The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage

By Forest Rohwer, Robert A. Edwards. Journal of Bacteriology, 2002

614 citations recorded by the source corpus.

Subfields: Ecology, Microbiology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c15d077331ed4c50c716cb766bd926fdf93f5cb2

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Citations in the corpus

The Marine Viromes of Four Oceanic Regions (2006, methodology): “edu/phage/Oceans) and was constructed as described previously [23].”
RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses (2005, background): “In addition, viruses do not have ubiquitously conserved genetic elements such as rDNA that can be used as diversity and evolutionary distance markers [15].”
Here a virus, there a virus, everywhere the same virus? (2005, background): “Phage specialization to different environments In general, officially recognized phage taxa [52] share similar suites of genes [ 26 ].”
Ecology of viruses in soils: Past, present and future perspectives (2008, background): “A recently developed genome-based taxonomy for phages divided Podoviridae into two groups of T7-like and PZA-like podophages (Rohwer and Edwards 2002).”
Use of bacteriophages to reduce Salmonella in chicken skin in comparison with chemical agents (2013, background): “…offer a number of desired properties such as speci ﬁ city for target bacteria, inability to infect human cells, capacity for self-replication and self-limiting, and ubiquitous presence in nature, that makes them excellent tools for food safety purposes (Mahony et al., 2011; Rohwer & Edwards, 2002).”
Viruses in aquatic ecosystems: important advancements of the last 20 years and prospects for the future in the field of microbial oceanography and limnology (2010, background): “A mean value of 10(7) virusml is equivalent to about 10(30) viruses in aquatic ecosystems, or roughly 90% of the total abundance of planktonic particles [2,38], but it corresponds to 510% of the carbon biomass because of the small size of viruses.”
Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities (2005, background): “The case of viral phylogeny is more complex, firstly, because it is not clear that all viruses are related by a tree, and, secondly, because viral taxonomy has traditionally not been based on molecular sequence data, though the Phage Proteomic Tree [59] represents a step in the direction of sequence”
Uncovering Earth’s virome (2016, background): “L21-Syr-AB, (6) molybdate ABC transporter in Desulfomicrobium thermophilum, (7) ABC transporter involved in multi-copper enzyme maturation in Desulfovibrio alkalitolerans; and (8) likely antibiotic resistance cassette in Geobacter soli.”
ACLAME: A CLAssification of Mobile genetic Elements, update 2010 (2009, methodology): “Capturing lateral gene transfer events, the mosaicism and genome rearrangement events observed in MGE populations and inferring evolutionary links between MGEs requires novel approaches distinct from the traditional tree-like based methods (21).”