% Generated by Paperpile. Check out http://paperpile.com for more information.
% BibTeX export options can be customized via Settings -> BibTeX.

@ARTICLE{Easterday2005-ev,
  title    = "Use of single nucleotide polymorphisms in the plcR gene for
              specific identification of Bacillus anthracis",
  author   = "Easterday, <NAME> and <NAME>, <NAME> and Simonson, <NAME>
              and Wagner, <NAME> and Kenefic, <NAME> and Allender, Christopher
              J and <NAME>",
  abstract = "A TaqMan-minor groove binding assay designed around a nonsense
              mutation in the plcR gene was used to genotype Bacillus
              anthracis, B. cereus, and B. thuringiensis isolates. The assay
              differentiated B. anthracis from these genetic near-neighbors and
              determined that the nonsense mutation is ubiquitous across 89
              globally and genetically diverse B. anthracis strains.",
  journal  = "J. Clin. Microbiol.",
  volume   =  43,
  number   =  4,
  pages    = "1995-1997",
  month    =  apr,
  year     =  2005,
  keywords = "BA Paper References",
  language = "en"
}

@MISC{Petit2015-qy,
  title        = "Searching for anthrax in the New York City subway metagenome",
  author       = "<NAME>, <NAME> and Ezewudo, Matthew and <NAME> and Read, <NAME>",
  month        =  apr,
  year         =  2015,
  howpublished = "\url{http://dx.doi.org/10.5281/zenodo.17158}",
  note         = "Accessed: 2019-1-2",
  keywords     = "BA Paper References"
}

@ARTICLE{Klee2010-ya,
  title    = "The genome of a Bacillus isolate causing anthrax in chimpanzees
              combines chromosomal properties of B. cereus with B. anthracis
              virulence plasmids",
  author   = "Klee, <NAME> and Brzuszkiewicz, <NAME> and Nattermann,
              Herbert and Br{\"u}ggemann, Holger and Dupke, Susann and
              Wollherr, Antje and Franz, Tatjana and Pauli, Georg and Appel,
              Bernd and Liebl, Wolfgang and Couacy-Hymann, Emmanuel and Boesch,
              Christophe and Meyer, Frauke-Dorothee and Leendertz, <NAME> and
              Ellerbrok, Heinz and Gottschalk, Gerhard and Grunow, Roland and
              Liesegang, Heiko",
  abstract = "Anthrax is a fatal disease caused by strains of Bacillus
              anthracis. Members of this monophyletic species are non motile
              and are all characterized by the presence of four prophages and a
              nonsense mutation in the plcR regulator gene. Here we report the
              complete genome sequence of a Bacillus strain isolated from a
              chimpanzee that had died with clinical symptoms of anthrax.
              Unlike classic B. anthracis, this strain was motile and lacked
              the four prohages and the nonsense mutation. Four replicons were
              identified, a chromosome and three plasmids. Comparative genome
              analysis revealed that the chromosome resembles those of non-B.
              anthracis members of the Bacillus cereus group, whereas two
              plasmids were identical to the anthrax virulence plasmids pXO1
              and pXO2. The function of the newly discovered third plasmid with
              a length of 14 kbp is unknown. A detailed comparison of genomic
              loci encoding key features confirmed a higher similarity to B.
              thuringiensis serovar konkukian strain 97-27 and B. cereus E33L
              than to B. anthracis strains. For the first time we describe the
              sequence of an anthrax causing bacterium possessing both anthrax
              plasmids that apparently does not belong to the monophyletic
              group of all so far known B. anthracis strains and that differs
              in important diagnostic features. The data suggest that this
              bacterium has evolved from a B. cereus strain independently from
              the classic B. anthracis strains and established a B. anthracis
              lifestyle. Therefore we suggest to designate this isolate as ``B.
              cereus variety (var.) anthracis''.",
  journal  = "PLoS One",
  volume   =  5,
  number   =  7,
  pages    = "e10986",
  month    =  jul,
  year     =  2010,
  keywords = "BA Paper References",
  language = "en"
}

@ARTICLE{Afshinnekoo2015-yw,
  title    = "Geospatial Resolution of Human and Bacterial Diversity with
              City-Scale Metagenomics",
  author   = "Afshinnekoo, Ebrahim and Meydan, Cem and Chowdhury, Shanin and
              Jaroudi, Dyala and Boyer, Collin and Bernstein, Nick and Maritz,
              <NAME> and Reeves, Darryl and Gandara, Jorge and Chhangawala,
              Sagar and Ahsanuddin, Sofia and Simmons, Amber and Nessel,
              Timothy and Sundaresh, Bharathi and Pereira, Elizabeth and
              Jorgensen, Ellen and Kolokotronis, Sergios-Orestis and
              Kirchberger, Nell and Garcia, Isaac and Gandara, David and
              Dhanraj, Sean and Nawrin, Tanzina and Saletore, Yogesh and
              Alexander, Noah and Vijay, Priyanka and H{\'e}naff, <NAME>
              and Zumbo, Paul and Walsh, Michael and O'Mullan, <NAME> and
              Tighe, Scott and Dudley, <NAME> and Dunaif, Anya and Ennis, Sean
              and O'Halloran, Eoghan and Magalhaes, <NAME> and Boone, Braden
              and Jones, <NAME> and Muth, Theodore R and Paolantonio, Katie
              Schneider and Alter, Elizabeth and Schadt, <NAME> and Garbarino,
              Jeanne and Prill, <NAME> and Carlton, <NAME> and Levy, Shawn
              and Mason, <NAME>",
  abstract = "The panoply of microorganisms and other species present in our
              environment influence human health and disease, especially in
              cities, but have not been profiled with metagenomics at a
              city-wide scale. We sequenced DNA from surfaces across the entire
              New York City (NYC) subway system, the Gowanus Canal, and public
              parks. Nearly half of the DNA (48\%) does not match any known
              organism; identified organisms spanned 1,688 bacterial, viral,
              archaeal, and eukaryotic taxa, which were enriched for harmless
              genera associated with skin (e.g., Acinetobacter). Predicted
              ancestry of human DNA left on subway surfaces can recapitulate
              U.S. Census demographic data, and bacterial signatures can reveal
              a station's history, such as marine-associated bacteria in a
              hurricane-flooded station. Some evidence of pathogens was found
              (Bacillus anthracis), but a lack of reported cases in NYC
              suggests that the pathogens represent a normal, urban microbiome.
              This baseline metagenomic map of NYC could help long-term disease
              surveillance, bioterrorism threat mitigation, and health
              management in the built environment of cities.",
  journal  = "Cell Syst",
  volume   =  1,
  number   =  1,
  pages    = "72-87",
  month    =  jul,
  year     =  2015,
  keywords = "BA Paper References",
  language = "en"
}

% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Afshinnekoo2015-tm,
  title     = "Modern Methods for Delineating Metagenomic Complexity",
  author    = "Afshinnekoo, Ebrahim and Meydan, Cem and <NAME> and
               Jaroudi, Dyala and Boyer, Collin and Bernstein, Nick and Maritz,
               <NAME> and Reeves, Darryl and <NAME> and Chhangawala,
               Sagar and Ahsanuddin, Sofia and Simmons, Amber and Nessel,
               Timothy and Sundaresh, Bharathi and Pereira, Elizabeth and
               Jorgensen, Ellen and Kolokotronis, Sergios-Orestis and
               Kirchberger, Nell and Garcia, Isaac and Gandara, David and
               Dhanraj, Sean and Nawrin, Tanzina and Saletore, Yogesh and
               <NAME> and Vijay, Priyanka and H{\'e}naff, <NAME>
               and Zumbo, Paul and Walsh, Michael and O'Mullan, <NAME> and
               Tighe, Scott and Dudley, <NAME> and Dunaif, Anya and Ennis, Sean
               and O'Halloran, Eoghan and Magalhaes, <NAME> and Boone, Braden
               and Jones, <NAME> and Muth, <NAME> and Paolantonio, Katie
               Schneider and Alter, Elizabeth and Schadt, <NAME> and Garbarino,
               Jeanne and Prill, <NAME> and Carlton, <NAME> and Levy, Shawn
               and Mason, <NAME>",
  abstract  = "Figure 3B has been corrected to show the general coverage of the
               Yersinia pestis pMT1 plasmid, but not the murine toxin gene
               (yMT). The initial claim of ``… consistent 20$\times$ coverage
               across the murine toxin gene…'' was erroneously based on looking
               at annotations from ...",
  journal   = "Cell Systems",
  publisher = "Elsevier",
  volume    =  1,
  number    =  1,
  pages     = "6-7",
  month     =  jul,
  year      =  2015,
  keywords  = "BA Paper References"
}
