SEA-PHAGES | Introductory Phage Papers

Link to this post \| posted 01 Sep, 2015 15:56
sbconant	I remember several people mentioning good research or introductory phage articles that they have their students read at the intro to this course. I can't, however seem to find in my notes what they were! Any help would be greatly appreciated. Thanks, Stephanie

Link to this post \| posted 01 Sep, 2015 16:17
DanRussell	Hi Stephanie, I moved your question to the "Papers" forum since it seems more at home here. One source to check out is the PhagesDB "PubGroups". These are groups of publications that share some theme. The "Faculty Favorites" are papers that come with recommendations by SEA-PHAGES faculty members. This page on seaphages.org also has papers that have been authored in part by SEA-PHAGES undergrads or faculty. Finally, here are just a few direct suggestions that might be good for getting students' feet wet. The secret lives of mycobacteriophages. (Review article.) Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches –Dan Edited 01 Sep, 2015 16:20

Link to this post | posted 01 Sep, 2015 16:17

DanRussell

Hi Stephanie,

I moved your question to the "Papers" forum since it seems more at home here.

One source to check out is the PhagesDB "PubGroups". These are groups of publications that share some theme. The "Faculty Favorites" are papers that come with recommendations by SEA-PHAGES faculty members.

This page on seaphages.org also has papers that have been authored in part by SEA-PHAGES undergrads or faculty.

Finally, here are just a few direct suggestions that might be good for getting students' feet wet.

The secret lives of mycobacteriophages. (Review article.)

Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage.

Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches

–Dan

Edited 01 Sep, 2015 16:20

Link to this post \| posted 01 Sep, 2015 16:56
sbconant	Thank you so much!

Link to this post \| posted 02 Sep, 2015 15:55
sbconant	Is there any way someone might be able to send me a pdf of "The secret lives of mycobacteriophages"?? I cant seem to access it through our or Wayne State's library system. Thanks!

Link to this post \| posted 02 Sep, 2015 21:09
DanRussell	sbconant Is there any way someone might be able to send me a pdf of "The secret lives of mycobacteriophages"?? I cant seem to access it through our or Wayne State's library system. Thanks! Hi Stephanie, As long as you're using it in line with the disclaimers on the first page, we should be fine sharing it with you (and others) directly. Here it is! –Dan

Link to this post \| posted 03 Sep, 2015 00:56
sbconant	Yes of course, thank you! Stephanie

Link to this post \| posted 20 Jun, 2023 19:25
mdgainey	This is a fun paper that I did in phage bioinformatics this year that my students enjoyed. We use code 11 (bacterial, archael and plant plastid code) for our annotations because TTG (UUG) and GTG (GUG)are used as start codons. This paper demonstrates the some human microbiome phages use code 15. In code 15 TAG(UAG) is not used as a stop codon and instead will code for the amino acid Glutamine. I thought it was very relevant to what we were doing and shows how much "better" these genomes look after annotation when the proper code was used. https://www.nature.com/articles/s41467-022-32979-6

Link to this post | posted 20 Jun, 2023 19:25

mdgainey

This is a fun paper that I did in phage bioinformatics this year that my students enjoyed. We use code 11 (bacterial, archael and plant plastid code) for our annotations because TTG (UUG) and GTG (GUG)are used as start codons.

This paper demonstrates the some human microbiome phages use code 15. In code 15 TAG(UAG) is not used as a stop codon and instead will code for the amino acid Glutamine. I thought it was very relevant to what we were doing and shows how much "better" these genomes look after annotation when the proper code was used.

https://www.nature.com/articles/s41467-022-32979-6

Link to this post \| posted 26 Oct, 2024 14:35
nic.vega	A few newer papers (and one old one) that may be of interest: Gallet, Romain, Sherin Kannoly, and Ing-Nang Wang. 2011. “Effects of Bacteriophage Traits on Plaque Formation.” BMC Microbiology 11 (1): 181. https://doi.org/10.1186/1471-2180-11-181. Germida, James J., and L. E. Casida. 1981. “Isolation of Arthrobacter Bacteriophage from Soil.” Applied and Environmental Microbiology 41 (6): 1389–93. Keen, Eric C. 2015. “A Century of Phage Research: Bacteriophages and the Shaping of Modern Biology.” BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology 37 (1): 6–9. https://doi.org/10.1002/bies.201400152. Zrelovs, Nikita, Andris Dislers, and Andris Kazaks. 2021. “Motley Crew: Overview of the Currently Available Phage Diversity.” Frontiers in Microbiology 11 (January). https://doi.org/10.3389/fmicb.2020.579452.

Link to this post | posted 26 Oct, 2024 14:35

nic.vega

A few newer papers (and one old one) that may be of interest:

Gallet, Romain, Sherin Kannoly, and Ing-Nang Wang. 2011. “Effects of Bacteriophage Traits on Plaque Formation.” BMC Microbiology 11 (1): 181. https://doi.org/10.1186/1471-2180-11-181.

Germida, James J., and L. E. Casida. 1981. “Isolation of Arthrobacter Bacteriophage from Soil.” Applied and Environmental Microbiology 41 (6): 1389–93.

Keen, Eric C. 2015. “A Century of Phage Research: Bacteriophages and the Shaping of Modern Biology.” BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology 37 (1): 6–9. https://doi.org/10.1002/bies.201400152.

Zrelovs, Nikita, Andris Dislers, and Andris Kazaks. 2021. “Motley Crew: Overview of the Currently Available Phage Diversity.” Frontiers in Microbiology 11 (January). https://doi.org/10.3389/fmicb.2020.579452.

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