Now showing items 1-20 of 342

    • RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response 

      Krishnan, Arjun; Gupta, Chirag; Ambavaram, Madana M. R.; Pereira, Andy (2017-09-20)
      Transcriptional profiling is a prevalent and powerful approach for capturing the response of crop plants to environmental stresses, e.g., response of rice to drought. However, functionally interpreting the resulting ...
    • Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome 

      Dinel, S; Bolduc, C; Belleau, P; Boivin, A; Yoshioka, M; Calvo, E; Piedboeuf, B; Snyder, EE; Labrie, F; St-Amand, J (2005-01-01)
      The serial analysis of gene expression (SAGE) method is used to study global gene expression in cells or tissues in various experimental conditions. However, its reproducibility has not yet been definitively assessed. In ...
    • Tomato Expression Database (TED): a suite of data presentation and analysis tools 

      Fei, Zhangjun; Tang, Xuemei; Alba, Rob; Giovannoni, James (2006-01-01)
      The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. ...
    • VMD: a community annotation database for oomycetes and microbial genomes 

      Tripathy, Sucheta; Pandey, Varun N.; Fang, Bing; Salas, Fidel; Tyler, Brett M. (2006-01-01)
      The VBI Microbial Database (VMD) is a database system designed to host a range of microbial genome sequences. At present, the database contains genome sequence and annotation data of two plant pathogens Phytophthora sojae ...
    • A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case 

      Yu, G. X.; Snyder, E. E.; Boyle, S. M.; Crasta, O. R.; Czar, M.; Mane, S. P.; Purkayastha, A.; Sobral, B.; Setubal, J. C. (2007-06)
      We present a bacterial genome computational analysis pipeline, called GenVar. The pipeline, based on the program GeneWise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence ...
    • 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 ...
    • GeneTrees: a phylogenomics resource for prokaryotes 

      Tian, Yuying; Dickerman, Allan W. (2007-01)
      The GeneTrees phylogenomics system pursues comparative genomic analyses from the perspective of gene phylogenies for individual genes. The GeneTrees project has the goal of providing detailed evolutionary models for all ...
    • MvirDB - a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications 

      Zhou, C. E.; Smith, J.; Lam, M.; Zemla, A.; Dyer, M. D.; Slezak, T. (2007-01)
      Knowledge of toxins, virulence factors and antibiotic resistance genes is essential for bio-defense applications aimed at identifying 'functional' signatures for characterizing emerging or engineered pathogens. Whereas ...
    • An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data 

      Zhang, C.; Crasta, O.; Cammer, S.; Will, R.; Kenyon, R.; Sullivan, D.; Yu, Q.; Sun, W.; Jha, R.; Liu, D.; Xue, T.; Zhang, Y.; Moore, M.; McGarvey, P.; Huang, H.; Chen, Y.; Zhang, J.; Mazumder, R.; Wu, C.; Sobral, B. (2008-01)
      The NIAID-funded Biodefense Proteomics Resource Center (RC) provides storage, dissemination, visualization and analysis capabilities for the experimental data deposited by seven Proteomics Research Centers (PRCs). The data ...
    • 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 ...
    • 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 ...
    • Writing DNA with GenoCAD (TM) 

      Czar, Michael J.; Cai, Yizhi; Peccoud, Jean (2009-07-01)
      Chemical synthesis of custom DNA made to order calls for software streamlining the design of synthetic DNA sequences. GenoCAD (TM) (www.genocad.org) is a free web-based application to design protein expression vectors, ...
    • Sequence verification of synthetic DNA by assembly of sequencing reads 

      Wilson, Mandy L.; Cai, Yizhi; Hanlon, Regina; Taylor, Samantha; Chevreux, Bastien; Setubal, Joao C.; Tyler, Brett M.; Peccoud, Jean (2013-01)
      Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the ...
    • 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 ...
    • GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs 

      Cai, Yizhi; Wilson, Mandy L.; Peccoud, Jean (2010-05)
      One of the foundations of synthetic biology is the project to develop libraries of standardized genetic parts that could be assembled quickly and cheaply into large systems. The limitations of the initial BioBrick standard ...
    • 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 ...
    • The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) 

      Overbeek, Ross; Olson, Robert; Pusch, Gordon D.; Olsen, Gary J.; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Parrello, Bruce; Shukla, Maulik; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang; Stevens, Rick (2014-01)
      In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED ...
    • EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles 

      Dittmar, W. James; McIver, Lauren; Michalak, Pawel; Garner, Harold R.; Valdez, Gregorio (2014-07-01)
      The wealth of publicly available gene expression and genomic data provides unique opportunities for computational inference to discover groups of genes that function to control specific cellular processes. Such genes are ...
    • GenoLIB: a database of biological parts derived from a library of common plasmid features 

      Adames, Neil R.; Wilson, Mandy L.; Fang, Gang; Lux, Matthew W.; Glick, Benjamin S.; Peccoud, Jean (2015-05-26)
      Synthetic biologists rely on databases of biological parts to design genetic devices and systems. The sequences and descriptions of genetic parts are often derived from features of previously described plasmids using ad ...
    • The Kub5-Hera/RPRD1B interactome: a novel role in preserving genetic stability by regulating DNA mismatch repair 

      Patidar, Praveen L.; Motea, Edward A.; Fattah, Farjana J.; Zhou, Yunyun; Morales, Julio C.; Xie, Yang; Garner, Harold R.; Boothman, David A. (2016-02-29)
      Ku70-binding protein 5 (Kub5)-Hera (K-H)/RPRD1B maintains genetic integrity by concomitantly minimizing persistent R-loops and promoting repair of DNA double strand breaks (DSBs). We used tandem affinity purification-mass ...