@conference {15271,
	title = {Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques},
	booktitle = {IEEE International Conference on Bioinformatics and Biomedicine, 2008. BIBM {\textquoteright}08},
	year = {2008},
	month = {2008/11/03/5},
	pages = {223 - 230},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {The evolutionary histories of viral genomes have received significant recent attention due to their importance in understanding virulence and the corresponding ramifications to public health. We present a novel framework to detect reassortment events in influenza based on the comparison of two distributions of phylogenetic trees, rather than a pair of, possibly unreliable, consensus trees. We show how to detect all high-probability inconsistencies between two distributions of trees by enumerating maximal bicliques within a defined incompatibility graph. In the process, we give the first quadratic delay algorithm for enumerating maximal bicliques within general bipartite graphs. We demonstrate the utility of our approach by applying it to several sets of influenza genomes (both human- and avian-hosted) and successfully identify all known reassortment events and a few novel candidate reassortments. In addition, on simulated datasets, our approach correctly finds implanted reassortments and rarely detects reassortments where none were introduced.},
	keywords = {avian hosted influenza genome, Bioinformatics, Capacitive sensors, Delay, diseases, Event detection, general bipartite graphs, genomic reassortments, Genomics, graph theory, high probability inconsistencies, History, human hosted influenza genome, incompatibility graph, Influenza, influenza strain, maximal biclique, maximal biclique enumeration, microorganisms, phylogenetic trees, Phylogeny, Public healthcare, quadratic delay algorithm, reassortment, reassortment event detection, Tree graphs, viral genome evolutionary history, virulence},
	isbn = {978-0-7695-3452-7},
	doi = {10.1109/BIBM.2008.78},
	author = {Nagarajan,N. and Kingsford, Carl}
}
@article {16949,
	title = {A telescope for high-dimensional data},
	journal = {Computing in Science \& Engineering},
	volume = {8},
	year = {2006},
	month = {2006/04//March},
	pages = {48 - 53},
	abstract = {Muscular dystrophy is a degenerative disease that destroys muscles and ultimately kills its victims. Researchers worldwide are racing to find a cure by trying to uncover the genetic processes that cause it. Given that a key process is muscle development, researchers at a consortium of 10 institutions are studying 1,000 men and women, ages 18 to 40 years, to see how their muscles enlarge with exercise. The 150 variables collected for each participant will make this data analysis task challenging for users of traditional statistical software tools. However, a new approach to visual data analysis is helping these researchers speed up their work. At the University of Maryland{\textquoteright}s Human-Computer Interaction Library, we developed an interactive approach to let researchers explore high-dimensional data in an orderly manner, focusing on specific features one at a time. The rank-by-feature framework lets them adjust controls to specify what they{\textquoteright}re looking for, and then, with only a glance, they can spot strong relationships among variables, find tight data clusters, or identify unexpected gaps. Sometimes surprising outliers invite further study as to whether they represent errors or an unusual outcome. Similar data analysis problems come up in meteorology, finance, chemistry, and other sciences in which complex relationships among many variables govern outcomes. The rank-by-feature framework could be helpful to many researchers, engineers, and managers because they can then steer their analyses toward the action},
	keywords = {Chemistry, Data analysis, data mining, data visualisation, degenerative disease, Degenerative diseases, diseases, Finance, genetic process, Genetics, high-dimensional data, interactive data analysis, medical computing, Meteorology, muscle, muscle development, Muscles, muscular dystrophy, Rank-by-feature framework, software, software libraries, software tools, Telescopes, visual data, visual data analysis},
	isbn = {1521-9615},
	doi = {10.1109/MCSE.2006.21},
	author = {Shneiderman, Ben}
}
@conference {16462,
	title = {Exploiting multiple paths to express scientific queries},
	booktitle = {16th International Conference on Scientific and Statistical Database Management, 2004. Proceedings},
	year = {2004},
	month = {2004/06/21/23},
	pages = {357 - 360},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {The purpose of this demonstration is to present the main features of the BioNavigation system. Scientific data collection needed in various stages of scientific discovery is typically performed manually. For each scientific object of interest (e.g., a gene, a sequence), scientists query a succession of Web resources following links between retrieved entries. Each of the steps provides part of the intended characterization of the scientific object. This process is sometimes partially supported by hard-coded scripts or complex queries that will be evaluated by a mediation-based data integration system or against a data warehouse. These approaches fail in guiding the scientists during the collection process. In contrast, the BioNavigation approach presented in the paper provides the scientists with information on the available alternative resources, their provenance, and the costs of data collection. The BioNavigation system enhances a mediation-based integration system and provides scientists with support for the following: to ask queries at a high conceptual level; to visualize the multiple alternative resources that may be exploited to execute their data collection queries; to choose the final execution path to evaluate their queries.},
	keywords = {access protocols, biology computing, BioNavigation system, complex queries, Costs, Data analysis, data handling, Data visualization, data warehouse, Data warehouses, Databases, diseases, distributed databases, hard-coded scripts, information resources, Information retrieval, mediation-based data integration system, multiple paths, query evaluation, Query processing, scientific data collection, scientific discovery, scientific information, scientific information systems, scientific object of interest, scientific queries, sequences, Web resources},
	isbn = {0-7695-2146-0},
	doi = {10.1109/SSDM.2004.1311231},
	author = {Lacroix,Z. and Moths,T. and Parekh,K. and Raschid, Louiqa and Vidal,M. -E}
}
@article {17849,
	title = {The virtual microscope},
	journal = {IEEE Transactions on Information Technology in Biomedicine},
	volume = {7},
	year = {2003},
	month = {2003/12//},
	pages = {230 - 248},
	abstract = {We present the design and implementation of the virtual microscope, a software system employing a client/server architecture to provide a realistic emulation of a high power light microscope. The system provides a form of completely digital telepathology, allowing simultaneous access to archived digital slide images by multiple clients. The main problem the system targets is storing and processing the extremely large quantities of data required to represent a collection of slides. The virtual microscope client software runs on the end user{\textquoteright}s PC or workstation, while database software for storing, retrieving and processing the microscope image data runs on a parallel computer or on a set of workstations at one or more potentially remote sites. We have designed and implemented two versions of the data server software. One implementation is a customization of a database system framework that is optimized for a tightly coupled parallel machine with attached local disks. The second implementation is component-based, and has been designed to accommodate access to and processing of data in a distributed, heterogeneous environment. We also have developed caching client software, implemented in Java, to achieve good response time and portability across different computer platforms. The performance results presented show that the Virtual Microscope systems scales well, so that many clients can be adequately serviced by an appropriately configured data server.},
	keywords = {biomedical optical imaging, client software, client/server architecture, Computer architecture, Computer Graphics, computer platforms, Computer simulation, Concurrent computing, configured data server, data server software, database management systems, database software, Database systems, digital slide images, digital telepathology, diseases, emulation, Environment, Equipment Design, Equipment Failure Analysis, high power light microscope, Image databases, Image Enhancement, Image Interpretation, Computer-Assisted, Image retrieval, Information retrieval, Information Storage and Retrieval, java, local disks, microscope image data, Microscopy, multiple clients, optical microscopy, PACS, software, Software design, software system, Software systems, Systems Integration, Telepathology, User-Computer Interface, virtual microscope design, Virtual reality, Workstations},
	isbn = {1089-7771},
	doi = {10.1109/TITB.2004.823952},
	author = {Catalyurek,U. and Beynon,M. D and Chang,Chialin and Kurc, T. and Sussman, Alan and Saltz, J.}
}
