Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 4

System / cell line: pairs ✕ Assay: cis-regulatory ✕ Clear

CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data.

PMID 41734268 · PMC12987762 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

Full-text index only

CIRCE re-implements the Cicero co-accessibility algorithm in Python, producing near-identical results while running much faster and using far less memory

bmmc pbmc foetal cis-regulatory enhancer-promoter scalability
Shaken not stirred: a global research cocktail served in Hinxton.

PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups

Full-text index only

Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process

budding caenorhabditis drosophila escherichia two-color double chip-chip
Genome-wide identification and characterization of germin-like protein family in Brassica juncea reveals their role against biotic stress.

PMID 41327045 · PMC12763953 · BMC plant biology · 2025 · 8 claims · 7 setups

Has reproduction · 58

Genome-wide identification revealed 102 GLPs in B. juncea, 51 in B. nigra, and 48 in B. rapa

juncea promoter duplicated super genome-wide phylogenetic synteny
Genome- and Transcriptome-Wide Characterization of AP2/ERF Transcription Factor Superfamily Reveals Their Relevance in Stylosanthes scabra Vogel Under Water Deficit Stress.

PMID 41515103 · PMC12787715 · Plants (Basel, Switzerland) · 2026 · 8 claims · 8 setups

Full-text index only

295 AP2/ERF transcription factor genes were identified and classified in the S. scabra genome

scabra representative hmm rna-seq qpcr

Experiments

CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data.

Shaken not stirred: a global research cocktail served in Hinxton.

Genome-wide identification and characterization of germin-like protein family in Brassica juncea reveals their role against biotic stress.

Genome- and Transcriptome-Wide Characterization of AP2/ERF Transcription Factor Superfamily Reveals Their Relevance in Stylosanthes scabra Vogel Under Water Deficit Stress.