data_id
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biomedicine_7
|
Most of the highquality MAGs had a contig number <250 and ≥18 of the standard tRNAs (Supplementary Fig. 8b, c). Of the 1358 high-quality MAGs, 36 had the 5S, 16S, and 23S rRNA genes together with at least 18 tRNAs, and conformed to the MIMAG standards for the ‘high quality’ MAG set by the Genomic Standards Consortium [CITATION].
|
[
{
"citation": "Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731 (2017).",
"title": "Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea",
"url": "https://www.semanticscholar.org/paper/Minimum-information-about-a-single-amplified-genome-Bowers-Kyrpides/de6b66013fcebf03d997d28b384497a1d3733670"
}
] |
biomedicine_3
|
Rarefaction analysis suggested that the number of PIGC90 clusters approached a saturation point when the sample number reached 100, which is in line with previous estimates [CITATION].
|
[
{
"citation": "Xiao, L. et al. A reference gene catalogue of the pig gut microbiome. Nat. Microbiol. 1, 16161 (2016).",
"title": "A reference gene catalogue of the pig gut microbiome",
"url": "https://www.semanticscholar.org/paper/A-reference-gene-catalogue-of-the-pig-gut-Xiao-Estell%C3%A9/232db55ff77c0a9fb991a6660a75ea03bbe3c2b9"
}
] |
biomedicine_2
|
Reference genes as well as high-quality microbial genomes are essential resources for understanding the functional role of specific microbes and quantifying their abundance in the gut microbiome [CITATION].
|
[
{
"citation": "Kyrpides, N. C. et al. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol. 12, e1001920 (2014).",
"title": "Metagenomic species profiling using universal phylogenetic marker genes",
"url": "https://www.semanticscholar.org/paper/Metagenomic-species-profiling-using-universal-genes-Sunagawa-Mende/072965fe4db20d2a1ba9412722a038388a41b588"
}
] |
biomedicine_8
|
There are 2,866 single-cell genomes and 4,622 genomes reconstructed from metagenomes, which are already registered in the Genomes OnLine Database (GOLD) [CITATION].
|
[
{
"citation": "Reddy, T.B.K. et al. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res. 43, D1099–D1106 (2015).",
"title": "The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification",
"url": "https://www.semanticscholar.org/paper/The-Genomes-OnLine-Database-(GOLD)-v.5%3A-a-metadata-Reddy-Thomas/298decd07895b3d3775157949bdbdad926c8a192"
}
] |
biomedicine_5
|
The number of protein clusters in the PIGC90 was six-fold compared with PGC, which contained 3,460,040 complete genes from a total of 7,685,872 nonredundant genes from 287 pigs, and 2,847,252 complete protein clusters at 90% protein identity (defined as PGC90) [CITATION].
|
[
{
"citation": "Xiao, L. et al. A reference gene catalogue of the pig gut microbiome. Nat. Microbiol. 1, 16161 (2016).",
"title": "A reference gene catalogue of the pig gut microbiome",
"url": "https://www.semanticscholar.org/paper/A-reference-gene-catalogue-of-the-pig-gut-Xiao-Estell%C3%A9/232db55ff77c0a9fb991a6660a75ea03bbe3c2b9"
}
] |
biomedicine_6
|
This result suggests a significant difference in the relative abundances of the same bacterial species in different gut locations. For example, consistent with our previous report [CITATION].
|
[
{
"citation": "Yang, H. et al. Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness. Sci. Rep. 6, 27427 (2016).",
"title": "Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness",
"url": "https://www.semanticscholar.org/paper/Uncovering-the-composition-of-microbial-community-Yang-Huang/7087b91f94358ba0dc5e144c7e82bd0a44bc4a79"
}
] |
biomedicine_9
|
Assembly of microbial genomes from metagenomic sequence reads was pioneered in 2004 by Tyson et al. [CITATION].
|
[
{
"citation": "Tyson, G.W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43 (2004).",
"title": "Community structure and metabolism through reconstruction of microbial genomes from the environment",
"url": "https://www.semanticscholar.org/paper/Community-structure-and-metabolism-through-of-from-Tyson-Chapman/7fb5f1d5710ec5060beb8cff53c3baa8196eb4c6"
}
] |
biomedicine_4
|
A reference gene catalog of the pig gut microbiome has also been constructed using 287 fecal samples, containing 7.7 million nonredundant genes (named PGC in this study) [CITATION].
|
[
{
"citation": "Xiao, L. et al. A reference gene catalogue of the pig gut microbiome. Nat. Microbiol. 1, 16161 (2016).",
"title": "A reference gene catalogue of the pig gut microbiome",
"url": "https://www.semanticscholar.org/paper/A-reference-gene-catalogue-of-the-pig-gut-Xiao-Estell%C3%A9/232db55ff77c0a9fb991a6660a75ea03bbe3c2b9"
}
] |
biomedicine_0
|
Cancer is a major societal, public health, and economic problem in the 21st century, responsible for almost one in six deaths (16.8%) and one in four deaths (22.8%) from noncommunicable diseases (NCDs) worldwide. The disease causes three in 10 global premature deaths from NCDs (30.3% in those aged 30–69 years), and it is among the three leading causes of death in this age group in 177 of 183 countries [CITATION].
|
[
{
"citation": "Bray F, Laversanne M, Weiderpass E, Soerjomataram I. The ever‐ increasing importance of cancer as a leading cause of premature death worldwide. Cancer. 2021;127(16):3029‐3030. doi:10.1002/ cncr.33587",
"title": "The ever‐increasing importance of cancer as a leading cause of premature death worldwide",
"url": "https://www.semanticscholar.org/paper/The-ever%E2%80%90increasing-importance-of-cancer-as-a-cause-Bray-Laversanne/6dd9af4b95992551c77eeaf179581865aa61cfe1"
}
] |
biomedicine_1
|
In addition to being an important barrier to increasing life expectancy, cancer is associated with substantial societal and macroeconomic costs that vary in degree across cancer types, geography, and gender [CITATION].
|
[
{
"citation": "Chen S, Cao Z, Prettner K, et al. Estimates and projections of the global economic cost of 29 cancers in 204 countries and territories from 2020 to 2050. JAMA Oncol. 2023;9(4):465‐472. doi:10.1001/ jamaoncol.2022.7826",
"title": "Estimates and Projections of the Global Economic Cost of 29 Cancers in 204 Countries and Territories From 2020 to 2050",
"url": "https://www.semanticscholar.org/paper/Estimates-and-Projections-of-the-Global-Economic-of-Chen-Cao/92359c698a05444a31e2cfecfef5e662b4b497d4"
}
] |
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