School of Graduate Studies

School of Graduate Studies
School of Graduate Studies

Hazem Ahmed

Ph.D candidate, Computing

Hazem Ahmed at his Master's Convocation

Hazem Ahmed at his Master's Convocation

What do Birds Flocking and Proteins Folding have in Common? Hazem Ahmed brings Swarm Intelligence to Bioinformatics

by Sharday Mosurinjohn
​February 2014

 In 2006–07, Hazem R. Ahmed was working in Egypt as a research and a teaching assistant in Ain Shams University, and a systems analyst at the university’s hospital drawing upon his education in computer and information sciences. He was also building on this background, taking what’s called a “pre-Master’s.” Among the ten courses required by this program was one on bioinformatics taught by a professor who came from the U.S. to raise the international profile of this emerging subfield in which computer science intersects with chemistry or biology. Captured by the interdisciplinarity of bioinformatics, Ahmed made contact at a conference with another professor from Queen’s University and applied to his home institution—the only university to which he applied—for an MSc. So in September 2007 Ahmed arrived at Queen’s under the supervision of Dr. Janice Glasgow, with a lot of background reading to do.

“Biochemistry wasn’t my thing, and luckily I didn’t need much of it,” explains Ahmed. “My problem was related more to structural modeling of proteins.” The function of proteins in the body has to do with their shape—in other words, in this case, function follows structure. Ahmed and his colleagues—some of whom are a research group in Italy—are trying to move from a one-dimensional protein sequence (basically a list of the amino acids that make up a given protein) to a two–dimensional representation of its three–dimensional structure (the shape it takes when it folds up), and eventually to build a physical three–dimensional model of the way the protein actually occupies space.

This has remained one of the biggest challenges in bioinformatics for the past decades for a host of reasons including the fact that there are thousands of proteins in the human body and each protein has a unique 3D structure. Not only that, but their shapes lively change to interact with other proteins. Ahmed elaborates: “One understanding at least is that proteins fold into energetically-favorable three-dimensional structures that achieve minimal energy conformations of its individual residues for the sake of stability.”

His own approach is a novel one that tackles the problem in a truly interdisciplinary way, using the concept of “swarm intelligence” (SI). SI refers to the natural intelligence  displayed by the collective behavior of social swarms like birds flocking or fish schooling. “I didn’t realize there was this kind of natural intelligence,” recalls Ahmed, who started familiarizing himself with the idea by “watching Discovery Channel programming and documentaries” that depicted these processes of the natural world. The idea behind SI is that, guided by just a few rules, interacting individuals can manifest strikingly complex emergent properties. This might be a way to understand how amino acids bond to create the unique shape of a specific protein.

With his research gaining ground, Ahmed was offered a teaching fellowship instructing “CISC-471: Computational Biology.” His PhD depth proposal was the sole exemplar selected to be available online on the school’s official electronic library for Queen’s School of Computing students. His 2011 NSERC application was not only successful, but also ranked in the top 10 out of several applications nationwide, and he has been granted the prestigious Alexander Graham Bell Canada Graduate Scholarship until 2014. All of these accomplishments attested to his viability as an intern in Dr. Igor Jurisica’s cancer informatics lab at the Ontario Cancer Institute in Toronto.

Ahmed made contact with Jurisica in winter 2012 when he was invited to Queen's university to give a seminar. After the talk, Ahmed approached him to discuss possible applications of his research to cancer informatics. Again, there was a lot of background to catch up on in a short time, but he was awarded the Graduate Dean's Travel Grant for Doctoral Field Research to support his 3–month summer visit to Jurisica's lab, and, says Ahmed, he also “received support from Jurisica's lab members for all my technical, biological, and cancer–related questions.” They weren’t all convinced, at first, of his research’s relevance to their lab’s work, so Ahmed had to argue his point. He developed in the process a love of good scholarly debate and a great deal of gratitude for the way they answered his questions “so patiently.”

The work went well, supplying the fodder for a successful application to attend the 2013 Bioinformatics for Cancer Genomics (BiCG) workshop and the BiCG Registration Award (provided by the Canadian Bioinformatics Workshops) to attend this important 5-day workshop in Toronto from May 27–31.

While he finishes his dissertation, Ahmed continues to work on a casual basis for the Equity Office, for whom he started several projects while he was a work study student there early on in his graduate career at Queen’s. He remains active in professional and pedagogical development, as well, becoming involved with Queen's Emerging Leadership Initiative last year, earning the School of Graduate Studies’ Expanding Horizons Professional Development Certificate in fall 2012, and completing SGS-901: Teaching and Learning in Higher Education, in winter 2012. He has also volunteered with the Society of Graduate and Professional Students (SGPS) and the Centre for Teaching and Learning (CTL), and in roles associated with the Queen’s Senate. In his spare time, Ahmed enjoys reading and writing short fiction, and film—creative products, which, as his entrée into SI through the Discovery Channel demonstrates, might just as well be potential gateways to novel conceptualizations of tough problems.

For more and latest information on Hazem R. Ahmed, go to his LinkedIn profile at