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DNA-sequence and epigenomic determinants of local rates of transcription elongation

Liu, L.; Zhao, Y.; Siepel, A.

2023-12-23 genomics
10.1101/2023.12.21.572932 bioRxiv

Matching journals

The top 3 journals account for 50% of the predicted probability mass.

1
Genome Biology
○ 637 papers in training set
Top 0.1%
34.3%
Similar papers in this journal
2
Nature Communications
○ 5641 papers in training set
Top 15%
11.9%
Similar papers in this journal
3
PLOS Computational Biology
● 1863 papers in training set
Top 4%
9.8%
Similar papers in this journal
50% of probability mass above
4
Genome Research
● 468 papers in training set
Top 0.6%
7.9%
Similar papers in this journal
5
Nature Methods
○ 385 papers in training set
Top 2%
5.5%
Similar papers in this journal
6
Nucleic Acids Research
◐ 1281 papers in training set
Top 4%
4.8%
7
eLife
● 5828 papers in training set
Top 39%
2.8%
8
PLOS Genetics
● 862 papers in training set
Top 5%
2.8%
9
Nature Genetics
○ 286 papers in training set
Top 3%
1.9%
10
Nature Biotechnology
○ 172 papers in training set
Top 3%
1.5%
11
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 30%
1.5%
12
Molecular Biology and Evolution
◐ 542 papers in training set
Top 4%
1.1%
13
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 3%
1.1%
14
GENETICS
◐ 483 papers in training set
Top 4%
1.0%
15
Cell Genomics
○ 172 papers in training set
Top 4%
0.8%
16
Nature Structural & Molecular Biology
236 papers in training set
Top 3%
0.8%
17
Communications Biology
○ 993 papers in training set
Top 35%
0.6%
18
Cell Systems
○ 201 papers in training set
Top 5%
0.6%
19
Nature Computational Science
○ 55 papers in training set
Top 2%
0.6%
20
Bioinformatics
◐ 1204 papers in training set
Top 9%
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.