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: lines ✕ Assay: fine ✕ Clear

Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts.

PMID 41618434 · PMC12930932 · Genome biology · 2026 · 8 claims · 7 setups

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PEFT enables accurate transfer of Borzoi to new datasets while significantly reducing GPU memory and runtime compared to joint training or full fine-tuning

gtex encode wi-38 thp-1 bulk eqtl variant-flowfish
Community assessment of methods to deconvolve cellular composition from bulk gene expression.

PMID 39191725 · PMC11350143 · Nature communications · 2024 · 8 claims · 4 setups

Has reproduction · 63

Most deconvolution methods accurately predict coarse-grained immune/stromal cell populations from bulk expression.

admixtures cancer tumor bulk bulk admixture crowdsourced
ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

PMID 41592570 · PMC13069865 · Cell genomics · 2026 · 8 claims · 7 setups

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ChromBERT is pre-trained via masked reconstruction on the Cistrome-Human-6K dataset (6,391 cistromes, 991 transcription regulators) to learn genome-wide interaction syntax of transcription regulators

lines chromosome embryonic transcription chip-seq chromhmm hi-c
Cross-ancestry genome-wide association studies of liver function biomarkers uncover pleiotropic variants, systemic disease links and therapeutic targets.

PMID 41689074 · PMC13005531 · Genome medicine · 2026 · 8 claims · 8 setups

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5,507 lead signals (P<5x10^-9) were identified for seven LFQBs across ancestries, including 210 novel loci

hope biobank combined cross-ancestry gwas cross-ancestry functional-informed

Experiments

Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts.

Community assessment of methods to deconvolve cellular composition from bulk gene expression.

ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

Cross-ancestry genome-wide association studies of liver function biomarkers uncover pleiotropic variants, systemic disease links and therapeutic targets.