Now showing items 203-222 of 323

    • 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 ...
    • Phytophthora sojae Avirulence Effector Avr3b is a Secreted NADH and ADP-ribose Pyrophosphorylase that Modulates Plant Immunity 

      Dong, Suomeng; Yin, Weixiao; Kong, Guanghui; Yang, Xinyu; Qutob, Dinah; Chen, Qinghe; Kale, Shiv D.; Sui, Yangyang; Zhang, Zhengguang; Dou, Daolong; Zheng, Xiaobo; Gijzen, Mark; Tyler, Brett M.; Wang, Yuanchao (PLOS Pathogens, 2011-11-10)
      Plants have evolved pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) to protect themselves from infection by diverse pathogens. Avirulence (Avr) effectors that ...
    • The Phytophthora sojae avirulence locus Avr3c encodes a multi-copy RXLR effector with sequence polymorphisms among different pathogen strains 

      Dong, Suomeng; Qutob, Dinah; Tedman-Jones, Jennifer; Kuflu, Kuflom; Wang, Yuanchao; Tyler, Brett M.; Gijzen, Mark (Public Library of Science, 2009-05-15)
      Root and stem rot disease of soybean is caused by the oomycete Phytophthora sojae. The avirulence (Avr) genes of P. sojae control race-cultivar compatibility. In this study, we identify the P. sojae Avr3c gene and show ...
    • PIG-the pathogen interaction gateway 

      Driscoll, Tim; Dyer, Matthew D.; Murali, T. M.; Sobral, Bruno W. (2009-01)
      Protein-protein interactions (PPIs) play a vital role in initiating infection in a number of pathogens. Identifying which interactions allow a pathogen to infect its host can help us to understand methods of pathogenesis ...
    • Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity 

      Rodrigues, Richard R.; Pineda, Rosana P.; Barney, Jacob N.; Nilsen, Eric T.; Barrett, John E.; Williams, Mark A. (PLOS, 2015-10-27)
    • The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions 

      Torto-Alalibo, Trudy; Collmer, Candace W; Gwinn-Giglio, Michelle (2009-02-19)
      All microbes that form beneficial, neutral, or pathogenic associations with hosts face similar challenges. They must physically adhere to and/or gain entry to host tissues; they must avoid, suppress, or tolerate host ...
    • Plasmids and Rickettsial Evolution: Insight from Rickettsia felis 

      Gillespie, Joseph J.; Beier, Magda S.; Rahman, M. Sayeedur; Ammerman, Nicole C.; Shallom, Joshua M.; Purkayastha, Anjan; Sobral, Bruno S.; Azad, Abdu F. (PLOS, 2007-03-07)
      Background The genome sequence of Rickettsia felis revealed a number of rickettsial genetic anomalies that likely contribute not only to a large genome size relative to other rickettsiae, but also to phenotypic oddities ...
    • PLoS Computational Biology Conference Postcards from PSB 2010 

      Datta, R. S.; Lux, Matthew W.; Bourne, Philip E. (Public Library of Science, 2010-04-29)
      Welcome to PLoS Conference Postcards. Postcards, as the name suggests, are designed to vividly recount to those not at a conference what happened at the event that was scientifically noteworthy and therefore make the reader ...