settles, M., Lucker, B., Skinner,
M. Epigenetic and Transgenerational Actions of
Vinclozolin
on the Rat Epigenome.
TECHNICAL SKILLS
General skills in computing, algorithm development and
statistics. Specific expertise and interests in:
· Computing platforms: Mac OS X, UNIX, Windows
XP.
· Programming Languages: Extensive experience with
C,C++ and R as a programming language; familiar
with Java, HTML and many others.
· Statistical Software: Extensive experience in R
and Bioconductor; moderate experience with SAS.
· Scientific text writing and formatting:
Extensive experience in LATEX.
PROFESSIONAL MEMBERSHIPS
Tau Beta Pi, Engineering Honor Society
Association for Computing Machinery (ACM)
Special Interest Group on Genetic and Evolutionary
Computation (SIGEVO)