Browsing Faculty Works, Biocomplexity Institute by Title

Now showing items 1-20 of 322

    • A Network Biology Approach to Denitrification in Pseudomonas aeruginosa 

      Arat, Seda; Bullerjahn, George S.; Laubenbacher, Reinhard (2015-02-23)
      Pseudomonas aeruginosa is a metabolically flexible member of the Gammaproteobacteria. Under anaerobic conditions and the presence of nitrate, P. aeruginosa can perform (complete) denitrification, a respiratory process of ...

    • A Simulation Optimization Approach to Epidemic Forecasting 

      Nsoesie, Elaine O.; Beckman, Richard J.; Shashaani, Sara; Nagaraj, Kalyani S.; Marathe, Madhav V. (PLOS, 2013-06-27)
      Reliable forecasts of influenza can aid in the control of both seasonal and pandemic outbreaks. We introduce a simulation optimization (SIMOP) approach for forecasting the influenza epidemic curve. This study represents ...

    • Abstracts from the 3rd Conference on Aneuploidy and Cancer: Clinical and Experimental Aspects 

      Cornish-Bowden, Athel; Cornish-Bowden, Athel; Rasnick, David; Heng, Henry H; Horne, Steven; Abdallah, Batoul; Liu, Guo; Ye, Christine J; Bloomfield, Mathew; Vincent, Mark D; Aldaz, C. M; Karlsson, Jenny; Valind, Anders; Jansson, Caroline; Gisselsson, David; Graves, Jennifer A M; Stepanenko, Aleksei A; Andreieva, Svitlana V; Korets, Kateryna V; Mykytenko, Dmytro O; Huleyuk, Nataliya L; Baklaushev, Vladimir P; Kovaleva, Oksana A; Chekhonin, Vladimir P; Vassetzky, Yegor S; Avdieiev, Stanislav S; Bakker, Bjorn; Taudt, Aaron S; Belderbos, Mirjam E; Porubsky, David; Spierings, Diana C J; de Jong, Tristan V; Halsema, Nancy; Kazemier, Hinke G; Hoekstra-Wakker, Karina; Bradley, Allan; de Bont, Eveline S J M; van den Berg, Anke; Guryev, Victor; Lansdorp, Peter M; Tatché, Maria C; Foijer, Floris; Liehr, Thomas; Baudoin, Nicolaas C; Nicholson, Joshua M; Soto, Kimberly; Quintanilla, Isabel; Camps, Jordi; Cimini, Daniela; Dürrbaum, M.; Donnelly, N.; Passerini, V.; Kruse, C.; Habermann, B.; Storchová, Z.; Mandrioli, Daniele; Belpoggi, Fiorella; Silbergeld, Ellen K; Perry, Melissa J; Skotheim, Rolf I; Løvf, Marthe; Johannessen, Bjarne; Hoff, Andreas M; Zhao, Sen; SveeStrømme, Jonas M; Sveen, Anita; Lothe, Ragnhild A; Hehlmann, R.; Voskanyan, A.; Fabarius, A.; Böcking, Alfred; Biesterfeld, Stefan; Berynskyy, Leonid; Börgermann, Christof; Engers, Rainer; Dietz, Josef; Fritz, A.; Sehgal, N.; Vecerova, J.; Stojkovicz, B.; Ding, H.; Page, N.; Tye, C.; Bhattacharya, S.; Xu, J.; Stein, G.; Stein, J.; Berezney, R.; Gong, Xue; Grasedieck, Sarah; Swoboda, Julian; Rücker, Frank G; Bullinger, Lars; Pollack, Jonathan R; Roumelioti, Fani-Marlen; Chiourea, Maria; Raftopoulou, Christina; Gagos, Sarantis; Duesberg, Peter; Bloomfield, Mat; Hwang, Sunyoung; Gustafsson, Hans T; O’Sullivan, Ciara; Acevedo-Colina, Aracelli; Huang, Xinhe; Klose, Christian; Schevchenko, Andrej; Dickson, Robert C; Cavaliere, Paola; Dephoure, Noah; Torres, Eduardo M; Stampfer, Martha R; Vrba, Lukas; LaBarge, Mark A; Futscher, Bernard; Garbe, James C; Zhou, Yi-Hong; Trinh, Andrew L; Zhou, Yi-Hong; Digman, Michelle (2017-06-22)

    • Accuracy of epidemiological inferences based on publicly available information: retrospective comparative analysis of line lists of human cases infected with influenza A(H7N9) in China 

      Lau, Eric HY; Zheng, Jiandong; Tsang, Tim K; Liao, Qiaohong; Lewis, Bryan; Brownstein, John S; Sanders, Sharon; Wong, Jessica Y; Mekaru, Sumiko R; Rivers, Caitlin; Wu, Peng; Jiang, Hui; Li, Yu; Yu, Jianxing; Zhang, Qian; Chang, Zhaorui; Liu, Fengfeng; Peng, Zhibin; Leung, Gabriel M; Feng, Luzhao; Cowling, Benjamin J; Yu, Hongjie (2014-05-28)
      Background Appropriate public health responses to infectious disease threats should be based on best-available evidence, which requires timely reliable data for appropriate analysis. During the early stages of epidemics, ...

    • Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles 

      Highnam, Gareth; Franck, Christopher; Martin, Andy; Stephens, Calvin; Puthige, Ashwin; Mittelman, David (2013-01)
      Repetitive sequences are biologically and clinically important because they can influence traits and disease, but repeats are challenging to analyse using short-read sequencing technology. We present a tool for genotyping ...

    • ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra 

      Hinkelmann, Franziska; Brandon, Madison; Guang, Bonny; McNeill, Rustin; Blekherman, Grigoriy; Veliz-Cuba, Alan; Laubenbacher, Reinhard (2011-07-20)
      Background Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The ...

    • Adaptive Imaging Cytometry to Estimate Parameters of Gene Networks Models in Systems and Synthetic Biology 

      Ball, David A.; Lux, Matthew W.; Adames, Neil R.; Peccoud, Jean (PLOS, 2014-09-11)
      The use of microfluidics in live cell imaging allows the acquisition of dense time-series from individual cells that can be perturbed through computer-controlled changes of growth medium. Systems and synthetic biologists ...

    • Age-related variations in the methylome associated with gene expression in human monocytes and T cells 

      Reynolds, Lindsay M.; Taylor, Jackson R.; Ding, Jingzhong; Lohman, Kurt; Johnson, Craig; Siscovick, David; Burke, Gregory L.; Post, Wendy; Shea, Steven; Jacobs, David R., Jr.; Stunnenberg, Hendrik; Kritchevsky, Stephen B.; Hoeschele, Ina; McCall, Charles E.; Herrington, David M.; Tracy, Russell P.; Liu, Yongmei (Springer Nature, 2014-11)
      Age-related variations in DNA methylation have been reported; however, the functional relevance of these differentially methylated sites (age-dMS) are unclear. Here we report potentially functional age-dMS, defined as ...

    • An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Strand Termination by Nucleoside Reverse Transcription Inhibitors 

      Wendelsdorf, Katherine V.; Song, Zhuo; Samuels, David C. (Public Library of Science, 2009-01-09)
      Nucleoside analogs used in antiretroviral treatment have been associated with mitochondrial toxicity. The polymerase-gamma hypothesis states that this toxicity stems from the analogs' inhibition of the mitochondrial DNA ...

    • Analysis of global gene expression changes in human bronchial epithelial cells exposed to spores of the allergenic fungus, Alternaria alternata 

      Babiceanu, M. C.; Howard, B. A.; Rumore, A. C.; Kita, H.; Lawrence, C. B. (Frontiers, 2013-07-19)
      Exposure and sensitivity to ubiquitous airborne fungi such as Alternaria alternata have long been implicated in the development, onset, and exacerbation of chronic allergic airway disorders. This present study is the first ...

    • Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype 

      Huang, J. L.; Zhao, Y. P.; Shiraigol, W.; Li, B.; Bai, D. Y.; Ye, W. X.; Daidiikhuu, D.; Yang, L. H.; Jin, Brqqg; Zhao, Q. A.; Gao, Y. H.; Wu, J.; Bao, Wydl; Li, A. A.; Zhang, Y. H. Percival; Han, H. G.; Bai, H. T.; Bao, Y. Q.; Zhao, L. L.; Zhai, Z. X.; Zhao, W. J.; Sun, Z. K.; Zhang, Y.; Meng, H.; Dugarjaviin, M. (Nature Publishing Group, 2014-05)
      Karyotypic diversification is more prominent in Equus species than in other mammals. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse ...

    • Analysis of Microsatellite Variation in Drosophila melanogaster with Population-Scale Genome Sequencing 

      Fondon III, John W.; Martin, Andy; Richards, Stephen; Gibbs, Richard A.; Mittelman, David (PLoS, 2012-03-12)
      Genome sequencing technologies promise to revolutionize our understanding of genetics, evolution, and disease by making it feasible to survey a broad spectrum of sequence variation on a population scale. However, this ...

    • Analysis of Schistosoma mansoni genes shared with Deuterostomia and with possible roles in host interactions 

      Venancio, Thiago M.; DeMarco, Ricardo; Almeida, Giulliana T.; Oliveira, Katia C.; Setubal, João C.; Verjovski-Almeida, Sergio (2007-11-08)
      Background: Schistosoma mansoni is a blood helminth parasite that causes schistosomiasis, a disease that affects 200 million people in the world. Many orthologs of known mammalian genes have been discovered in this parasite ...

    • Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages 

      Mian, MA Rouf; Zhang, Yan; Wang, Zeng-Yu; Zhang, Ji-Yi; Cheng, Xiaofei; Chen, Lei; Chekhovskiy, Konstantin; Dai, Xinbin; Mao, Chunhong; Cheung, Foo; Zhao, Xuechun; He, Ji; Scott, Angela D; Town, Christopher D; May, Gregory D (2008-03-04)
      Background Tall fescue (Festuca arundinacea Schreb) is a major cool season forage and turf grass species grown in the temperate regions of the world. In this paper we report the generation of a tall fescue expressed sequence ...

    • Analysis system using brokers that access information sources 

      Virginia Polytechnic Institute and State Univ.; Marathe, Madhav V.; Barrett, Christopher L.; Bisset, Keith R. (United States Patent and Trademark Office, 2018-01-16)
      Systems, methods, and computer-readable media for generating a data set are provided. One method includes generating a data set based on input data using a plurality of brokers. The method further includes receiving a ...

    • An analytical framework for optimizing variant discovery from personal genomes 

      Highnam, Gareth; Wang, Jason J.; Kusler, Dean; Zook, Justin; Vijayan, Vinaya; Leibovich, Nir; Mittelman, David (Springer Nature, 2015-02)
      The standardization and performance testing of analysis tools is a prerequisite to widespread adoption of genome-wide sequencing, particularly in the clinic. However, performance testing is currently complicated by the ...

    • An anomalous type IV secretion system in Rickettsia is evolutionarily conserved 

      Gillespie, Joseph J.; Ammerman, Nicole C.; Dreher-Lesnick, Sheila M.; Rahman, Sayeedur; Worley, Micah J.; Setubal, João C.; Sobral, Bruno S.; Azad, Abdu F. (Public Library of Science, 2009-03-12)
      Background: Bacterial type IV secretion systems (T4SSs) comprise a diverse transporter family functioning in conjugation, competence, and effector molecule (DNA and/or protein) translocation. Thirteen genome sequences from ...

    • Antimicrobial Resistance Prediction in PATRIC and RAST 

      Davis, James J.; Boisvert, Sebastien; Brettin, Thomas; Kenyon, Ronald W.; Mao, Chunhong; Olson, Robert; Overbeek, Ross; Santerre, John; Shukla, Maulik; Wattam, Alice R.; Will, Rebecca; Xia, Fangfang; Stevens, Rick (Springer Nature, 2016-06-14)
      The emergence and spread of antimicrobial resistance (AMR) mechanisms in bacterial pathogens, coupled with the dwindling number of effective antibiotics, has created a global health crisis. Being able to identify the genetic ...

    • Arlington County Emergency Alerts: Enhancing Enrollment and Effectiveness 

      Grant, Milicent; Tyner, Samantha; Ziemer, Kathryn (Virginia Tech, 2017)
      Emergency alerts are an efficient tool for keeping populations well informed during high-risk situations. In collaboration with Arlington County, our laboratory conducted a pilot study to identify messaging patterns that ...

    • Assessing Glucose Uptake through the Yeast Hexose Transporter 1 (Hxt1) 

      Roy, Adhiraj; Dement, Angela D.; Cho, Kyu Hong; Kim, Jeong-Ho (PLOS, 2015-03-27)
      The transport of glucose across the plasma membrane is mediated by members of the glucose transporter family. In this study, we investigated glucose uptake through the yeast hexose transporter 1 (Hxt1) by measuring ...