Research articles, presentations, and other scholarship

Recent Submissions

  • 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 ...
  • Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans 

    Quilez, Javier; Guilmatre, Audrey; Garg, Paras; Highnam, Gareth; Gymrek, Melissa; Erlich, Yaniv; Joshi, Ricky S.; Mittelman, David; Sharp, Andrew J. (2016-05-05)
    Despite representing an important source of genetic variation, tandem repeats (TRs) remain poorly studied due to technical difficulties. We hypothesized that TRs can operate as expression (eQTLs) and methylation (mQTLs) ...
  • Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center 

    Wattam, Alice R.; Davis, James J.; Assaf, Rida; Boisvert, Sebastien; Brettin, Thomas; Bun, Christopher; Conrad, Neal; Dietrich, Emily M.; Disz, Terry; Gabbard, Joseph L.; Gerdes, Svetlana; Henry, Christopher S.; Kenyon, Ronald W.; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K.; Olsen, Gary J.; Murphy-Olson, Daniel E.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Vonstein, Veronika; Warren, Andrew; Xia, Fangfang; Yoo, Hyunseung; Stevens, Rick L. (2017-01-04)
    The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that ...
  • Quantifying spatio-temporal variation of invasion spread 

    Goldstein, J.; Park, J.; Haran, M.; Liebhold, A.; Bjørnstad, O.N. (Royal Society Publishing, 2019-01-09)
    The spread of invasive species can have far-reaching environmental and ecological consequences. Understanding invasion spread patterns and the underlying process driving invasions are key to predicting and managing invasions. ...
  • Endocytic Markers Associated with the Internalization and Processing of Aspergillus fumigatus Conidia by BEAS-2B Cells 

    Clark, H.R.; Powell, A.B.; Simmons, K.A.; Ayubi, T.; Kale, S.D. (NLM (Medline), 2019-02-06)
    Aspergillus fumigatus is a ubiquitous mold that produces small airborne conidia capable of traversing deep into the respiratory system. Recognition, processing, and clearance of A. fumigatus conidia by bronchial airway ...
  • 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 ...
  • 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 ...
  • 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 ...
  • Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting 

    Lemos, Leandro N.; Pereira, Roberta V.; Quaggio, Ronaldo B.; Martins, Layla F.; Moura, Livia M. S.; da Silva, Amanda R.; Antunes, Luciana P.; da Silva, Aline M.; Setubal, Joao C. (Frontiers, 2017-04-19)
    Microbial consortia selected from complex lignocellulolytic microbial communities are promising alternatives to deconstruct plant waste, since synergistic action of different enzymes is required for full degradation of ...

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