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Phylogeny and Metadata Network Database for Epidemiologic Surveillance

Stott, G. L.; Lyu, L.; Veytsel, G.; Kuo, J.; Lewis, R.; Brown, A.; Fujimoto, K.; Bahl, J.

2022-04-19 evolutionary biology
10.1101/2022.04.19.488067 bioRxiv
Show abstract

AO_SCPLOWBSTRACTC_SCPLOWThe ongoing SARS-CoV-2 pandemic has highlighted the difficulty in integrating disparate data sources for epidemiologic surveillance. To address this challenge, we have created a graph database to integrate phylogenetic trees, associated metadata, and community surveillance data for phylodynamic inference. As an example use case, we divided 22,713 SARS-CoV-2 samples into 5 groups, generated maximum likelihood trees, and inferred a potential transmission network from a forest of minimum spanning trees built on patristic distances between samples. We then used Cytoscape to visualize the resultant graphs.

Matching journals

The top 6 journals account for 50% of the predicted probability mass.

1
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Top 0.1%
15.3%
Similar papers in this journal
2
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12.9%
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○ 176 papers in training set
Top 0.7%
3.3%
50% of probability mass above
7
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Top 35%
3.2%
8
Molecular Biology and Evolution
◐ 542 papers in training set
Top 2%
2.8%
9
G3 Genes|Genomes|Genetics
◐ 351 papers in training set
Top 2%
2.5%
10
Ecology and Evolution
○ 267 papers in training set
Top 3%
2.4%
11
Viruses
○ 332 papers in training set
Top 2%
2.4%
12
PeerJ
◐ 308 papers in training set
Top 4%
2.2%
13
G3: Genes, Genomes, Genetics
◐ 252 papers in training set
Top 2%
2.2%
14
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○ 15 papers in training set
Top 0.1%
1.5%
15
Journal of Open Source Software
● 25 papers in training set
Top 0.2%
1.5%
16
Bioinformatics Advances
◐ 203 papers in training set
Top 3%
1.4%
17
Gigabyte
● 62 papers in training set
Top 0.8%
1.1%
18
Scientific Reports
○ 3612 papers in training set
Top 66%
1.1%
19
Genome Biology
○ 637 papers in training set
Top 8%
1.1%
20
Biology Open
● 156 papers in training set
Top 3%
1.1%
21
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○ 14 papers in training set
Top 0.1%
0.9%
22
Journal of Computational Biology
○ 48 papers in training set
Top 1.0%
0.9%
23
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○ 23 papers in training set
Top 0.4%
0.9%
24
BMC Genomics
○ 406 papers in training set
Top 7%
0.9%
25
Protein Science
○ 246 papers in training set
Top 3%
0.9%
26
PLOS Biology
● 486 papers in training set
Top 11%
0.9%
27
Virus Evolution
◐ 155 papers in training set
Top 1%
0.9%
28
Journal of Molecular Biology
○ 232 papers in training set
Top 4%
0.6%
29
mSphere
● 302 papers in training set
Top 7%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.