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Decoding the Variables of Life

By Lynn Mahoney

The recent explosion in genomic information has created an unprecedented need for computational tools, making the field of Bioinformatics one of the fundamental disciplines of the 21st century. The Computational Science and Bioinformatics Laboratory thrusts AUB scientists and graduate students at the forefront of this field, which has altered the methods by which diseases and medicines are discovered. 

Bioinformatics is a mixed marriage, aptly melding computer science and biology. This revolutionary field, which is changing the way scientists do science, has created advanced information and computational technologies to tackle problems in biology, particularly molecular biology, by storing, retrieving, and analyzing biological data, such as nucleic acid (DNA/RNA) and protein sequences, structures, functions, pathways, and genetic interactions.

Bioinformatics first appeared back in the 1950s and 1960s with early applications of computers to molecular biology. However, with the completion of the Human Genome Sequence (HGS) in 2000, the discipline has taken off.

Arguably one of the greatest scientific discoveries of the millennium, the HGS was completed in early April 2003—two years ahead of schedule and less than three years after finishing the working draft of the three billion DNA letters that comprise a human being’s genetic make-up.

“The June 2000 HGS working draft was 97 percent
complete but the recently published HGS approaches 100 percent,” explains Kinda Khalaf, assistant professor in the Faculties of Medicine and Engineering and Architecture, who is the coordinator of the Computational Science and Bioinformatics Laboratory at AUB. “A 3 percent difference may seem insignificant, but one needs to remember that it is a less than 4 percent DNA variation that distinguishes humans from primates,” she says smiling.
In genetics, a tiny difference really does make all the
difference. The human genome dictates every character of our being. While differences in the codes from one person to another can be extremely minute, they have the powerful ability to create a massive phenotypic variation. Now that scientists know exact genetic sequences from the HGS, they can compare this information with their research conducted on the genotypes of persons with genetic diseases. Their findings are expected to yield countless breakthroughs in combating different types of illnesses, including but not limited to congenital diseases. To a non-science person, like myself, this is pretty amazing stuff that touches on every aspect of one’s own life as well as of friends and family. Bioinformatics, in short, is changing the way we research and treat
illnesses.

I keep all this in mind while walking down the corridor of the third floor in the Diana Tamari Sabbagh Building, which is located on the AUB campus just off the Medical Gate. There is some degree of surprise entering the Computational Science and Bioinformatics Laboratory. The room is filled with the most high tech computers I have ever seen; but wait, I wondered aloud—where is the “wet lab” filled with beakers and solutions that one would usually expect. “This is the latest method of scientific research,” explains Khalaf. “And AUB has it.” 

The lab is filled with 22 computers and Silicon Graphics machines with the latest graphic software, such as Discovery Studio Gene, Insight II, Catalyst, and the Wisconsin package, which allows chemists and biologists to apply new genetic sequences to the HGS and all the associated genetic research. The software also aids molecular biological and biochemistry research by analyzing sequences and observing the evolution of various genes in different species through computations as well as by displaying stunning visuals of proteins and genes. “With the recent completion of the HGS project, the applications are literally endless,” says Khalaf. “Now a graduate student who is trying to isolate and amplify some DNA for further testing can do so more rapidly and easily by knowing the exact sequences upstream and downstream the gene of interest, as well as the exact mapping of the gene on the respective chromosome.”

Lab administrator, biochemistry graduate student Hassan Al-Ali, enthusiastically adds “For so long, every drug we casually obtained from over the counter was the fruit of thousands of experiments, the relentlessness of one or more scientists, the lives of countless lab animals, and certainly a large dose of luck. Computational sciences now offer an approach with lesser trials—and a much lesser probability for error. It is changing the way we are studying science at AUB.”


The Computational Science and Bioinformatics Laboratory came about through the persistence and efforts of Khalaf and AUB Vice President of Medical Affairs and Dean of the Faculty of Medicine Nadim Cortas. “Bioinformatics is important for AUB because it is the tool with which we can unravel the nature and function of gene products in a timely manner. Really, it is a brain intensive rather than an equipment intensive discipline—despite all the computer hardware Bioinformatics entails,” Cortas explains. “The Computational Sciences and Bioinformatics Laboratory is an extremely important tool for researchers at AUB; it gives them the same technology that is being utilized around the world at top institutions.” An American Schools and Hospital (ASHA) grant provided the funding for the equipment and technology of the lab—totaling some $240,000. Khalaf adds, “The lab is visionary. It’s the first in Lebanon and the first comprehensive lab in the region.” As such, Khalaf has organized training workshops on the software for fellow researchers at AUB, with more planned throughout Lebanon and the region in the future. She hopes that ultimately researchers at AUB will make full use of the state-of-the-art supercomputing facilities for their current research and make bioinformatics a national effort in Lebanon.

Since the lab’s opening in November 2002, it has already significantly boosted research, particularly in the field of proteomics, a direct and more sophisticated descendant of genomics that emerged after the completion of the Human Genome Project. Hassan explains that through quantum computing and complex algorithms, scientists can go from the DNA sequence to the structure and even the function of proteins. “Comparing mutations on DNA to the alterations they induce in the structure and function of the proteins that DNA expresses allows us to understand how these codes control the way proteins interact.”

AUB biology and chemistry students now have an added edge, Khalaf stresses. “We have the same protein data bank that is being used in the best institutions around the world—AUB is now better equipped to join efforts with the international science community.”

Graduate student Hassan Al-Ali is one of those budding AUB-trained scientists benefiting from the lab. A graduate of the Lebanese University, he will finish his master’s in 2003 at AUB and is currently preparing for his thesis-defense. An articulate, enthusiastic young man, Hassan has ambitions of pursuing his PhD in organic chemistry and rational drug design in the United States or England. Hassan, who originally comes from northern Lebanon, is also an artist. “Really the Computational Science and Bioinformatics Laboratory and its technology are not far from art. This software almost gives you a painting of a DNA or protein sequence.” Khalaf adds, “Hassan is highly motivated. Like so many of the other AUB students in engineering and medicine, they have the drive and potential. Now, with the Computational Science and Bioinformatics Laboratory they have the resources and technology to succeed in the field.”

Khalaf, a recent addition to the Faculties of Medicine and Engineering and Architecture, who arrived at AUB during the 2001-02 academic year as a visiting professor, was instrumental in establishing the new laboratory at AUB. Her joint appointment is the first of its kind between the two faculties. Born in London, Khalaf is of Jordanian descent and moved to the United States at the age of 16. There she went on to study at Ohio State University, where she received her PhD in biomedical engineering, then took an appointment as assistant professor at the University of Miami in Coral Gables. Her interest in combining the biological sciences and technology can be traced back to her father. “My father was a physician, and even though I am an engineer I have always been fascinated by medicine.” She finds her teaching experiences and the interdisciplinary exchanges with her AUB colleagues rewarding and dynamic.

As my meeting with Hassan and Khalaf ended, it became apparent to me that the new Computational Science and Bioinformatics Laboratory will unharness the potential of researchers and graduate students alike—and that AUB will participate in the data and international research that has been unleashed through the HGS. This new science, Bioinformatics, has the potential to identify persons with propensities towards cancers, help children afflicted with genetic diseases like cerebral palsy or cystic fibrosis, and aid scientists in finding new antibiotics to battle bacterial infections. And AUB has the technology, all quietly tucked away on the third floor of the Diana Tamari Sabbagh Building.