{"109721":{"#nid":"109721","#data":{"type":"news","title":"$8.5 Million Research Initiative Will Study Best Approaches for Quantum Memories","body":[{"value":"\u003Cp\u003EThe U.S. Air Force Office of Scientific Research (AFOSR) has awarded $8.5 million to a consortium of seven U.S. universities that will work together to determine the best approach for generating quantum memories based on interaction between light and matter. \u0026nbsp;\u003C\/p\u003E\u003Cp\u003EThe team will consider three different approaches for creating entangled quantum memories that could facilitate the long-distance transmission of secure information. The five-year Multidisciplinary University Research Initiative (MURI) will be led by the Georgia Institute of Technology and include scientists from Columbia University, Harvard University, the Massachusetts Institute of Technology, the University of Michigan, Stanford University and the University of Wisconsin.\u003C\/p\u003E\u003Cp\u003E\u201cWe want to develop a set of novel and powerful approaches to quantum networking,\u201d said \u003Ca href=\u0022https:\/\/www.physics.gatech.edu\/user\/alex-kuzmich\u0022\u003EAlex Kuzmich\u003C\/a\u003E, a professor in Georgia Tech\u2019s \u003Ca href=\u0022http:\/\/www.physics.gatech.edu\/\u0022\u003ESchool of Physics\u003C\/a\u003E and the MURI\u2019s principal investigator.\u0026nbsp; \u201cThe three basic capabilities will be (1) storing quantum information for longer periods of time, on the order of seconds, (2) converting the information to light, and (3) transmitting the information over long distances. We aim to create large-scale systems that use entanglement for quantum communication and potentially also quantum computing.\u201d\u003C\/p\u003E\u003Cp\u003EThe MURI scientists will study three different physical platforms for designing the matter-light interaction used to generate the entangled photons.\u0026nbsp; These include neutral atom memories with electronically-excited Rydberg-level interactions, nitrogen-vacancy (NV) defect centers in diamonds, and charged quantum dots.\u003C\/p\u003E\u003Cp\u003E\u201cA large body of work has been initiated in this area over the past 15 years by our team members and their research groups,\u201d Kuzmich noted. \u201cThe physical approaches are different, but the goals are closely related, so there are significant opportunities for synergistic activities. Through this MURI, we will be able to interact more closely, communicate more quickly and provide new opportunities for our students and postdoctoral fellows.\u201d\u003C\/p\u003E\u003Cp\u003EOverall, the MURI has four major goals:\u003C\/p\u003E\u003Cul\u003E\u003Cli\u003ETo implement efficient light-matter interfaces using three different approaches to entanglement;\u003C\/li\u003E\u003Cli\u003ETo realize entanglement lifetimes of more than one second in both the nitrogen-vacancy centers and atomic quantum memories;\u003C\/li\u003E\u003Cli\u003ETo implement two-qubit quantum states within memory nodes;\u003C\/li\u003E\u003Cli\u003ETo integrate different components and physical implementations into small units capable of significant quantum processing tasks.\u003C\/li\u003E\u003C\/ul\u003E\u003Cp\u003EQuantum memories generated from the interaction of neutral atoms and light now have maximum lifetimes of approximately 200 milliseconds.\u0026nbsp; But improvements beyond memory lifetime will be needed before practical systems can be created.\u003C\/p\u003E\u003Cp\u003E\u201cWe aim to be able to combine systems, so that instead of just one memory entangled with one photon, perhaps we could have four of them,\u201d Kuzmich added.\u0026nbsp; \u201cThis may look like a straightforward thing to do, but this is not easy in the laboratory.\u0026nbsp; The improvements must be made at every level, so the difficulty is significant.\u201d\u003C\/p\u003E\u003Cp\u003EAmong the challenges ahead are maintaining separation between the different memory systems, and minimizing loss of light as signals propagate through the optical fiber systems that would be used to transmit entangled photons. \u0026nbsp;\u003C\/p\u003E\u003Cp\u003E\u201cLight is easily lost, and there\u2019s not much that can be done about that from a fundamental physics standpoint,\u201d said Kuzmich.\u0026nbsp; \u201cThe rates of these protocols go down rapidly as you try to scale up the systems.\u201d \u003C\/p\u003E\u003Cp\u003EKuzmich and his Georgia Tech research team have been developing quantum memory based on the interaction of light with neutral atoms such as rubidium.\u0026nbsp; They have made substantial progress over the past decade, but he says it\u2019s not clear which approach will ultimately be used to create large-scale quantum communication system.\u003C\/p\u003E\u003Cp\u003EThe most immediate applications for the quantum memory are in secure communications, in which the entanglement of photons with matter would provide a new form of encryption.\u003C\/p\u003E\u003Cp\u003E\u201cThe immediate focus is on communication, including memories and distributed systems, which is important for sharing and transmitting information,\u201d Kuzmich explained.\u0026nbsp; \u201cIt also has implications for quantum computation because similar techniques are often used.\u201d\u003C\/p\u003E\u003Cp\u003EIn addition to Kuzmich, collaborators in the MURI include:\u003C\/p\u003E\u003Cul\u003E\u003Cli\u003ELuming Duan, professor of physics in the School of Physics at the University of Michigan, Ann Arbor, Michigan.\u003C\/li\u003E\u003Cli\u003EDirk Englund, assistant professor of electrical engineering and applied physics in the School of Engineering and Applied Science at Columbia University, New York, New York.\u003C\/li\u003E\u003Cli\u003EMarko Lonkar, associate professor of electrical engineering in the School of Engineering and Applied Sciences at Harvard University, Cambridge, Massachusetts.\u003C\/li\u003E\u003Cli\u003EBrian Kennedy, professor of physics in the School of Physics at the Georgia Institute of Technology, Atlanta, Georgia.\u003C\/li\u003E\u003Cli\u003EMikhail Lukin, professor of physics in the Department of Physics at Harvard University, Cambridge, Massachusetts.\u003C\/li\u003E\u003Cli\u003EMark Saffman, professor of physics in the Department of Physics at the University of Wisconsin, Madison, Wisconsin.\u003C\/li\u003E\u003Cli\u003EJelena Vuckovic, associate professor of electrical engineering in the Department of Electrical Engineering at Stanford University, Stanford, California.\u003C\/li\u003E\u003Cli\u003EVladan Vuletic, the Lester Wolfe Professor of Physics in the School of Physics at Massachusetts Institute of Technology, Cambridge, Massachusetts.\u003C\/li\u003E\u003Cli\u003EThad Walker, professor of physics in the Department of Physics at the University of Wisconsin, Madison, Wisconsin.\u003C\/li\u003E\u003C\/ul\u003E\u003Cp\u003E\u201cIf we are successful with this over the next five years, long-distance quantum communications may become promising for real-world implementation,\u201d Kuzmich added.\u0026nbsp; \u201cIntegrating these advances with existing infrastructure \u2013 optical fiber that\u2019s in the ground \u2013 will continue to be an important engineering challenge.\u201d\u003C\/p\u003E\u003Cp\u003E\u003Cem\u003EThis material is based upon work conducted under contract FA9550-12-1-0025.\u0026nbsp; Any opinions, findings and conclusions or recommendations expressed are those of the researchers and do not necessarily reflect the views of the Air Force Office of Scientific Research.\u003C\/em\u003E\u003Cbr \/\u003E\u003Cbr \/\u003E\u003Cstrong\u003EResearch News \u0026amp; Publications Office\u003Cbr \/\u003EGeorgia Institute of Technology\u003Cbr \/\u003E75 Fifth Street, N.W., Suite 314\u003Cbr \/\u003EAtlanta, Georgia\u0026nbsp; 30308\u0026nbsp; USA\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EMedia Relations Contacts\u003C\/strong\u003E: John Toon (404-894-6986)(\u003Ca href=\u0022mailto:jtoon@gatech.edu\u0022\u003Ejtoon@gatech.edu\u003C\/a\u003E) or Abby Robinson (404-385-3364)(\u003Ca href=\u0022mailto:abby@innovate.gatech.edu\u0022\u003Eabby@innovate.gatech.edu\u003C\/a\u003E).\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EWriter\u003C\/strong\u003E: John Toon\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":[{"value":"Air Force Office of Scientific Research Supports Multiple Universities"}],"field_summary":[{"value":"\u003Cp\u003EThe U.S. Air Force Office of Scientific Research (AFOSR) has awarded $8.5 million to a consortium of seven U.S. universities that will work together to determine the best approach for generating quantum memories based on interaction between light and matter. \u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":[{"value":"An $8.5 million contract will support evaluation of multiple approaches for producing quantum memory."}],"uid":"27303","created_gmt":"2012-02-15 16:52:16","changed_gmt":"2016-10-08 03:11:44","author":"John Toon","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2012-02-15T00:00:00-05:00","iso_date":"2012-02-15T00:00:00-05:00","tz":"America\/New_York"},"extras":[],"hg_media":{"109701":{"id":"109701","type":"image","title":"Quantum Memory Research Equipment","body":null,"created":"1449178201","gmt_created":"2015-12-03 21:30:01","changed":"1475894728","gmt_changed":"2016-10-08 02:45:28","alt":"Quantum Memory Research Equipment","file":{"fid":"194056","name":"quantum-information134.jpg","image_path":"\/sites\/default\/files\/images\/quantum-information134_0.jpg","image_full_path":"http:\/\/www.tlwarc.hg.gatech.edu\/\/sites\/default\/files\/images\/quantum-information134_0.jpg","mime":"image\/jpeg","size":1449159,"path_740":"http:\/\/www.tlwarc.hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/quantum-information134_0.jpg?itok=qJEt9koE"}}},"media_ids":["109701"],"groups":[{"id":"1188","name":"Research Horizons"}],"categories":[{"id":"147","name":"Military Technology"},{"id":"150","name":"Physics and Physical Sciences"}],"keywords":[{"id":"24201","name":"Alex Kuzmich"},{"id":"3135","name":"entanglement"},{"id":"1744","name":"quantum"},{"id":"24191","name":"quantum memory"},{"id":"166937","name":"School of Physics"},{"id":"171187","name":"secure communication"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003EJohn Toon\u003C\/p\u003E\u003Cp\u003EResearch News \u0026amp; Publications Office\u003C\/p\u003E\u003Cp\u003E404-894-6986\u003C\/p\u003E\u003Cp\u003E\u003Ca href=\u0022mailto:jtoon@gatech.edu\u0022\u003Ejtoon@gatech.edu\u003C\/a\u003E\u003C\/p\u003E","format":"limited_html"}],"email":["jtoon@gatech.edu"],"slides":[],"orientation":[],"userdata":""}},"109641":{"#nid":"109641","#data":{"type":"news","title":"Bo Hong Wins Best Paper Award","body":[{"value":"\u003Cp\u003EBo Hong received the Best Paper Award at the \n2011 IEEE International Conference on Bioinformatics and Biomedicine, \nheld November 12-15 in Atlanta.\u003C\/p\u003E\u003Cp\u003EAn assistant professor in the School of Electrical and Computer Engineering (ECE) at Georgia Tech, Dr. Hong was honored for his paper, \u0022Improving Prediction Accuracy of Protein-DNA Docking with GPU Computing.\u0022 He shares this award with two coauthors\u2013Jiadong Wu, his Ph.D. student, and Jun-tao Guo, a colleague from the Department of Bioinformatics and Biomedicine at the University of North Carolina at Charlotte.\u003C\/p\u003E\u003Cp\u003EProtein-DNA docking represents one of the most challenging problems in structural bioinformatics. Knowledge of how proteins interact with DNA is critical for understanding many key biological processes and for structure-based drug design. This paper describes a high performance computing method that Dr. Hong and his team have developed to tackle the protein-DNA docking problem using a GPU cluster. This protein-DNA docking algorithm integrates Monte-Carlo simulation and a simulated annealing method and has achieved 10.4 TFLOPS of sustained performance using 128 GPU cards, which represents 4\u00d7 speed up over a traditional cluster with 1000 CPU cores. Such improved computation capability accelerates the conformational space sampling for the docking algorithm and increases the chance of finding near-native protein-DNA structures.\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003EECE Assistant Professor Bo Hong on receiving the Best Paper Award at the 2011 IEEE International Conference on Bioinformatics and Biomedicine, held November 12-15, 2011 in Atlanta.\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":[{"value":"ECE Assistant Professor Bo Hong received the Best Paper Award at the 2011 IEEE International Conference on Bioinformatics and Biomedicine, held November 12-15 in Atlanta."}],"uid":"27241","created_gmt":"2012-02-15 16:01:37","changed_gmt":"2016-10-08 03:11:44","author":"Jackie Nemeth","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2012-02-15T00:00:00-05:00","iso_date":"2012-02-15T00:00:00-05:00","tz":"America\/New_York"},"extras":[],"hg_media":{"57047":{"id":"57047","type":"image","title":"photo of Bo Hong","body":null,"created":"1449175474","gmt_created":"2015-12-03 20:44:34","changed":"1475894483","gmt_changed":"2016-10-08 02:41:23","alt":"photo of Bo Hong","file":{"fid":"190528","name":"thm68998.jpg","image_path":"\/sites\/default\/files\/images\/thm68998_0.jpg","image_full_path":"http:\/\/www.tlwarc.hg.gatech.edu\/\/sites\/default\/files\/images\/thm68998_0.jpg","mime":"image\/jpeg","size":5213,"path_740":"http:\/\/www.tlwarc.hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/thm68998_0.jpg?itok=vp5SnWpy"}}},"media_ids":["57047"],"groups":[{"id":"1255","name":"School of Electrical and Computer Engineering"}],"categories":[{"id":"134","name":"Student and Faculty"},{"id":"145","name":"Engineering"}],"keywords":[{"id":"1316","name":"Bo Hong"},{"id":"109","name":"Georgia Tech"},{"id":"166855","name":"School of Electrical and Computer Engineering"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003EJackie Nemeth\u003C\/p\u003E\u003Cp\u003ESchool of Electrical and Computer Engineering\u003C\/p\u003E\u003Cp\u003E404-894-2906\u003C\/p\u003E\u003Cp\u003E\u003Ca href=\u0022mailto:jackie.nemeth@ece.gatech.edu\u0022\u003Ejackie.nemeth@ece.gatech.edu\u003C\/a\u003E\u003C\/p\u003E","format":"limited_html"}],"email":["jackie.nemeth@ece.gatech.edu"],"slides":[],"orientation":[],"userdata":""}},"108191":{"#nid":"108191","#data":{"type":"news","title":"Baylor and Georgia Tech Teams Collaborating on Protein and Metabolite Markers for Ovarian Cancer","body":[{"value":"\u003Cp\u003EScientists from Baylor College of Medicine and the Georgia Institute of Technology have won $900,000 from the Ovarian Cancer Research Fund to investigate the early detection of ovarian cancer.\u003C\/p\u003E\u003Cp\u003EThe research, which comprises three separate projects, includes work with a new mouse model of ovarian cancer to identify early detection biomarkers; an effort to characterize proteins and protein variants secreted from ovarian tumors that could serve as serum biomarkers; and work to identify metabolic changes that could help diagnose the disease.\u003C\/p\u003E\u003Cp\u003E\u0022This grant is a program project development grant, and the idea is to bring together a number of individuals around a common theme,\u0022 Martin Matzuk, a BCM professor of pathology and immunology and one of the leaders of the project, told ProteoMonitor. \u0022We were previously funded by OCRF along with a number of investigators to focus on the role of microRNAs in ovarian cancer. That work has gone very well, so we put together another proposal in which we decided to focus on biomarkers, whether they\u0027re protein or small molecule.\u0022\u003C\/p\u003E\u003Cp\u003EMatzuk is collaborating on the work with his BCM colleague Laising Yen as well as John McDonald, a professor, the associate dean for biology program development in the school of Biology at Georgia Tech, and a chief research scientist at Atlanta\u0027s Ovarian Cancer Institute.\u003Cbr \/\u003EMcDonald, who will head up the search for metabolomic biomarkers, leads a research team that published a paper in August 2010 detailing a metabolomic ovarian cancer diagnostic that identified women with ovarian cancer with 100 percent accuracy in a 94-subject trial (PM 8\/20\/2010).\u003C\/p\u003E\u003Cp\u003EThat test used direct-analysis-in-real-time mass spectrometry to measure thousands of metabolites in subjects\u0027 blood samples, classifying them with a functional support vector machine-based machine-learning algorithm. McDonald\u0027s team is still validating their findings, McDonald told ProteoMonitor this week, but thus far \u0022everything is looking good,\u0022 and, he said, the researchers hope to finish validating the results sometime within the year.\u003C\/p\u003E\u003Cp\u003EUnder the OCRF grant, the Georgia Tech team plans to use LC-MS\/MS to identify specific metabolites detected by their DART-MS work in hopes of combining them with protein biomarkers identified by Matzuk\u0027s lab to build an early detection panel for ovarian cancer.\u003Cbr \/\u003EThe DART analysis \u0022gives us thousands of features, and for most of them we don\u0027t know what they are,\u0022 McDonald said. \u0022From a diagnostic point of view we don\u0027t really care as long as it\u0027s a reliable diagnostic. But at the same time we\u0027re now running LC-MS\/MS to try to whittle it down to identify \u2026 the specific metabolites involved.\u0022\u003C\/p\u003E\u003Cp\u003E\u0022The idea is that we\u0027ll put it together [with Matzuk\u0027s markers] to see what an optimal diagnostic might consist of,\u0022 he said.\u003C\/p\u003E\u003Cp\u003EMatzuk and the BCM researchers will be looking for protein biomarkers using a recently developed mouse model of high-grade serous ovarian cancer in which the cancer actually begins in the fallopian tube as opposed to the ovary itself. The model reflects an alternate view of ovarian cancer development \u0022that is gaining a lot of support,\u0022 Matzuk said.\u003C\/p\u003E\u003Cp\u003EBecause ovarian cancer is difficult to detect early, often by the time patient samples are collected it\u0027s \u0022too late to be trying to figure out what are the changes with regard to proteins or metabolic changes,\u0022 he said. \u0022The nice thing about having a mouse model is that these animals get cancers universally, and so you can open the animals up at a certain period and say, \u0027OK, at this time point what are the expression changes in these cancers? What are the earliest time points [they are visible]?\u0022\u003C\/p\u003E\u003Cp\u003E\u0022The goal of all three projects is to [identify] the various transcripts that are out there in these cancers,\u0022 Matzuk said. \u0022The idea is, once we catalog all of them, to go back in and then screen or develop antibodies to new variants of proteins or new secreted proteins and see whether or not those could be better markers.\u0022\u003C\/p\u003E\u003Cp\u003EThe ultimate goal of the work, he said, \u0022is to generate enough data so that we could actually go into the National Institutes of Health for a bigger project that we could start not only between our groups, but also with other groups and centers to look at various biomarkers.\u0022\u003C\/p\u003E\u003Cp\u003EPrice will be a major consideration for any early detection test, Matzuk said, noting that he thinks even existing triage tests like Vermillion\u0027s OVA1 don\u0027t offer enough to justify their cost. Given the low prevalence of ovarian cancer in the general population, he said, any broad screening test for the disease would need to cost under $50 for it to be covered widely by insurers.\u003C\/p\u003E\u003Cp\u003E\u0022I run a clinical chemistry laboratory in the county hospital, and for us to be doing this kind of screening of healthy women you need to have the cost low,\u0022 he said.\u003Cbr \/\u003EHowever, Matzuk suggested, declining instrumentation prices could help bring costs down in the future \u2013 particularly in the case of mass spec-based tests, where multiplexing could significantly lower the price of multi-analyte assays.\u003C\/p\u003E\u003Cp\u003E\u0022Maybe everyone will have [mass spec] analysis of their serum at some point,\u0022 he said. \u0022I think right now the instrumentation is too expensive and the testing is too expensive to go ahead and say this is for general [screening] tests, but if it turns out that these tests are extremely valuable, people are going to find a way to make them cheaper.\u0022\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003EScientists from Baylor College of Medicine and the Georgia Institute of Technology have won $900,000 from the Ovarian Cancer Research Fund to investigate the early detection of ovarian cancer.\u003Cbr \/\u003EThe research, which comprises three separate projects, includes work with a new mouse model of ovarian cancer to identify early detection biomarkers; an effort to characterize proteins and protein variants secreted from ovarian tumors that could serve as serum biomarkers; and work to identify metabolic changes that could help diagnose the disease.\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":[{"value":"Scientists from Baylor College of Medicine and the Georgia Institute of Technology have won $900,000 from the Ovarian Cancer Research Fund to investigate the early detection of ovarian cancer."}],"uid":"27245","created_gmt":"2012-02-09 13:06:08","changed_gmt":"2016-10-08 03:11:40","author":"Troy Hilley","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2012-02-09T00:00:00-05:00","iso_date":"2012-02-09T00:00:00-05:00","tz":"America\/New_York"},"extras":[],"hg_media":{"99241":{"id":"99241","type":"image","title":"John McDonald :: Photo By Gary Meek","body":null,"created":"1449178150","gmt_created":"2015-12-03 21:29:10","changed":"1475894712","gmt_changed":"2016-10-08 02:45:12"}},"media_ids":["99241"],"related_links":[{"url":"http:\/\/www.biology.gatech.edu\/people\/john-mcdonald","title":"John McDonald"},{"url":"http:\/\/www.biology.gatech.edu\/","title":"School of Biology"}],"groups":[{"id":"1275","name":"School of Biological Sciences"}],"categories":[{"id":"140","name":"Cancer Research"}],"keywords":[{"id":"23511","name":"Collaborating on Protein and Metabolite Markers for Ovarian Cancer"},{"id":"11814","name":"John McDonad"},{"id":"2372","name":"ovarian cancer"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[],"email":["david.terraso@cos.gatech.edu"],"slides":[],"orientation":[],"userdata":""}},"107661":{"#nid":"107661","#data":{"type":"news","title":"Georgia Tech Develops Software for the Rapid Analysis of Foodborne Pathogens","body":[{"value":"\u003Cp\u003E2011 brought two of the deadliest bacterial outbreaks the\nworld has seen during the last 25 years. The two epidemics accounted for more\nthan 4,200 cases of infectious disease and 80 deaths. Software developed at\nGeorgia Tech was used to help characterize the bacteria that caused each\noutbreak. This helps scientists to better understand the underlying\nmicrobiologic features of the disease-causing organisms and shows promise for supporting\nfaster and more efficient outbreak investigations in the future. \u003C\/p\u003E\n\n\u003Cp\u003EFrom 2008 to 2010, a team of bioinformatics graduate\nstudents, led by School of Biology Associate Professor King Jordan, worked in\nclose collaboration with the Centers for Disease Control and Prevention (CDC)\nto create an integrated suite of computational tools for the analysis of\nmicrobial genome sequences.\u0026nbsp; At that\ntime, CDC scientists were in need of a fast and accurate system that could\nautomate the analysis of sequenced genomes from disease-causing bacteria. They\nturned to the Jordan lab at Georgia Tech to help develop such a tool. The\nGeorgia Tech scientists created an open source software package, the \u003Ca href=\u0022http:\/\/jordan.biology.gatech.edu\/jordan\/images\/pubs\/kislyuk-bioinformatics-2010.pdf\u0022\u003EComputational\nGenomics Pipeline\u003C\/a\u003E (CG-pipeline), to help meet CDC\u2019s need. The software\nplatform is now used worldwide in public health research and response efforts. \n\n\u003C\/p\u003E\u003Cp\u003E\u201cDetermining the order of DNA bases for an entire genome has\nbecome relatively cheap and easy in recent years because of technological\nadvancements,\u201d said Jordan. \u201cThe hard part is figuring out what the genome\nsequence information means. Our software takes that next step. It analyzes the sequences,\nfinds the genes and provides clues as to which genes are involved in making\npeople sick. Manually, this process used to take weeks, months or a year. Now\nit takes us about 24 hours.\u201d \u003C\/p\u003E\u003Cp\u003EThe CG-pipeline software has been used to analyze last\nsummer\u2019s outbreak of \u0026nbsp;severe Escherichia coli\n(E. coli) infections that started in Germany and eventually led to illnesses in\n16 European countries, Canada and the United States. It was one of the largest E.\ncoli outbreaks in history, causing 50 deaths and 4,075 confirmed worldwide\ncases. The bacterium was traced to sprouts. Andrey Kislyuk, a graduate of the Bioinformatics\nPh.D. program who helped Jordan create the software, used the CG-pipeline while\nworking at Pacific Biosciences to understand why the strain of the bacteria\nthat caused the outbreak was so virulent. \u003C\/p\u003E\n\n\u003Cp\u003E\u201cThe software was used to determine that genetic material\nfrom two previously distinct strains of E. coli \u003Cem\u003E\u003Cem\u003E\u0026nbsp;\u003C\/em\u003E\u003C\/em\u003Ewas combined in a new, hyper-virulent strain,\u201d said Kislyuk. \u201cThe\nresulting hybrid strain seems to be more lethal than either of the parent\nstrains.\u201d \u003C\/p\u003E\u003Cp\u003EAnother Bioinformatics Ph.D. graduate who helped design and\nimplement the pipeline, Lee Katz, analyzed the bacteria that caused last year\u2019s\noutbreak of listeriosis in the United States while working at the CDC.\u0026nbsp; That outbreak was traced back to cantaloupes\nfrom a single farm in Colorado that were tainted with Listeria. Over the span\nof several months, there were 146 confirmed cases of listeriosis and 30 deaths,\nmaking it the deadliest outbreak of foodborne illness in the U.S. in 25 years.\nUsing the CG-pipeline, Katz was able to identify an important epidemiological genomic\nmarker, which will help track invasive strains of Listeria. \n\n\u003C\/p\u003E\u003Cp\u003EThe CG-pipeline software platform can be used to analyze any\nmicrobial genome sequence. It has already been applied to bacteria that cause a\nvariety of infectious diseases, including cholera, salmonella and bacterial\nmeningitis. \n\n\u003C\/p\u003E\u003Cp\u003EKatz continues to work closely with the Jordan lab to\nimprove the software. This collaboration is important in CDC\u2019s efforts to mine\ngenome sequence information in the service of public health using software\ndeveloped at Georgia Tech.\n\n\u003C\/p\u003E\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\n\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":[{"value":"Tool can help save lives by quickly tracing origins"}],"field_summary":[{"value":"\u003Cp\u003E2011 brought two of the deadliest bacterial\noutbreaks the world has seen during the last 25 years. The two epidemics accounted\nfor more than 4,200 cases of infectious disease and 80 deaths. Software\ndeveloped at Georgia Tech was used to help characterize the bacteria that\ncaused each outbreak.\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":[{"value":"Georgia Tech software was used to analyze two recent, deadly worldwide outbreaks."}],"uid":"27560","created_gmt":"2012-02-08 14:06:50","changed_gmt":"2016-10-08 03:11:40","author":"Jason Maderer","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2012-02-08T00:00:00-05:00","iso_date":"2012-02-08T00:00:00-05:00","tz":"America\/New_York"},"extras":[],"hg_media":{"83641":{"id":"83641","type":"image","title":"Tech Tower","body":null,"created":"1449178095","gmt_created":"2015-12-03 21:28:15","changed":"1475894700","gmt_changed":"2016-10-08 02:45:00"}},"media_ids":["83641"],"related_links":[{"url":"http:\/\/www.biology.gatech.edu\/graduate-programs\/bioinformatics\/","title":"Computational Biology and Bioinformatics"},{"url":"http:\/\/www.biology.gatech.edu\/","title":"School of Biology"},{"url":"http:\/\/www.cos.gatech.edu\/","title":"College of Sciences"}],"groups":[{"id":"1183","name":"Home"}],"categories":[{"id":"135","name":"Research"}],"keywords":[{"id":"2546","name":"bioinformatics"},{"id":"23381","name":"DNA sequencing"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003EJason Maderer\u003Cbr \/\u003EGeorgia Tech Media Relations\u003Cbr \/\u003E404-385-2966\u003Cbr \/\u003E\u003Ca href=\u0022mailto:maderer@gatech.edu\u0022\u003Emaderer@gatech.edu\u003C\/a\u003E\u003C\/p\u003E","format":"limited_html"}],"email":["maderer@gatech.edu"],"slides":[],"orientation":[],"userdata":""}},"105911":{"#nid":"105911","#data":{"type":"news","title":"Ming Yuan Awarded Coca-Cola Junior Professorship","body":[{"value":"\u003Cp\u003EMing\nYuan, associate professor in the H. Milton Stewart School of Industrial and\nSystems Engineering (ISyE), has been awarded the Coca-Cola Junior Professorship\nfor a three-year term.\u003C\/p\u003E\u003Cp\u003E\u201cDuring Dr. Yuan\u2019s time on the ISyE faculty, he has made valuable contributions\nin research, teaching, and service. Dr. Yuan\u2019s exceptional teaching ability is\nevident in the excellent teaching evaluations and student praise he\nreceives.\u0026nbsp; We are fortunate to have him as a colleague and now as the\nISyE\u2019s newest Coca-Cola Junior Professor,\u201d said Jane C. Ammons, H. Milton and\nCarolyn J. Stewart School Chair.\u003C\/p\u003E\u003Cp\u003EThe Coca-Cola Junior Professorship is supported by a gift from Coca-Cola, in\norder to support research and development in ISyE. Endowed professorships, such\nas this one, are awarded to outstanding faculty, ensuring them the resources\nthey need to remain at the forefront of their fields and to lead teaching and\nresearch efforts in their key areas.\u003C\/p\u003E\u003Cp\u003EIn addition to this recent honor, Yuan was the recipient of the National\nScience Foundation Career Award in 2009 for his exemplary work in sparse\nmodeling and estimation with high-dimensional data.\u0026nbsp; He was also named as\na Distinguished Cancer Scholar from the Georgia Cancer Coalition in 2007, and\nwas the recipient of the John van Ryzin Award in 2004.\u003C\/p\u003E\u003Cp\u003EYuan received his PhD in statistics from the University of Wisconsin at\nMadison. He also holds a master\u2019s in computer science from the University of\nWisconsin, and a bachelor\u2019s in electrical engineering and information science\nfrom the University of Science \u0026amp; Technology of China. Yuan\u0027s current\nresearch interests include statistical learning, bioinformatics, and methods of\nregularization.\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003EMing Yuan, associate professor in the H. Milton Stewart School of\n    Industrial and Systems Engineering (ISyE), has been awarded the\n    Coca-Cola Junior Professorship for a three-year term.\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":"","uid":"27511","created_gmt":"2012-02-03 14:49:00","changed_gmt":"2016-10-08 03:11:37","author":"Ashley Daniel","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2012-02-03T00:00:00-05:00","iso_date":"2012-02-03T00:00:00-05:00","tz":"America\/New_York"},"extras":[],"hg_media":{"105921":{"id":"105921","type":"image","title":"Ming Yuan, PhD","body":null,"created":"1449178174","gmt_created":"2015-12-03 21:29:34","changed":"1475894723","gmt_changed":"2016-10-08 02:45:23","alt":"Ming Yuan, PhD","file":{"fid":"193969","name":"ming_yuan.jpg","image_path":"\/sites\/default\/files\/images\/ming_yuan_0.jpg","image_full_path":"http:\/\/www.tlwarc.hg.gatech.edu\/\/sites\/default\/files\/images\/ming_yuan_0.jpg","mime":"image\/jpeg","size":1894283,"path_740":"http:\/\/www.tlwarc.hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/ming_yuan_0.jpg?itok=b4_YwnKk"}}},"media_ids":["105921"],"groups":[{"id":"1242","name":"School of Industrial and Systems Engineering (ISYE)"}],"categories":[{"id":"134","name":"Student and Faculty"}],"keywords":[{"id":"22671","name":"Coca-Cola Junior Professorship"},{"id":"1202","name":"H. Milton Stewart School of Industrial and Systems Engineering"},{"id":"6107","name":"Ming Yuan"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003E\u003Ca href=\u0022mailto:barbara.christopher@isye.gatech.edu\u0022\u003E\u003Cstrong\u003EBarbara Christopher\u003C\/strong\u003E\u003C\/a\u003E\u003Cbr \/\u003EIndustrial and Systems Engineering\u003Cbr \/\u003E\u003Cstrong\u003E404.385.3102\u003C\/strong\u003E\u003C\/p\u003E","format":"limited_html"}],"email":[],"slides":[],"orientation":[],"userdata":""}},"98891":{"#nid":"98891","#data":{"type":"news","title":"Four IAC Faculty Honored at GTRC 75th Anniversary","body":[{"value":"\u003Cp\u003EFour IAC faculty members were presented with awards during the 75th Anniversary\u0026nbsp;Gala Celebration of Georgia Tech Research Corporation. The\u0026nbsp;awards were presented for Excellence in Research, Industry Engagement, and Technology Transfer. \u003C\/p\u003E\u003Cp\u003EThe following awards were presented to IAC faculty:\u003C\/p\u003E\u003Cp\u003E\u003Cem\u003E\u003Cstrong\u003EBig Data Award\u003C\/strong\u003E\u003C\/em\u003E\u003Cbr \/\u003E\u003Cstrong\u003EAlan L. Porter\u003C\/strong\u003E, Professor Emeritus, Schools of Public Policy and Industrial \u0026amp; Systems Engineering\u003C\/p\u003E\u003Cp\u003EThe Big Data Award recognizes a Georgia Tech researcher or research group that has successfully established a strong research relationship with industry and commercialized technology for the management and application of large complex datasets to solve problems in society and industry and, in so doing, developed new tools and methods for capture, storage, analysis, searching and visualization of information.\u003C\/p\u003E\u003Cp\u003E\u003Cem\u003E\u003Cstrong\u003EPeople and Technology Award\u003C\/strong\u003E\u003C\/em\u003E\u003Cbr \/\u003E\u003Cstrong\u003EMichael L. Best\u003C\/strong\u003E, Associate Professor, The Sam Nunn School of International Affairs and School of Interactive Computing;\u0026nbsp;Editor-in- Chief,\u003Cem\u003E Information Technologies \u0026amp; International Development\u003C\/em\u003E\u003C\/p\u003E\u003Cp\u003EThe People and Technology Award honors the efforts of Georgia Tech researchers whose pursuit of research in the interaction between humans and technology demonstrates a transformative societal impact in improving the human condition.\u003C\/p\u003E\u003Cp\u003E\u003Cem\u003E\u003Cstrong\u003EPublic Service, Leadership, and Policy Award\u003C\/strong\u003E\u003C\/em\u003E\u003Cbr \/\u003E\u003Cstrong\u003EDan Breznitz\u003C\/strong\u003E, Associate Professor, The Sam Nunn School of International Affairs\u003C\/p\u003E\u003Cp\u003EThe Public Service, Leadership, and Policy Award recognized a Georgia Tech researcher or research group that has made a significant contribution to the study of innovation and policies that promote and sustain research for public benefit.\u003C\/p\u003E\u003Cp\u003E\u003Cem\u003E\u003Cstrong\u003EInnovation in Literature and Communication Award\u003C\/strong\u003E\u003C\/em\u003E\u003Cbr \/\u003E\u003Cstrong\u003EThomas N. Lux\u003C\/strong\u003E, Professor, School of Literature, Communication, and Culture; Founder and Director of Poetry@Tech\u003C\/p\u003E\u003Cp\u003EThe Innovation in Literature and Communication Award is given in recognition for innovation in communication and literature in science, engineering, and technology.\u003C\/p\u003E\u003Cp\u003EThe Gala Celebration\u0026nbsp;Honoring Innovators and Inventors \u0026amp; GTRC for 75 years of Service to\u0026nbsp;Georgia Tech Faculty\u0026nbsp;took place December 12, 2011 at the Georgia Tech Hotel and Conference Center Ballroom.\u003C\/p\u003E\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003EFour IAC faculty members were presented awards during the 75th Anniversary\u0026nbsp;Gala Celebration of Georgia Tech Research Corporation.\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":"","uid":"27418","created_gmt":"2012-02-01 13:31:38","changed_gmt":"2016-10-08 03:11:02","author":"Lauren Langley","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2012-02-01T00:00:00-05:00","iso_date":"2012-02-01T00:00:00-05:00","tz":"America\/New_York"},"extras":[],"hg_media":{"63131":{"id":"63131","type":"image","title":"Ivan Allen College of Liberal Arts","body":null,"created":"1449176649","gmt_created":"2015-12-03 21:04:09","changed":"1475894552","gmt_changed":"2016-10-08 02:42:32","alt":"Ivan Allen College of Liberal Arts","file":{"fid":"191746","name":"IAC_facade_200x300_rk.jpg","image_path":"\/sites\/default\/files\/images\/IAC_facade_200x300_rk_0.jpg","image_full_path":"http:\/\/www.tlwarc.hg.gatech.edu\/\/sites\/default\/files\/images\/IAC_facade_200x300_rk_0.jpg","mime":"image\/jpeg","size":48077,"path_740":"http:\/\/www.tlwarc.hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/IAC_facade_200x300_rk_0.jpg?itok=nA6TqvsH"}}},"media_ids":["63131"],"groups":[{"id":"1281","name":"Ivan Allen College of Liberal Arts"}],"categories":[{"id":"134","name":"Student and Faculty"}],"keywords":[{"id":"21131","name":"GTRC 75th anniversary"},{"id":"21121","name":"GTRC Research Awards"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003ERebecca Keane 404-894-1720\u003C\/p\u003E","format":"limited_html"}],"email":["rebecca.keane@iac.gatech.edu"],"slides":[],"orientation":[],"userdata":""}}}