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datadrivenhypothesis.org: A resource for metabolic gene discovery through integrated pathway co-essentiality mapping

Hirschey, M.; Castellano-Escuder, P.; Bradley, J.

2026-02-12 systems biology
10.64898/2026.02.11.705287 bioRxiv
Show abstract

datadrivenhypothesis.org (DDH) integrates gene dependency, expression, literature data, and beyond from [~]20,000 human genes to reveal hidden metabolic connections. Through pathway-level co-essentiality analysis with novelty scoring, DDH uncovered unexpected links including Complex II coupled to purine nucleotide biosynthesis. This broad platform offers intuitive tools for hypothesis generation via gene queries, pathway analysis, and network visualization, plus publication-ready downloads. Automated updates make DDH a dynamic resource, bridging genes with unknown function to actionable metabolic insights.

Matching journals

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

1
Molecular Systems Biology
○ 162 papers in training set
Top 0.1%
21.3%
Similar papers in this journal
2
Nucleic Acids Research
◐ 1281 papers in training set
Top 2%
9.4%
Similar papers in this journal
3
Molecular Cell
○ 350 papers in training set
Top 1%
6.1%
Similar papers in this journal
4
npj Systems Biology and Applications
○ 125 papers in training set
Top 0.3%
5.4%
Similar papers in this journal
5
Nature Communications
○ 5641 papers in training set
Top 28%
5.3%
Similar papers in this journal
6
Cell Systems
○ 201 papers in training set
Top 1.0%
4.7%
50% of probability mass above
7
Nature Methods
○ 385 papers in training set
Top 3%
3.4%
8
Nature Biotechnology
○ 172 papers in training set
Top 1%
3.1%
9
Genome Biology
○ 637 papers in training set
Top 4%
2.7%
10
Cell Reports Methods
○ 165 papers in training set
Top 0.8%
2.6%
11
Nature Metabolism
○ 69 papers in training set
Top 0.8%
2.6%
12
eLife
● 5828 papers in training set
Top 44%
2.3%
13
Cell
○ 431 papers in training set
Top 5%
2.3%
14
Bioinformatics
◐ 1204 papers in training set
Top 6%
2.1%
15
iScience
○ 1154 papers in training set
Top 19%
1.7%
16
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 3%
1.7%
17
Nature
○ 645 papers in training set
Top 7%
1.7%
18
Cell Reports
○ 1498 papers in training set
Top 19%
1.7%
19
PLOS Computational Biology
● 1863 papers in training set
Top 15%
1.6%
20
Bioinformatics Advances
◐ 203 papers in training set
Top 3%
1.5%
21
Cell Genomics
○ 172 papers in training set
Top 3%
1.3%
22
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 39%
1.0%
23
Nature Genetics
○ 286 papers in training set
Top 5%
0.9%
24
Patterns
○ 78 papers in training set
Top 3%
0.8%
25
Genome Medicine
○ 183 papers in training set
Top 5%
0.8%
26
Science Advances
● 1243 papers in training set
Top 32%
0.8%
27
Life Science Alliance
● 285 papers in training set
Top 8%
0.8%
28
Genome Research
● 468 papers in training set
Top 7%
0.8%
29
BMC Genomics
○ 406 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.