Now showing items 196-215 of 323

    • Named Entity Recognition for Bacterial Type IV Secretion Systems 

      Ananiadou, Sophia; Sullivan, Dan; Black, William; Levow, Gina-Anne; Gillespie, Joseph J.; Mao, Chunhong; Pyysalo, Sampo; Kolluru, BalaKrishna; Tsujii, Junichi; Sobral, Bruno (Public Library of Science, 2011-03-29)
      Research on specialized biological systems is often hampered by a lack of consistent terminology, especially across species. In bacterial Type IV secretion systems genes within one set of orthologs may have over a dozen ...
    • Near-Optimal and Practical Algorithms for Graph Scan Statistics 

      Cadena, J; Chen, F; Vullikanti, AK (Siam, 2017-04-27)
    • Network Effects of Risk Behavior Change Following Prophylactic Interventions 

      Rajaraman, Rajmohan; Sun, Zhifeng; Sundaram, Ravi; Vullikanti, Anil Kumar S. (PLOS, 2013-08-01)
      We formulated a network-based model to understand how risk behavior change in conjunction with failure of prophylactic interventions can lead to unintended outcomes where “less (intervention) is more (effective).” Our model ...
    • Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis 

      Dias-Neto, Emmanue; Nunes, Diana N.; Giordano, Ricardo J.; Sun, Jessica; Botz, Gregory H.; Yang, Kuan; Setubal, João C.; Pasqualini, Renata; Arap, Wadih (Public Library of Science, 2009-12-17)
      Background: Combinatorial phage display has been used in the last 20 years in the identification of protein-ligands and protein-protein interactions, uncovering relevant molecular recognition events. Rate-limiting steps ...
    • 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 ...
    • Novel roles for scleraxis in regulating adult tenocyte function 

      Nichols, Anne E C; Settlage, Robert E; Werre, Stephen R; Dahlgren, Linda A (2018-08-07)
      Abstract Background Tendinopathies are common and difficult to resolve due to the formation of scar tissue that reduces the mechanical integrity of the tissue, leading to ...
    • Nucleotide diversity inflation as a genome-wide response to experimental lifespan extension in Drosophila melanogaster 

      Michalak, Pawel; Kang, Lin; Sarup, Pernille M; Schou, Mads F; Loeschcke, Volker (2017-01-14)
      Abstract Background Evolutionary theory predicts that antagonistically selected alleles, such as those with divergent pleiotropic effects in early and late life, may often ...
    • Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools 

      Tran, Hong; Porter, Jacob; Sun, Ming-an; Xie, Hehuang; Zhang, Liqing (Hindawi, 2014-04-15)
      Background. Large-scale bisulfite treatment and short reads sequencing technology allow comprehensive estimation of methylation states of Cs in the genomes of different tissues, cell types, and developmental stages. Accurate ...
    • Origin, Evolution, and Genotyping of Emergent Porcine Epidemic Diarrhea Virus Strains in the United States 

      Huang, Yao-Wei; Dickerman, Allan W.; Pineyro, Pablo; Li, Long; Fang, Li; Kiehne, Ross; Opriessnig, Tanja; Meng, Xiang-Jin (American Society for Microbiology, 2013-09)
      Coronaviruses are known to infect humans and other animals and cause respiratory and gastrointestinal diseases. Here we report the emergence of porcine epidemic diarrhea virus (PEDV) in the United States and determination ...
    • Oscillatory Dynamics of Cell Cycle Proteins in Single Yeast Cells Analyzed by Imaging Cytometry 

      Ball, D. A.; Marchand, J.; Poulet, M.; Baumann, W. T.; Chen, K. C.; Tyson, John J.; Peccoud, J. (PLOS, 2011-10-26)
      Progression through the cell division cycle is orchestrated by a complex network of interacting genes and proteins. Some of these proteins are known to fluctuate periodically during the cell cycle, but a systematic study ...
    • Overlap microtubules link sister k-fibres and balance the forces on bi-oriented kinetochores 

      Kajtez, Janko; Solomatina, Anastasia; Novak, Maja; Polak, Bruno; Vukusic, Kruno; Ruediger, Jonas; Cojoc, Gheorghe; Milas, Ana; Sestak, Ivana Sumanovac; Risteski, Patrik; Tavano, Federica; Klemm, Anna H.; Roscioli, Emanuele; Welburn, Julie; Cimini, Daniela; Gluncic, Matko; Pavin, Nenad; Tolic, Iva M. (Springer Nature, 2016-01)
      During metaphase, forces on kinetochores are exerted by k-fibres, bundles of microtubules that end at the kinetochore. Interestingly, non-kinetochore microtubules have been observed between sister kinetochores, but their ...
    • Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011 

      Pyysalo, Sampo; Ohta, Tomoko; Rak, Rafal; Sullivan, Dan; Mao, Chunhong; Wang, Chunxia; Sobral, Bruno WS; Tsujii, Jun'ichi; Ananiadou, Sophia (2012-06-26)
      We present the preparation, resources, results and analysis of three tasks of the BioNLP Shared Task 2011: the main tasks on Infectious Diseases (ID) and Epigenetics and Post-translational Modifications (EPI), and the ...
    • PATRIC, the bacterial bioinformatics database and analysis resource 

      Wattam, Alice R.; Abraham, David; Dalay, Oral; Disz, Terry L.; Driscoll, Timothy; Gabbard, Joseph L.; Gillespie, Joseph J.; Gough, Roger; Hix, Deborah; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K.; Olson, Robert; Overbeek, Ross; Pusch, Gordon D.; Shukla, Maulik; Schulman, Julie; Stevens, Rick L.; Sullivan, Daniel E.; Vonstein, Veronika; Warren, Andrew; Will, Rebecca; Wilson, Meredith J. C.; Yoo, Hyun Seung; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno W. (2014-01)
      The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious ...
    • PATRIC: The VBI PathoSystems Resource Integration Center 

      Snyder, E. E.; Kampanya, N.; Lu, J.; Nordberg, E. K.; Karur, H. R.; Shukla, M.; Soneja, J.; Tian, Y.; Xue, T.; Yoo, H.; Zhang, F.; Dharmanolla, C.; Dongre, N. V.; Gillespie, J. J.; Hamelius, J.; Hance, M.; Huntington, K. I.; Jukneliene, D.; Koziski, J.; Mackasmiel, L.; Mane, S. P.; Nguyen, V.; Purkayastha, A.; Shallom, J.; Yu, G.; Guo, Y.; Gabbard, J.; Hix, D.; Azad, A. F.; Baker, S. C.; Boyle, S. M.; Khudyakov, Y.; Meng, X. J.; Rupprecht, C.; Vinje, J.; Crasta, O. R.; Czar, M. J.; Dickerman, A.; Eckart, J. D.; Kenyon, R.; Will, R.; Setubal, J. C.; Sobral, B. W. S. (2007-01)
      The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a data and analysis resource ...
    • PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database 

      Davis, James J.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Pusch, Gordon D.; Shukla, Maulik; Vonstein, Veronika; Wattam, Alice R.; Yoo, Hyunseung (Frontiers, 2016-02-08)
      The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein ...
    • Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction 

      Yang, Kuan; Zhang, Liqing (2008-03)
      Phylogenetic tree reconstruction requires construction of a multiple sequence alignment (MSA) from sequences. Computationally, it is difficult to achieve an optimal MSA for many sequences. Moreover, even if an optimal MSA ...
    • Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland 

      Susanti, Dwi; Johnson, Eric F; Lapidus, Alla; Han, James; Reddy, T. B K; Pilay, Manoj; Ivanova, Natalia N; Markowitz, Victor M; Woyke, Tanja; Kyrpides, Nikos C; Mukhopadhyay, Biswarup (2016-01-13)
      This report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, an obligate anaerobic hyperthermophilic crenarchaeon that was isolated from acidic hot springs in Hveravellir, ...
    • Phosphorylation of PPAR gamma Affects the Collective Motions of the PPAR gamma-RXR alpha-DNA Complex 

      Lemkul, J. A.; Lewis, S. N.; Bassaganya-Riera, J.; Bevan, David R. (PLOS, 2015-05-08)
      Peroxisome-proliferator activated receptor-γ (PPARγ) is a nuclear hormone receptor that forms a heterodimeric complex with retinoid X receptor-α (RXRα) to regulate transcription of genes involved in fatty acid storage and ...
    • Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity 

      Schwartz, Allison R.; Potnist, Neha; Milsina, Sujan; Wilson, Mark; Patane, Jose; Martins, Joaquim, Jr.; Minsavage, Gerald V.; Dahlbeck, Douglas; Akhunova, Alina; Almeida, Nalvo; Vallad, Gary E.; Barak, Jeri D.; White, Frank F.; Miller, Sally A.; Ritchie, David; Goss, Erica; Bart, Rebecca S.; Setubal, Joao C.; Jones, Jeffrey B.; Staskawicz, Brian J. (Frontiers, 2015-06-03)
      Bacterial spot disease of pepper and tomato is caused by four distinct Xanthomonas species and is a severely limiting factor on fruit yield in these crops. The genetic diversity and the type Ill effector repertoires of a ...
    • Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance 

      Maldonado-Contreras, Ana; Mane, Shrinivasrao P; Zhang, Xue-Song; Pericchi, Luis; Alarcón, Teresa; Contreras, Monica; Linz, Bodo; Blaser, Martin J; Domínguez-Bello, María G (2013-09-19)
      Background: Helicobacter pylori has diverged in parallel to its human host, leading to distinct phylogeographic populations. Recent evidence suggests that in the current human mixing in Latin America, European H. pylori ...