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: predicted ✕ Assay: stochastic ✕ Clear

Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage.

PMID 41779826 · PMC12959883 · eLife · 2026 · 8 claims · 5 setups

Full-text index only

DeepTX is an interpretable, scalable deep learning inference framework that links mechanistic transcription models to scRNA-seq data to infer genome-wide transcriptional burst kinetics

synthetic embryonic colorectal computational stochastic scrna-seq deep
Age Deceleration and Reversal Gene Patterns in Dauer Diapause.

PMID 41104926 · PMC12686545 · Aging cell · 2025 · 8 claims · 8 setups

Has reproduction · 88

Dauer arrest, regardless of duration, does not cause lasting functional decline in lifespan, brood size, or developmental resumption

daf-2 wild-type same dauer developmental lifespan brood
spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 8 setups

Has reproduction · 53

spliceJAC uses unspliced and spliced mRNA count matrices to construct cell state-specific gene-gene regulatory interaction (Jacobian) matrices from scRNA-seq data

bistable three-gene emt circuits simulation mixed-state grn
Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.

PMID 40990923 · PMC12687342 · Evolution; international journal of organic evolution · 2025 · 8 claims · 5 setups

Has reproduction · 64

The LWS opsin gene was identified in 13 species of caecilians spanning 8 of 10 recognized families

caecilian caecilia archival lws pcr eye histology

Experiments

Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage.

Age Deceleration and Reversal Gene Patterns in Dauer Diapause.

spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.