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Comparative genomic analysis of DNA motif frequency across the animal kingdom

DuFriend, D.; Valderrama, E.; Annor, E.; Rosler, C.; Davis, E.; Anthem, Y. L.; Velasquez, C.; Wheat, S.; Goelzer, M. H.; Goelzer, J. A.

2025-08-11 bioinformatics
10.1101/2025.08.10.669586 bioRxiv
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Withdrawal StatementThe authors have withdrawn this pre-print manuscript because of some inadvertent errors and inconclusive data discovered upon further review. Therefore, the authors do not wish this work to be cited as reference for research and review articles from other research groups. If you have any questions, please contact the corresponding author.

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The top 5 journals account for 50% of the predicted probability mass.

1
Genome Biology and Evolution
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6
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PLOS ONE
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Top 36%
3.2%
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Top 0.7%
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10
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Top 0.9%
2.8%
11
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Top 8%
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12
Scientific Reports
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1.7%
13
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Top 7%
1.7%
14
Current Biology
○ 665 papers in training set
Top 7%
1.4%
15
Molecular Ecology Resources
○ 171 papers in training set
Top 1%
1.3%
16
Nature Communications
○ 5641 papers in training set
Top 48%
1.3%
17
Frontiers in Genetics
○ 230 papers in training set
Top 4%
1.1%
18
F1000Research
○ 88 papers in training set
Top 2%
1.1%
19
BMC Evolutionary Biology
○ 18 papers in training set
Top 0.1%
1.1%
20
PeerJ
◐ 308 papers in training set
Top 9%
1.1%
21
Genomics
○ 64 papers in training set
Top 2%
0.8%
22
eLife
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Top 67%
0.8%
23
G3: Genes, Genomes, Genetics
◐ 252 papers in training set
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BMC Bioinformatics
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25
Mobile DNA
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26
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"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.