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Articles by Patrick S. G
Methods for safely sharing dual-use genetic data
ORIGINAL RESEARCH article Front. Microbiol. Sec. Systems Microbiology This article is part of the Research TopicArtificial Intelligence and the Future of BiosecurityView all articles Methods for safely sharing dual-use genetic data Provisionally accepted 1GeneInfoSec Inc., Boulder, United States 2Los Alamos National Laboratory, Los Alamos, United States The final, formatted version of the article will be published soon.
Combining Compositional Data Sets Introduces Error in Covariance Network Reconstruction
Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques.
The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research
Microbiome, Aug 2023 As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae.
Metabolic versatility of Caldarchaeales from geothermal features of Hawai’i and Chile as revealed by five metagenome-assembled genomes
Introduction The archaeal candidate phylum Aigarchaeota belongs to the TACK superphylum, which initially consisted of the Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota phyla (Guy and Ettema, 2011; Adam et al., 2017). The TACK superphylum now comprises several additional phyla discovered since 2011, including Bathyarchaeota (Meng et al., 2014), Verstraetearchaeota (Vanwonterghem et al., 2016), Geothermarchaeota (Jungbluth et al., 2017), and Nezhaarchaeota (Wang et al., 2019).
Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles
Introduction Volcanic features in Hawai‘i, such as lava caves and fumaroles, are often oligotrophic, yet they host unexpectedly high microbial diversity (Northup and Lavoie, 2015; Riquelme et al., 2015; Wall et al., 2015). Lava caves and tubes form when the surface of flowing molten lava cools, crust over, and the molten lava beneath continues to flow, leaving tube-like structures or pockets behind that to form caves.
The National Microbiome Data Collaborative: enabling microbiome science - Nature Reviews Microbiology
To harness the potential of microbiome science across the broad range of relevant disciplines, new approaches to data infrastructure and transdisciplinary collaboration are necessary. The National Microbiome Data Collaborative (NMDC) is a new initiative to support microbiome data exploration and discovery through a collaborative, integrative data science ecosystem.
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