Community structure and metabolism through reconstruction of microbial genomes from the environment

By Gene W. Tyson, Jarrod Chapman, Philip Hugenholtz, Eric E. Allen, Rachna J. Ram, Paul Richardson, Victor V. Solovyev, Edward M. Rubin, D. Rokhsar, Jillian F. Banfield. Nature, 2004

2,363 citations recorded by the source corpus.

Subfields: Biomedical Engineering, Environmental Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7fb5f1d5710ec5060beb8cff53c3baa8196eb4c6

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Citations in the corpus

An ORFome assembly approach to metagenomics sequences analysis. (2008, background): “In the second project, a handful of genomes of bacteria 9 then, many more metagenomics projects have been conducted, involving broadened applications from ecology and environmental sciences to chemical industry 10 and human health, e.g., the human gut microbiome projects 11 , 12 .”
Next-generation DNA sequencing methods. (2008, background): “Several early metagenomic studies utilized DNA sequence sampling by capillary sequencing to investigate an acidophilic biofilm (49), an acid mine site (12) and the Sargasso Sea (52).”
Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes (2015, positive): “Sequencing has become an indispensible tool in modern microbiology, dramatically changing the resolution and speed of studies of biodiversity [1], evolution [2-6], and molecular biology [7], and improving pathogen surveillance [8] and clinical diagnostics [9,10].”
Metagenomics: Application of Genomics to Uncultured Microorganisms (2004, background): “The recent monumental sequencing efforts, which include reconstruction of the genomes of uncultured organisms in a community in acid mine drainage (141) and the Sargasso Sea (142), illustrate the power of large-scale sequencing efforts to enrich our understanding of uncultured communities.”
Interactive metagenomic visualization in a Web browser (2011, methodology): “All three programs were used to visualize the famous metagenome of an acid mine drainage biofilm [21].”
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes (2013, background): “Tracking and visualization of paired-end connections between scaffolds [10].”
Exploring the Vast Diversity of Marine Viruses (2007, background): “…to previously described sequences (Breitbart et al., 2002, 2004; Angly et al., 2006; Culley et al., 2006), as opposed to ~ 10% for cellular metagenomic surveys (Tyson et al., 2004; Venter et al., 2004), suggesting that we have only begun to scratch the surface of marine viral sequence diversity.”
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2020, background): “Since early studies of environmental and host-associated microbial communities (Gill et al., 2006; Tyson et al., 2004; Venter et al., 2004) , it has been clear that many aspects of intercellular and inter-species signaling, short-and long-term evolution, and regulatory programs are exercised by…”
Linking pangenomes and metagenomes: the Prochlorococcus metapangenome (2018, background): “…bioactive molecules ( Lorenz & Eck, 2005 ; Thies et al., 2016 ), investigate the functional potential of ecosystems ( Tringe et al., 2005 ; Al-Amoudi et al., 2016 ), and access the genomic context of uncultivated microorganisms ( Tyson et al., 2004 ; Haroon et al., 2016 ; Delmont et al., 2017 ).”