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Breakthrough in Understanding Human Evolution Due to Computational Genomics

The fragile regions in mammals’ genomes that are thought to play a key role in evolution go through a "birth and death" process, according to new work by University of South Carolina and University of California-San Diego researchers. The study, published in the journal Genome Biology, could help researchers identify the current fragile regions in the human genome – information that may reveal how the human genome will evolve in the future. “We made a step towards understanding the mechanism of genome rearrangements that ‘shuffle’ genomic architectures and represent one of the major driving forces behind evolutionary diversity. In contrast to previous studies, our results allow one not only to analyze the evolution in retrospect but also to predict the future changes in genomic architectures,” said Dr. Max Alekseyev, one of the study’s authors and a computer science and engineering professor in the College of Engineering and Computing at USC. Alekseyev worked with Dr. Pavel Pevzner from UC-San Diego. The two researchers study genomes and genome evolution from a computational perspective. An important question in evolutionary studies is whether there are "fragile" regions where genome rearrangements are happening over and over again. The fragile regions are prone to “genomic earthquakes” that can trigger genome rearrangements, disrupt genes, alter gene regulation and otherwise play an important role in the evolution and emergence of new species. For example, humans have 23 chromosomes while some apes have 24 chromosomes, a consequence of a genome rearrangement that fused two chromosomes in our ape ancestor into human chromosome 2. Although nearly all recent studies support the existence of these fragile regions, there have been some doubts about their existence, raised from a comparative analysis of multiple mammalian genomes. “Our findings imply that fragile regions migrate to different locations in different mammals, and it explains why there are only a few fragile regions shared between different lineages,” said Alekseyev. The research demonstrates that the fragile regions undergo a birth and death process over evolutionary timescales and provides a clue to where the fragile regions in the human genome are located. The researchers conclude that these regions in the human genome are likely to be affected by the coming genome rearrangements. “We hope that further analysis of the identified fragile regions in the human genome would provide insights into current trends in the human evolution”, said Alekseyev. The researchers are now working on confirmation of a conjecture that genomic fragility is promoted by matching segmental duplications. The researchers also hope that their approach may be useful for understanding genome rearrangements at the level of individuals, rather than entire species. In the future, they plan to apply similar analysis for the genome rearrangements that occur within the cells of individual cancer patients in order to develop new cancer diagnostics and drugs.

Organizational Meeting of the Computer Science Teachers Association

A meeting will be held on 7 December 2010 at USC with statewide participation via video or conference call to organize a South Carolina chapter of the Computer Science Teachers Association. All K-12 teachers of computer science and information technology especially, and other interested parties from the computing community, are encouraged to attend and/or participate. More details can be found at bit.ly/sccsta.

BottleMI: Another Startup from our Students

Through a recent University of South Carolina project, students from the business and computer science and engineering schools have teamed up to develop a unique social networking website known as “BottleMi.com”. This website, designed by your very own fellow classmates, could possibly be the next Facebook or Twitter. Currently it is exclusive to USC students and we want you to be a part of its development by actively participating on BottleMi.com. Your feedback is crucial and will dictate what the site ultimately becomes. As the dailygamecock mentions, the website was built by Jimmy Parker, Beattie Daniels and Josh Mabry. Go check it out We wish them luck!

Dr. Cannon Named Fellow of ABET

Dr. Robert Cannon, distinguished professor emeritus, has been named a Fellow of the Accreditation Board for Engineering and Technology (ABET), an award bestowed upon him "for his leadership in the orderly transition of computing accreditation into ABET operations; and for his commitment to diversity through the development of ABET's Policy Statement on Diversity." More information can be found on the ABET press release. Bob’s work with accreditation began when the Computing Sciences Accreditation Board – now CSAB – was founded in 1985. He served on CSAB’s Board of Directors, and as the organization’s President in 1999, he led the team that worked with ABET to merge the two organizations’ services. His leadership enabled the Computing Science Accreditation Commission to integrate into the new Computing Accreditation Commission with minimal disruption to accreditation processes. Bob went on to represent CSAB on the ABET Board of Directors from 2000 to 2005, the first five years after CSAB became a participating body of ABET. In addition, he chaired the committee that created ABET’s first policy statement on diversity, in 2002.

Bob is a Senior Member of IEEE and of the Association for Computing Machinery, and he is a CSAB Fellow.

Three CSE Graduate Students win Travel Grants

Three of our graduate students have won university grants to travel to conferences to present their research! The result will be great experience for them, increased visibility for USC by their presence at these conferences, increased visibility for their advisors, and recognition locally for their research. Congratulations to:
  • Mr. Achraf El Allali and his advisor Dr. John Rose for "International Conference on Bioinformatics and Computational Biology"
  • Ms. Laura Boccanfuso and her advisor Dr. Jason O'Kane for "International Conference on Social Robotics"
  • Mr. Yiwei Zhang and his advisor Dr. Jijun Tang for "IEEE International Conference on Bioinformatics & Biomedicine"

CSE Students Help South Carolina Fix its Computers

The ACM Student Chapter at USC held its first Fix-IT Day on Sunday the 25th where student volunteers helped to fix computers brought in by anyone who wanted to attend. The event received wide publicity, with articles written about it in The State newspaper and a news segment on WISTV. “The event was a great success. We helped an estimated 200 or more number of people,” recalled Dr. Valafar, a Computer Science professor who coordinated the event. “We are still receiving phone calls from the community inquiring whether we will have any more events like this. We received participant from as far as Charlotte and several of smaller rural communities in SC that do not have extensive computer shops,” he added. The event was held from noon to 6pm. Attendees were given tickets when they arrived and told how long they would be expected to wait. The computer problems were then separated intro either hardware or software problems. Two large conference rooms in the Swearingen building were used: one to handle hardware problems and the other for software problems. Each room had about a dozen USC computer students diligently working to fix the problems with the computers. Attendees were very grateful for the free service, some saying that they could not afford to get their computer fixed, other stating that they had paid to get it fixed but the fix did not work. Some attendees even left messages of encouragement on the poster board. It is clear that if the ACM student group held the event again that even more people would show up. The ACM student chapter has shown their sincere commitment to helping the community, and this commitment was appreciated by the community. The students are now in the process of compiling their experience and data, revising their protocol, and planning for the next event. If you are interested in more information, or you are a Computer student interested in joining the ACM student chapter the just send them an email. You can also take a look at the photos taken at the event.

Dr. Valafar Receives NIH Grant

Dr. Valafar has received a grant from the National Center for Research Resources (NCRR)/NIH for his project "South Carolina IDeA Network of Biomedical Research Excellence (INBRE) - Bioinformatics Core." This is part of the umbrella INBRE grant of $17M.

USC CSE To Assist SPAWAR

This article in the Charleston Post and Courier explains how we are among a pool of seven schools selected to compete for $30 million over the next six years from the U.S. Space and Naval Warfare Systems Center.

Car Tire Pressure Monitor Systems Exposed

Update 11/16/2011: This work was also mentioned in a CACM article Wireless tire pressure monitoring systems designed to alert drivers to problems with low tire pressure can be intercepted or forged, causing possible security or privacy threats, according to research at the University of South Carolina and Rutgers University. Dr. Wenyuan Xu, an assistant professor in the department of computer science and engineering at USC and the lead investigator on the project, said tire pressure monitoring communications systems in many new cars are not properly secured, allowing anyone to eavesdrop on the wireless communication and send false messages to drivers.

Most new cars manufactured or sold in the U.S. after 2007 are equipped with the tire pressure monitoring system. As technology evolves and more wireless sensors and devices are introduced into cars, Xu said carmakers need to pay more attention to securing wireless communication before more serious vulnerabilities emerge. For example, although not a reality yet, if the tire pressure reading is used to assist the stability control, then sending a forged message with the wrong tire pressure could be dangerous. USC researchers and their colleagues at Rutgers University studied tire-pressure monitoring systems (TPMS), the devices that monitor air pressure inside tires and trigger a dashboard warning if a tire’s pressure drops.

Researchers were able to intercept the wireless signals 120 feet away from the car using a simple receiver. “Hopefully, as a result of our project, the security and privacy concerns from consumers will push the car industry to design in-car wireless networks with security and privacy in mind,” Xu said. Virtually all new cars use direct TPMS, which relies on wireless technologies. Since wireless communication is prone to eavesdropping and malicious hacking, the researchers wanted to analyze the security and privacy aspects of the first widely used wireless systems, Xu said. “Since the wireless communication contains unique identifiers of each car, it is possible to track vehicles by listening to the tire pressure monitoring system’s wireless communication,” Xu said. “Further, we have shown that we can transmit false messages to make the car trigger the ‘low pressure warning light’ on the dashboard while all tire pressures are normal. We managed to ‘damage’ the tire pressure monitoring system by sending false messages.”

Xu is a co-author of the paper, “Security and Privacy Vulnerabilities of In-Car Wireless Networks: A Tire Pressure Monitoring System Case Study,” and presented it at the USENIX Security Symposium in Washington, D.C., earlier this month. The automotive security and privacy research project is a joint project between USC and the Wireless Information Network Laboratory (WINLAB) at Rutgers. USC students Ishtiaq Rouf, Hossen Mustafa and Travis Taylor, along with Rob Miller, Sangho Oh, Marco Gruteser, Wade Trappe and Ivan Seskar from Rutgers participated in the project. Most of the experiments were conducted at USC. Computerworld has an article on the research into the vulnerabilities of cars' tire pressure monitor systems performed by Dr. Xu and her collaborators. MIT's Technology Review has another similar article.

Smart App Shows Inside of Horseshoe Buildings

The new app was developed by students in computer science courses taught by Duncan Buell, standing at left, and assistant professor of new media studies Heidi Cooley, at right.

The new entry, "Virtual USC," is taking shape at the College of Engineering and Computing to provide an insider's virtual tour of the Carolina Horseshoe. "This is going to be very cool," said Duncan Buell, the professor of computer science who guided a group of 10 undergraduate students involved in the software application's development during the spring semester. Buell is aiming for a prototype smart phone tour of the Horseshoe in which users can click on Gamecock icons embedded in a campus map to reveal historic and contemporary interior pictures of several buildings.

Among highlights will be the South Caroliniana Library and the Gressette Room in Harper College. University Archives provided historical photos and University Technology Services provided current pictures. "Once we get the first couple of stops on the tour done adding more of them won't be conceptually difficult," said Buell, adding that tours of each building will take users through an animation that walks them to a starting point where they can then access other available images. "With a program like this, once you get the basic structure of the app done, adding locations means a little more work and having to worry about bandwidth and things like that, but it's not that much more of an effort."

Buell embarked on the project with the intent of producing an app for an Android smart phone that would be relevant to a National Endowment for the Humanities-funded computer gaming institute at the University this summer. The institute is a project of the University's Digital Humanities Initiative. "The first couple of weeks the students just brainstormed on various ideas along the lines of, ‘What could you do with a mobile phone like this, and how could you use a location awareness to know where you were and pull up something of interest?' "Gradually, we converged on this project as something that could be done in 15 weeks and end up with close to a 100 percent professional product. It's not really a game, but once you get an app like this built out you can change the content and the programming and easily put it into something else, like a scavenger hunt. "The hard part of the programming is getting all the pieces to fit together with the maps, overlays, and the images," said Buell. "It's not hard dealing with the content once you have it. So this project is partly an adaptation to what we could undertake that was interesting and relevant."

The 10 students were drawn from three different computer science courses. They had worked as programmers and helped come up with the design and structure of the overall software. Once the Android app is working, the next project will be to port it to the iPhone, "a huge difference because the programming is very different," Buell said. The group has also drawn on the expertise of faculty members in the University's Digital Humanities Initiative who offered guidance on such things as the app's visual elements and other factors that would add to its user friendliness and appeal. Buell anticipates that once the app is perfected for both Android and iPhones, it could be adapted to a wide variety of other campus uses. These could include wider virtual tours of the campus, plant or museum tours envisioned by Allison Marsh, an assistant professor of history who supervises the museum track in the history department's public history program, or applications like teaching outdoor courses that link GPS coordinates with radio frequency ID chips positioned at various locations on campus. "You could do a lot of fun applications like this and even expand it to Columbia and the Vista," Buell said. By Office of Publications