1. PhD graduate, Jerry S. Chen recently published
an article in the PLOS Computational Biology
Journal of June 2014. The article, “An Expanded
Notch-Delta Model Exhibiting Long-Range Patterning
and Incorporating MicroRNA Regulation,” was
featured on the cover of the publication as well. Jerry
contributed along
with SDSU faculty
and co-authors,
Joseph Mahaffy and Robert Zeller, on how
building upon classical Notch-Delta models,
the experimental data led to the formulation of
an expanded mathematical model that explains
the irregular patterning (marine invertebrate’s
spacings ranging from one cell to thirteen cells
between consecutive neurons).
T
he aim of Computational Biology and
Bioinformaticsistheunderstandingofliving
systems at all scales through the application
of data-analytical and theoretical methods,
mathematical modeling and computational
simulation techniques.
In the last decade, biology has become a digital
science. Moving away from science lead by
descriptive natural historical approaches,
reductionist biology flourished with molecular
techniques and especially DNA sequencing.
Duringthatperiod,anewareaofbiologicalsciences
– computational biology and bioinformatics
yielded insights into the cell and the workings of
individual organisms. The recent resurgence of holistic approaches to explore and study our
environments, again driven by DNA sequencing, has pushed the demand for computational
biology graduates into a new area which we call quantitative biology. These approaches
embrace computer science, applied mathematics, statistics, biochemistry, chemistry,
biophysics, molecular biology, genetics, ecology, evolution, anatomy, neuroscience, and
visualization to understand how genes and proteins combine to form cells, how cells combine
to form organisms, how organisms combine to form communities, and how the environments
that house those communities are driven by the biological processes at the heart of the systems.
The quantitative biology program at SDSU, a tract within the Computational Science PhD
program, has already graduated eight PhD students and three MSc students. Another six
students are currently studying in the program. Our recent graduates have worked in a variety
of quantitative biology fields including:
Metagenomics: The holistic study of the environment by sequencing all of the species in the
environment and using computational models to separate out the contributions of individual
organisms.
Viral genomics: Developing new tools to analyze
viral genomes to drive insights into the emergence
of novel viruses that may affect us.
Computational tools: To analyze the contraction of
heart cells to aid our understanding of cardiac health
and prevent heart disease.
SDSU
Computational Science
Graduate Programs:
PhD, Computational Science
PhD, Concentration in Statistics
Master of Science Degree
Master of Science Degree with
Concentration in Professional
Applications
Contact the CSRC or Be Placed on
the Mailing List:
Computational Science
Research Center
GMCS Building, Room 206
San Diego State University
5500 Campanile Drive
San Diego, CA 92182-1245
Telephone: (619) 594-3430
csrc@mail.sdsu.edu
Give to the Computational Science
Research Center for the Graduate
Student Research Projects Fund:
Donations to the CSRC can be made in the
following ways:
By check made out to:
The SDSU Campanile Foundation
or through credit card by contacting the
Computational Science Research Center
GMCS Building, Room 206
College of Sciences
San Diego State University
5500 Campanile Drive
San Diego, CA 92182-1245
Telephone: (619) 594-3430
csrc@mail.sdsu.edu
Donate online at the following
SDSU link:
http://www.csrc.sdsu.edu/csrc/
Click on “Donate here” under
Donate to the CSRC
COMPUTATIONAL SCIENCE
ODYSSEY is published twice a year by the
Computational Science Research Center
for the faculty, friends and supporters of
San Diego State University.
Your comments, suggestions and bulletin
submissions are welcome. Please call
Parisa Plant at (619) 594-2260 or e-mail:
parisa.plant@sdsu.edu
Jose E. Castillo Editor-in-Chief
Parisa Plant Editor/Publication
Designer/Coordinator THE
CSRC Alumni Spotlight
O D Y S S E Y
C O M P U TAT I O N A L S C I E N C E
Executive Board
Director
Jose E. Castillo, PhD
Associate Directors
Andrew Cooksy, PhD
Satchi Venkataraman, PhD
Paul Paolini, PhD
Computer Support Coordinator
James Otto, PhD
Industry Projects Coordinator
Ezra Bejar, PhD
CSRC Advisory Board
John Newsam, Chair
Tioga Research, Inc.
Gary Fogel
Natural Selection, Inc.
Mark E. Pflieger
Source Signal Imaging, Inc.
Bill Bartling
SR2020, Inc.
Bob Parker
SPAWAR
Scott Kahn
Illumina, Inc.
Victor Pereyra
Stanford University
Antonio Redondo
Los Alamos National Laboratory
SPRING
2015
In This Issue
Quantitative Biology.........Page 1
Director’s Corner..............Page 2
Pan-American Workshop.Page 3
Student Spotlights.............Page 4
Q u a n t i t a t i v e B i o l o g y c o n t i n u e d o n P a g e 3 . . .
After receiving her Bachelor’s degree in Physics
from UCSD, Priscilla Kelly began her MS studies
in SDSU’s Computational Science degree program in
2014. She is a recipient of the S-STEM Scholarship
from Computational Science Research Center. The
Scholarships for Graduate Student Participation in
Computational Science and Engineering Research
program is supported by a grant from the National
Science Foundation and managed by SDSU’s
Computational Science Research Center. Priscilla
is working in the area of nanophotonics in the research group of Professor
Kuznetsova, Physics Department. Her research is focused on the study of
nanolayeredAl:ZnO/ZnO andAl/SiO2 metamaterials with hyperbolic dispersion.
This recently discovered intriguing class of metamaterials could potentially be
used for nano-laser devices and ultrafast LEDS for a variety of applications, from
optical communications to biological nanoparticles sensing.
CSRC PhD Spotlight
CSRC MS Spotlight
We are pleased to announce that our PhD student,
Rong Zablocki, has been selected to receive an
Inamori Fellowship from San Diego State University
for 2015. Competition for Inamori Fellowships are
highly competitive. Applicants represent both masters
and doctoral candidates from almost every college of
the University. Each application was first reviewed and
ranked by the corresponding college-level research
committee. The Student Research Committee took
those recommendations into serious consideration
when they selected the final ten recipients. Rong is a multidisciplinary statistician
with a medical background interested in biostatistics and bioinformatics.
Currently, she is in her third year of the SDSU and CGU Joint Doctoral Program
in Computational Science with a concentration in Statistics. Her research focuses
on the application of Markov Chain Monte Carlo (MCMC) methods and Bayesian
statistical inferences in Genome-Wide Association Studies (GWAS) and other
health related studies.
Quantitative Biology at the CSRC

2. Director’s Corner - Jose Castillo
Dear Friends,
It is always a pleasure putting together our Computational Science Odyssey bringing news about
the accomplishment of our students and faculty. We now have 51 Doctoral students and 13 Master’s
students and have graduated 34 Doctoral students and 18 Master’s students so far. We would like
to congratulate our recent 2014 graduates: Mary Thomas and Mohammad Abouali. Also, we would
like to thank all our participants in the Student Research Symposium and congratulate Mariangel
Garcia for receiving the Dean’s Best Oral Presentation Award and Kelly Spoon for receiving the
Provost’s Best Poster Award. A warm welcome goes out to our new students as they finish their first
year as part of the CSRC family. CSRC is very excited about our new faculty members: Jerome
Giles, Ilenia Battiato, Bo-Wen Shen and Tony Luque; who bring a lot of energy and new research
opportunities to our students and faculty. I would also like to thank our staff who are doing an ex-
cellent job in making our goals possible.
The SDSU Computational Science Research Center
(CSRC) is primarily a graduate student program, with
13 Master’s degree candidates currently in the Center’s
Master’s Degree program, and 51 students in the CSRC
Doctoral Program. The Doctoral program can take 4 to
6 years to complete, and is offered jointly by SDSU and
the Claremont Graduate University, located about a two
hour’s drive north from SDSU. However, the CSRC also
conducts several undergraduate programs as part of its
mission to encourage student pursuit of computational
science and engineering skills.
Bridges: For twenty years, the SDSU Bridges Program
(supported by the National Institutes of Health) has
worked to inform students at several San Diego commu-
nity colleges of opportunities of how to transfer to San
Diego State University or to another four year university.
The Bridges Coordinator at SDSU, Maureen Gibbins, vis-
its each campus monthly to meet with students interested
in applying to the Bridges Summer Research Immersion
Program. Students at the Bridges partner community
colleges, plus students at San Diego Mesa College, San
Diego Miramar College, Mira Costa College, Cuyamaca
College and Palomar College are also invited to partici-
pate. Please contact Maureen Gibbins @ 619-200-4940
for more information.
Visit SDSU to hear about STEM research: Twenty-
four community college students in the STEM disciplines
expressing an interest in transferring to SDSU were in-
vited to attend SDSU’s Student Research Symposium
(SRS) held in early March. They experienced our stu-
dents’ poster and oral presentations discussing research
accomplished by undergraduates and graduates working
in faculty members’ laboratories.
CSRC Student Training
The SRS program highlighted a speech by SDSU’s President
Hirschman, a ceremony involving handouts of scholarship
awards, and, various selections of oral presentations.
We are scheduling the appearance of six enthusiastic senior
undergraduates from representative labs in SDSU’s physical
and life sciences and engineering disciplines, to visit each of
the partner campuses in the fall, to talk about their research
experiences and answer questions about what their research
immersion has meant to them. More information coming
soon!
ICSERT: The main objective of this National Science Foun-
dation program, the Interdisciplinary Computational Science
and Engineering Research Traineeship, is to recruit and sup-
port talented graduate students to broaden participation in
Interdisciplinary Computational Science and Engineering
Research (ICSERT). Currently, there are eight students in
the program, with accommodations for 32.
S-STEM: The program, sponsored by the National Science
Foundation and conducted for the past four years, is expiring
this semester. However, we are hopeful of the program re-
turning next year. S-STEM has supported 85 undergraduate
students, of whom 40 have graduated, 24 have entered grad-
uate programs and 21 are working in industry or research
laboratories in their area of specialization. Stay tuned!
RSRF Laboratory: The laboratory facility (LS 316, 316A
and 391A) moved from the Rees-Stealy Research Founda-
tion site on Grape Street to our SDSU campus in 2003.
This Laboratory serves as the wet-bench site for quantita-
tive bioscience training in the CSRC. The lab is used by the
Genomic explorations into Ciona intestinalis: The most
primordial chordate (animal with a backbone) where research
is allowing us to understand the evolution of other chordates
including humans; computational tools to track and monitor
the outbreak of antibiotic resistance in bacteria that threatens.
You can find out more about the research CSRC students are
performing at http://www.csrc.sdsu.edu/students_bio.html.
Quantitative Biology continued from Page 1...
Bridges program to introduce its students to basic bio-
medical laboratory bench science and computational
biomedical methods. Approximately a dozen students
continue their training with Dr. Paolini as they complete
their bachelor’s, master’s or doctoral degrees and re-
search projects.
Student Training continued from Page 2...
CSRC Student Training continued on Page 3...
Upcoming ACSESS Event, April 17, 2015
Join us for the 12th annual ACSESS for Industry Event being held April 17, 2015 on the SDSU
campus. The forum is a great place for our local industry to interact with CSRC faculty, staff, and
graduate students. Here are industry co-sponsors of this event:
Barranquilla, Colombia was the host of the Eighth Pan-American
Workshop in Computational and Applied Mathematics. As in previous
events, a cross section of numerical and applied mathematicians from the
Americas and Europe met in a very congenial atmosphere to exchange ideas,
new results and to establish lasting professional contacts.
As usual, we met not in the capital, Bogota, but in a smaller city, with fewer
distractions. One of the objectives of these workshops has always been to help
young students and faculty that may have had no opportunity to experience
an international meeting of high quality.
More than 83 participants from 11 countries
presented 85 papers. Seven invited presentations dealt with a variety of subjects of current interest.
There was a strong emphasis on Mimetic Discretizations for PDE’s, but we also heard talks on
many other topics, such as Financial Applications, Energy and Climate Change, Oil Exploration and
Seismology.
The local Committee was ably led by Jorge E. Ospino P.
and did an excellent logistic job that resulted in a smoothly
functioning conference. The meeting was co-sponsored by
the Computational Science Research Center, San Diego State
University, Universidad del Norte, Barranquilla, Colombia,
IMACS and the Barcelona Supercomputing Center.
Several of the foreign visitors had the opportunity to visit the neighboring famous
historical town of Cartagena de Indias, funded by Spanish explorers in 1533. Jose
Castillo, V. Pereyra and G. Scherer were the organizers of the workshop.
VIII Pan-American Workshop
in Applied and Computational Mathematics
July 21-25, 2014