Winter Enrichment Program (WEP)
King Abdullah University of Science and Technology at Thuwal, Kingdom of Saudi Arabia
BEACON 2012 January 2012 / Safar 1433 Volume 2, Issue No.5
the
turn to pages 4 – 5
www.kaust.edu.sa
Student contribution key to new dragon system
Student Speaker Ali Al-Dawood
Two KAUST PhD students are among the shared first authors on a recent paper published in Guest Speak Dr. Charles Vest
Bioinformatics, the leading journal in the field, which describes the development of a new system to further identify poly(A) motifs in human DNA: the Dragon PolyA Spotter (DPS). The DPS system is accessible as a free web-based tool. While recognizing poly(A) signals in RNA is relatively straightforward, the task of identifying poly(A) motifs in the primary genomic DNA sequence that correspond to poly(A) signals in RNA presents a far more challenging problem. Recognition of the poly(A) motifs is important for better gene annotation and understanding of the gene reg-
Commencement 2011
ulation mechanisms. The accuracy of predictions by the KAUSTdeveloped DPS system constitutes a distinct improvement over the existing solutions. Not only does DPS achieve higher sensitivity and specificity, it also provides a more consistent
“I was having lunch in the dining hall at Edinburgh University . . .
level of accuracy for 12 poly(A) motif variants.
when I heard two postgraduate students talking about a fast-spread-
Distinguished KAUST Trustee, Professor Charles Vest, President
Already colleagues at the BC Cancer Agency,
ing email they had received about a graduate-level research university
of the National Academy of Engineering, President Emeritus of
Genome Sciences Centre, Vancouver, Canada,
called KAUST,” recalled Ali Al-Dawood, in his speech at the 2011
Massachusetts Institute of Technology (MIT), and distinguished guest
have requested a version to use in one of their
Commencement Ceremony. “Intrigued, I googled KAUST later that day
speaker, shared with the students the advice of another former MIT
large-scale studies.
and found, to my total amazement, that a research university was open-
President, Professor Jerome Wiesner. He recounted, “One day long
hold the promise, in turn, to shape our collective future.”
Manal Kalkatawi, a Saudi computer science
ing in Saudi Arabia. This did not seem possible to me . . . I’d been
after his (Prof. Wiesner’s) service came to an end, an MIT alumnus
graduate who completed her undergraduate
searching for the best master’s programs in the world, but I had never
approached him, asking ‘Professor Wiesner, do you remember me?
studies at King AbdulAziz University in Jeddah
considered that I could find such a program at home.”
You shook my hand as I walked across the stage at my graduation
and her master’s by thesis at KAUST, was
For Al-Dawood, returning to Saudi Arabia to continue his gradu-
ceremony several years ago and you gave me some profound advice.'
one of the scholarship students in the KAUST
ate studies was something
“Now Professor Wiesner
founding class. Upon her arrival at KAUST,
he’d never seriously contem-
had shaken the hands of thou-
Kalkatawi switched the focus of her major from
plated. Now as a member of
computer systems to bioinformatics after she
the Class of 2011, he looks
took a class in artificial intelligence; in fact the
back on his experience at
topic of her master’s thesis was related to rec-
KAUST as one of inspired
ognition of poly(A) motifs. The paper evolved
discovery, intense learning,
from graduate seminar research that she and
and a dream fulfilled—a jour-
co-author Farania Rangkuti began during
ney that culminated in standing before the KAUST Board of Trustees,
“‘You looked at me,’ the alumnus replied, ‘you shook my hand, you
their second semester at KAUST. Kalkatawi
University leadership and faculty, and fellow graduates, as the Class of
waved your arm, and said, “Keep on moving, keep on moving!”’ And that's
and Rangkuti played key roles in the project
2011 Student Speaker.
my advice to you new KAUST alumni, keep on moving, keep on moving."
“This is it . . . the moment we have all waited for and worked so hard to enjoy.”
sands of graduates in his term as president and couldn't remember the alumnus, but he very diplomatically asked,
— Ali Al-Dawood, MS ‘11 Student Commencement Speaker
‘Well, what was this profound advice?'
by discovering and using new characteris-
A total of 244 graduates were conferred master's degrees at the
Graduates and KAUST family alike were heartened by Prof. Vest’s
tics and features to describe the problem and
University’s second Commencement Ceremony on Friday, December 16,
humorous anecdote, an apropos reminder at a time when many might
develop related artificial neural network pre-
2011. Amid applause, cheering, smiles, and the tears of proud parents,
be tempted to slacken their pace to “keep on moving,” whether it is in
dictive models. “I particularly enjoyed the
students and their families, University staff, faculty, and members of the
the studies, research, or work of the individual continuing on the jour-
challenge of building the system,” Kalkatawi
community gathered together for this memorable ceremony to recog-
ney to shape our collective future.
told The Beacon. “While this tool has proved
nize the accomplishments of the new graduates.
The feelings of attainment and accomplishment were captured when
more effective for human DNA, in my further
University President, Professor Choon Fong Shih, congratulated the Class
Al-Dawood closed reflecting, “This is it . . . the moment we have all
studies I will be investigating a similar prob-
of 2011 and remarked, “As you give your best in all that you do, I see your
waited for and worked so hard to enjoy . . . Believe me, it's not only the
lem with Arabidopsis Thaliana, a plant widely
KAUST education multiplying through the people you work with and come
certificate that matters. It’s the science and knowledge that we obtained;
used as a model in biology whose poly(A)
to influence positively. I see your education also multiplying through your
it’s the skills of problem solving and communications that will make
characteristics are very different than those
children, through your children’s children, and for future generations to
us competent professionals. Our degrees are keys to open doors to the
in humans.”
come. Indeed, your ideas and values, shaped by your KAUST education,
many opportunities and challenges waiting for us.”
STUDENT PAPER | Continued on p.2
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