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: validated ✕ Assay: cross-species ✕ Clear

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups

Full-text index only

Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters

orthologous randomized high-score promoters pssm-based comparative motif
CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

PMID 41498638 · PMC12948241 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

Full-text index only

CellPolaris is a unified computational framework performing TF-centered GRN construction, master TF identification, and TF perturbation simulation

bulk previously round paired transfer-learning cross-species
Predicting enhancers in mammalian genomes using supervised hidden Markov models.

PMID 30917778 · PMC6437899 · BMC bioinformatics · 2019 · 8 claims · 8 setups

Has reproduction · 70

eHMM predicts enhancers with high precision and recall comparable to state-of-the-art methods and consistently outperforms them in accuracy and resolution

esc atac-seq chip-seq cage
A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females.

PMID 35471187 · PMC9113746 · eLife · 2022 · 8 claims · 5 setups

Has reproduction · 73

Created Aegypti-Atlas, an online RNAseq resource covering Ae. aegypti body parts, gut regions, and a blood meal digestion time course

dissected five anterior midguts rnaseq rt-qpcr

Experiments

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

Predicting enhancers in mammalian genomes using supervised hidden Markov models.

A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females.