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DOME Copilot: Making transparency and reproducibility for artificial intelligence methods simple

Farrell, G.; Attafi, O. A.; Fragkouli, S.-C.; Heredia, I.; Fernandez Tobias, S.; Harrison, M.; Hermjakob, H.; Jeffryes, M.; Obregon Ruiz, M.; Pearce, M.; Pechlivanis, N.; Lopez Garcia, A.; Psomopoulos, F.; Tosatto, S. C. E.

2026-04-19 bioinformatics
10.64898/2026.04.16.718888 bioRxiv
Show abstract

Unprecedented breakthroughs are being made in life science research through the application of artificial intelligence (AI). However, adherence to method reporting guidelines is necessary to support their reusability and reproducibility. The DOME Copilot solution extracts structured reports of AI methods using a large language model to help interpret manuscripts. It is a fast and efficient resource capable of scaling to annotate the corpus of global AI literature, unlocking value and trust in published methods.

Matching journals

The top 11 journals account for 50% of the predicted probability mass.

1
Nucleic Acids Research
◐ 1128 papers in training set
Top 2%
8.4%
2
Bioinformatics
◐ 1061 papers in training set
Top 4%
6.8%
3
Nature Communications
○ 4913 papers in training set
Top 28%
6.4%
4
PLOS ONE
● 4510 papers in training set
Top 31%
4.9%
5
GigaScience
◐ 172 papers in training set
Top 0.3%
4.9%
6
Scientific Data
○ 174 papers in training set
Top 0.3%
4.9%
7
Genome Biology
○ 555 papers in training set
Top 2%
3.6%
8
Nature Biotechnology
○ 147 papers in training set
Top 2%
3.6%
9
eLife
● 5422 papers in training set
Top 29%
3.1%
10
Journal of Molecular Biology
○ 217 papers in training set
Top 0.8%
3.1%
11
Nature Methods
○ 336 papers in training set
Top 3%
2.9%
50% of probability mass above
12
BMC Bioinformatics
○ 383 papers in training set
Top 3%
2.9%
13
PLOS Biology
● 408 papers in training set
Top 5%
2.7%
14
Nature
○ 575 papers in training set
Top 8%
2.7%
15
iScience
○ 1063 papers in training set
Top 10%
2.1%
16
Cell Systems
○ 167 papers in training set
Top 6%
1.9%
17
NAR Genomics and Bioinformatics
◐ 214 papers in training set
Top 2%
1.8%
18
Scientific Reports
○ 3102 papers in training set
Top 58%
1.7%
19
Molecular Systems Biology
○ 142 papers in training set
Top 0.6%
1.7%
20
Proceedings of the National Academy of Sciences
● 2130 papers in training set
Top 36%
1.3%
21
Bioinformatics Advances
◐ 184 papers in training set
Top 4%
1.2%
22
Genomics, Proteomics & Bioinformatics
◐ 171 papers in training set
Top 4%
1.2%
23
Nature Genetics
○ 240 papers in training set
Top 6%
1.1%
24
Computational and Structural Biotechnology Journal
● 216 papers in training set
Top 7%
1.0%
25
Patterns
○ 70 papers in training set
Top 2%
1.0%
26
Genome Medicine
○ 154 papers in training set
Top 6%
1.0%
27
Briefings in Bioinformatics
◐ 326 papers in training set
Top 6%
0.9%
28
Communications Biology
○ 886 papers in training set
Top 19%
0.9%
29
PLOS Computational Biology
● 1633 papers in training set
Top 23%
0.8%
30
Database
◐ 51 papers in training set
Top 0.8%
0.8%