News & Events
THE DEPARTMENT OF COMPUTER AND INFORMATION SCIENCE AND ENGINEERING WELCOMES HUSBAND-WIFE TEAM TAMER KAHVECI AND TUBA YAVUZ-KAHVECI
January 18, 2005
GAINESVILLE, Fla. --- They are both new parents, both recently received their doctoral degrees in computer science, and they just kicked off their academic careers with the UF Computer and Information Science and Engineering Department.
Tamer Kahveci, an Assistant Professor with research interests in bioinformatics, and Tuba Yavuz-Kahveci, a Lecturer whose research interests lie in software engineering, reliability and model checking, are both looking forward to the opportunities that being a part of the University of Florida provide.
First and foremost, they are hoping to have the chance to collaborate and work together on problems at the upcoming Florida Bioinformatics Workshop in February 2005.
The bioinformatics field has experienced exponential growth in the last 10 to 15 years since the human genome project began. Tamer's research focuses on indexing, storing, accessing and using bioinformatics data. His interest in bioinformatics is such because it provides the "ability to retrieve and look at raw data as functional information to understand the implications in life," he said.
For
example, DNA and protein sequences need to be analyzed to determine if a relationship
exists between certain proteins and their order. Through advanced computer
methods, the sequencing and related data can be examined to narrow down the
search and reduce the number of experiments required in testing these sequences,
which thereby also reduces the cost and time involved.
Tuba's research focuses on developing and designing tools to ensure software reliability. Especially when software is relied upon to meet safety critical ends, such as in air or space flight, a software failure can be catastrophic, resulting in the loss of human life. In her dissertation, Tuba developed symbolic model checking tools to automatically verify concurrent software systems in a case study of an airport ground traffic control system.
The field of bioinformatics offers a large network of research problems in which Tamer and Tuba hope to collaborate. Bioinformatics brings together numerous fields of research: medicine, genetics, mathematics, biology, veterinary medicine, computer science and more. What researchers in bioinformatics have in common is the processing of large amounts of biologically-derived information, whether DNA sequences, heart X-rays or protein modeling.
Developing the query language for the data utilized in solving bioinformatics research problems is where Tuba's expertise comes in. First of all, a technique to translate these questions into computer language is necessary, and then the next step is verifying that the results are accurate and reliable. With Tamer's capabilities in managing data, through indexing and searching, he can work to restrict this huge database of information into a smaller network of data in order to find correlations in a much more efficient, timely manner.
There are more than 3 billion chemical base pairs that make up human DNA. In order to determine what the functions are within the sequences of these pairs, imagine the multiple alignment possibilities, the thousands, upon thousands, of sequences of numbers. "The number of cases you would need to explore is larger than the number of particles in the universe," Tamer said.
Through the process of indexing, the data is summarized; the DNA sequence is changed from a sequence of letters to integers, whereby approximately 1,000 letters is changed into a couple integers. When the data is summarized, it is simplified, and common sets are categorized together. So as a researcher begins to hunt for information, he or she only explores those sets that are similar to the ones he or she is researching.
The bioinformatics field provides cross-disciple collaborative opportunities as well. While biologists and medical doctors have the expertise necessary to comprehend the human DNA sequence, the work of computer scientists like Tamer Kahveci and Tuba Yavuz-Kahveci is integral to the success of research in bioinformatics. The manipulation of data in this arena is the key to solving research problems.
Both Tamer and Tuba, natives of Turkey, are accomplished researchers, just beginning in their careers. They both graduated in 2004 with their Ph.D.s in computer science from the University of California in Santa Barbara. Tamer credits 13 conference papers, four journal articles and a book chapter to the beginning of his academic career, while Tuba notes eight refereed conference papers, five grant awards, four conference presentations and a journal article. Their first child, less than a year old, is a boy named Omer, after a friend of the prophet Muhammed in Islamic history.
The department welcomes Tamer and Tuba and looks forward to their collaborative
research opportunities!
Writer: Mandelyn Hutcherson, 352-392-4700 ext. 5011, HutchersonM@mail.vetmed.ufl.edu
Sources: Tamer Kahveci, 352-392-6849, tamer@cise.ufl.edu
Tuba Yavuz-Kahveci, 352-392-6888, tyavuz@cise.ufl.edu
