Now showing items 41-60 of 254

    • Service-based analysis of biological pathways 

      Zheng, George; Bouguettaya, Athman (2009-10-01)
      Background Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at ...
    • An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications 

      Pan, Deng; Zhang, Liqing (PLOS, 2009-10-23)
      The notion that gene duplications generating new genes and functions is commonly accepted in evolutionary biology. However, this assumption is more speculative from theory rather than well proven in genome-wide studies. ...
    • A Pattern Analysis of Gene Conversion Literature 

      Lawson, Mark J.; Jiao, Jian; Fan, Weiguo; Zhang, Liqing (Hindawi Publishing Corporation, 2009-11-15)
      Gene conversion is an important biological process that involves the transfer of genetic (sequence) information from one gene to another. This can have a variety of effects on an organism, both short-term and long-term and ...
    • First-order quantum phase transition in adiabatic quantum computation 

      Amin, M. H. S.; Choi, V. (American Physical Society, 2009-12-01)
      We investigate the connection between local minima in the problem Hamiltonian and first-order quantum phase transitions during adiabatic quantum computation. We demonstrate how some properties of the local minima can lead ...
    • Keystroke-Dynamics Authentication Against Synthetic Forgeries 

      Stefan, Deian; Yao, Danfeng (Daphne) (IEEE, 2010)
      We describe the use of keystroke-dynamics patterns for authentication and detecting infected hosts, and evaluate its robustness against forgery attacks. Specifically, we present a remote authentication framework called ...
    • Designing for Schadenfreude (or, how to express well-being and see if youʼre boring people) 

      André, Paul; Schraefel, M.C.; Dix, Alan; White, Ryen W.; Bernstein, Michael; Luther, Kurt (ACM, 2010)
      This position paper presents two studies of content not normally expressed in status updates—well-being and status feedback—and considers how they may be processed, valued and used for potential quality-of-life benefits ...
    • Global estimates of CO sources with high resolution by adjoint inversion of multiple satellite datasets (MOPITT, AIRS, SCIAMACHY, TES) 

      Kopacz, M.; Jacob, D. J.; Fisher, J. A.; Logan, J. A.; Zhang, L.; Megretskaia, I. A.; Yantosca, R. M.; Singh, K.; Henze, D. K.; Burrows, J. P.; Buchwitz, M.; Khlystova, I.; McMillan, W. W.; Gille, J. C.; Edwards, D. P.; Eldering, A.; Thouret, V.; Nedelec, P. (Copernicus Publications, 2010)
      We combine CO column measurements from the MOPITT, AIRS, SCIAMACHY, and TES satellite instruments in a full-year (May 2004-April 2005) global inversion of CO sources at 4 degrees x 5 degrees spatial resolution and monthly ...
    • Elucidating the Evolutionary Relationships among Bos taurus Digestive Organs Using Unigene Expression Data 

      Beck, D. C.; Jiang, Honglin; Zhang, Liqing (Hindawi, 2010-02-08)
      Although the nature of ruminant evolution is still disputed, current theory based on physiology and genetic analysis suggests that the abomasum is the evolutionarily oldest stomach compartment, the rumen evolved some time ...
    • Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding 

      Aguilar, B.; Anandakrishnan, Ramu; Ruscio, J. Z.; Onufriev, Alexey V. (CELL PRESS, 2010-03-01)
      This work investigates statistical prevalence and overall physical origins of changes in charge states of receptor proteins upon ligand binding. These changes are explored as a function of the ligand type (small molecule, ...
    • Missing genes in the annotation of prokaryotic genomes 

      Warren, Andrew S.; Archuleta, Jeremy; Feng, Wu-chun; Setubal, João C. (2010-03-15)
      Background Protein-coding gene detection in prokaryotic genomes is considered a much simpler problem than in intron-containing eukaryotic genomes. However there have been reports that prokaryotic gene finder programs have ...
    • Got the Flu (or Mumps)? Check the Eigenvalue! 

      Prakash, B. Aditya; Chakrabarti, Deepayan; Faloutsos, Michalis; Valler, Nicholas; Faloutsos, Christos (Virginia Tech, 2010-03-30)
      For a given, arbitrary graph, what is the epidemic threshold? That is, under what conditions will a virus result in an epidemic? We provide the super-model theorem, which generalizes older results in two important, orthogonal ...
    • Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp aurantifolii 

      Moreira, Leandro M.; Almeida, Nalvo F., Jr.; Potnis, Neha; Digiampietri, Luciano A.; Adi, Said S.; Bortolossi, Julio C.; da Silva, Ana C.; da Silva, Aline M.; de Moraes, Fabrício E.; de Oliveira, Julio C.; de Souza, Robson F.; Facincani, Agda P.; Ferraz, André L.; Ferro, Maria I.; Furlan, Luiz R.; Gimenez, Daniele F.; Jones, Jeffrey B.; Kitajima, Elliot W.; Laia, Marcelo L.; Leite, Rui P., Jr; Nishiyama, Milton Y.; Rodrigues Neto, Julio; Nociti, Letícia A.; Norman, David J.; Ostroski, Eric H.; Pereira, Haroldo A., Jr; Staskawicz, Brian J.; Tezza, Renata I.; Ferro, Jesus A.; Vinatzer, Boris A.; Setubal, João C. (Biomed Central Ltd, 2010-04-13)
      Background Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different ...
    • Personal Anomaly Detection and Smart-Phone Security 

      Xiong, Huijun; Yao, Danfeng (Daphne) (Virginia Tech, 2010-04-22)
      Mobile devices increasingly become the computing platform for networked applications such as Web and email. This development requires strong guarantees on the system integrity and data security of mobile devices against ...
    • Functional bias in molecular evolution rate of Arabidopsis thaliana 

      Warren, Andrew S; Anandakrishnan, Ramu; Zhang, Liqing (2010-05-01)
      Background Characteristics derived from mutation and other mechanisms that are advantageous for survival are often preserved during evolution by natural selection. Some genes are conserved in many organisms because they ...
    • Experiments on the Random Packing of Tetrahedral Dice 

      Jaoshvili, A.; Esakia, A.; Porrati, M.; Chaikin, P. M. (American Physical Society, 2010-05-07)
      Tetrahedra may be the ultimate frustrating, disordered glass forming units. Our experiments on tetrahedral dice indicate the densest (volume fraction phi = 0.76 +/- .02, compared with phi(sphere) = 0.64), most disordered, ...
    • Learning probabilistic models of connectivity from multiple spike train data 

      Patnaik, Debprakash; Laxman, Srivatsan; Ramakrishnan, Naren (2010-07-20)
      Neuronal circuits or cell assemblies carry out brain function through complex coordinated firing patterns [1]. Inferring topology of neuronal circuits from simultaneously recorded spike train data is a challenging problem ...
    • Applications and Security of Next-Generation, User-Centric Wireless Systems 

      Ramstetter, Jerry Rick; Yang, Yaling; Yao, Danfeng (Daphne) (MDPI, 2010-07-28)
      Pervasive wireless systems have significantly improved end-users quality of life. As manufacturing costs decrease, communications bandwidth increases, and contextual information is made more readily available, the role of ...
    • Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis 

      Dalloul, Rami A.; Long, JA; Zimin, AV; Aslam, L; Beal, K; Blomberg, LA; Bouffard, P; Burt, DW; Crasta, O; Crooijmans, RPMA; Cooper, K; Coulombe, RA; De, S; Delany, ME; Dodgson, JB; Dong, JJ; Evans, C; Frederickson, KM; Flicek, P; Florea, L; Folkerts, O; Groenen, MAM; Harkins, TT; Herrero, J; Hoffmann, S; Megens, H-J; Jiang, A; de Jong, P; Kaiser, P; Kim, H; Kim, K-W; Kim, S; Langenberger, D; Lee, M-K; Lee, T; Mane, S; Marcais, G; Marz, M; McElroy, AP; Modise, T; Nefedov, M; Notredame, C; Paton, IR; Payne, WS; Pertea, G; Prickett, D; Puiu, D; Qioa, D; Raineri, E; Ruffier, M; Salzberg, SL; Schatz, MC; Scheuring, C; Schmidt, CJ; Schroeder, S; Searle, SMJ; Smith, EJ; Smith, J; Sonstegard, TS; Stadler, PF; Tafer, H; Tu, ZJ; Van Tassell, CP; Vilella, AJ; Williams, KP; Yorke, JA; Zhang, L; Zhang, H-B; Zhang, X; Zhang, Y; Reed, Kent M. (PLOS, 2010-09-01)
      A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). ...
    • Charge State of the Globular Histone Core Controls Stability of the Nucleosome 

      Fenley, Andrew T.; Adams, D. A.; Onufriev, Alexey V. (CELL PRESS, 2010-09-01)
      Presented here is a quantitative model of the wrapping and unwrapping of the DNA around the histone core of the nucleosome that suggests a mechanism by which this transition can be controlled: alteration of the charge state ...
    • The Effects of Higher Levels of Immersion on Procedure Memorization Performance and Implications for Educational Virtual Environments 

      Ragan, Eric D.; Sowndararajan, Ajith; Kopper, Regis; Bowman, Doug A. (MIT Press, 2010-12-01)
      Researchers have proposed that immersion could have advantages for tasks involving abstract mental activities, such as conceptual learning; however, there are few empirical results that support this idea. We hypothesized ...