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bioinformatics:public [2014/05/05 17:41]
chrissch
bioinformatics:public [2015/10/15 22:37] (current)
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-  * [[bioinformatics:​scripts:​sup05|Cultivation-independent exploration ​of SUP05 host-virus interactions in a model Oxygen Minimum Zone]]\\ +  * [[bioinformatics:​scripts:​sup05|Ecology and evolution ​of viruses infecting uncultivated ​SUP05 bacteria as revealed by single-cell genomics and metagenomics]]\\ 
-    * This package includes the script used in "​Cultivation-independent exploration ​of SUP05 host-virus interactions in a model Oxygen Minimum Zone".+    * This package includes the script used in  ​[[http://​elifesciences.org/​content/​3/​e03125#​sthash.sskQREWU.dpuf|Roux,​ S., Hawley, A.K., Torres Beltran, M., Scofield, M., Schwientek, P., Stepanauskas,​ R., Woyke, T., Hallam, S.J., Sullivan, M.B. (doi:​10.7554/​eLife.03125). Ecology and evolution ​of viruses infecting uncultivated ​SUP05 bacteria as revealed by single-cell genomics and metagenomics]].
  
   *[[bioinformatics:​scripts:​Nature|Viral tagging reveals discrete populations in Synechococcus viral genome sequence space]]\\   *[[bioinformatics:​scripts:​Nature|Viral tagging reveals discrete populations in Synechococcus viral genome sequence space]]\\
-     * This includes the scripts used in Deng, L., Ignacio-Espinoza,​ J.C., Gregory, A., Poulos, B.T., Weitz, J.S., Hugenholtz, P., Sullivan, M.B. (accepted). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature.+     * This includes the scripts used in [[http://​www.nature.com/​nature/​journal/​vaop/​ncurrent/​full/​nature13459.html|Deng, L., Ignacio-Espinoza,​ J.C., Gregory, A., Poulos, B.T., Weitz, J.S., Hugenholtz, P., Sullivan, M.B. (doi:​10.1038/​nature13459). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature.]]
  
   * [[bioinformatics:​scripts:​pov|The Pacific Ocean Virome (POV)]]\\   * [[bioinformatics:​scripts:​pov|The Pacific Ocean Virome (POV)]]\\
-    * This package includes the scripts used in [[http://​www.plosone.org/​article/​info%3Adoi%2F10.1371%2Fjournal.pone.0057355|Hurwitz,​ B.L., & Sullivan, M.B. (2013). The Pacific Ocean Virome (POV): A marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One. 8(2), e57355.]].+    * This package includes the scripts used in [[http://​www.plosone.org/​article/​info%3Adoi%2F10.1371%2Fjournal.pone.0057355|Hurwitz,​ B.L., & Sullivan, M.B. (2013). The Pacific Ocean Virome (POV): A marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One. 8(2), e57355.]]
  
   *[[bioinformatics:​scripts:​quantitative_assessment|Quantitative assessment of concentration,​ purification and replication in viral metagenomics]]\\   *[[bioinformatics:​scripts:​quantitative_assessment|Quantitative assessment of concentration,​ purification and replication in viral metagenomics]]\\
-    * This package includes the scripts used in [[http://​onlinelibrary.wiley.com/​doi/​10.1111/​j.1462-2920.2012.02836.x/​full|Hurwitz,​ B.L., Deng, L., Poulos, B.T., & Sullivan, M.B. (2012). Evaluation of methods to concentrate and purify ocean virus communities through comparative,​ replicated metagenomics. Environ Microbiol. 15(5), 1428–1440.]].+    * This package includes the scripts used in [[http://​onlinelibrary.wiley.com/​doi/​10.1111/​j.1462-2920.2012.02836.x/​full|Hurwitz,​ B.L., Deng, L., Poulos, B.T., & Sullivan, M.B. (2012). Evaluation of methods to concentrate and purify ocean virus communities through comparative,​ replicated metagenomics. Environ Microbiol. 15(5), 1428–1440.]]
  
   *[[bioinformatics:​scripts:​cyanophage|Phylogenomics of T4 cyanophages:​ Lateral gene transfer in the '​core'​ and origins of host genes.]]\\   *[[bioinformatics:​scripts:​cyanophage|Phylogenomics of T4 cyanophages:​ Lateral gene transfer in the '​core'​ and origins of host genes.]]\\
-      * This includes the scripts used in [[http://​onlinelibrary.wiley.com/​doi/​10.1111/​j.1462-2920.2012.02704.x/​abstract|Ignacio-Espinoza,​ J.C., & Sullivan, M.B. (2012). Phylogenomics of T4 cyanophages:​ Lateral gene transfer in the '​core'​ and origins of host genes. Environ Microbiol. 14(8), 2113-2126.]].+      * This includes the scripts used in [[http://​onlinelibrary.wiley.com/​doi/​10.1111/​j.1462-2920.2012.02704.x/​abstract|Ignacio-Espinoza,​ J.C., & Sullivan, M.B. (2012). Phylogenomics of T4 cyanophages:​ Lateral gene transfer in the '​core'​ and origins of host genes. Environ Microbiol. 14(8), 2113-2126.]] 
 + 
 +  * [[bioinformatics:​scripts:​vsb|Viral dark matter and virus–host interactions resolved from publicly available microbial genomes.]]\\ 
 +    * This package includes the script used in Roux, S., Hallam, S.J., Woyke, T., Sullivan, M.B. Viral dark matter and virus–host interactions resolved from publicly available microbial genomes.
  
  
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