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 8

System / cell line: prediction ✕ Assay: dimensionality ✕ Clear

Improving genomic prediction accuracy for methane emission and feed efficiency in sheep: integrating rumen microbial PCA with host genomic variation using neural network GBLUP (NN-GBLUP).

PMID 40676527 · PMC12273308 · Genetics, selection, evolution : GSE · 2025 · 6 claims · 8 setups

Has reproduction · 85

PCA effectively reduces the dimensionality of high-dimensional RMC data while retaining essential biological information.

sheep rumen rmc genomic rumen snp
Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

PMID 40871599 · PMC12388828 · Molecules (Basel, Switzerland) · 2025 · 8 claims · 8 setups

Has reproduction · 87

TrioFold integrates base-pairing clues from thermodynamic- and DL-based methods via ensemble learning and a convolutional block attention mechanism to enhance RSS prediction generalizability.

testseta bprna-new ts-inter individual jaccard pca ensemble
scArchon: a scalable benchmarking framework for assessing single-cell perturbation models.

PMID 42121287 · PMC13162514 · Genome biology · 2026 · 8 claims · 8 setups

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scArchon is a reproducible, modular, Snakemake-based benchmarking platform that evaluates perturbation response prediction tools in a standardized, containerized, extensible manner.

pbmcs epithelial liver glioblastoma scrna-seq gene dimensionality
Machine learning-predicted chromatin organization landscape across pediatric tumors.

PMID 41904260 · PMC13039956 · Scientific reports · 2026 · 8 claims · 5 setups

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SuPreMo-Akita (built on the Akita CNN) enables systematic in silico prediction of somatic SV effects on 3D genome folding across large SV cohorts where experimental testing is infeasible

somatic per-sample tumor paired mutagenesis dimensionality h3k27ac
scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

PMID 41507436 · PMC12859067 · Communications biology · 2026 · 7 claims · 7 setups

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scXDR outperforms seven methods that transfer drug response information from bulk RNA-seq to single-cell data, across all four evaluated scenarios

single-cell scrna-seq scxdr gse117872 heterogeneous benchmarking type
Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy.

PMID 41820396 · PMC13121706 · Nature communications · 2026 · 8 claims · 7 setups

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TRIM, a conditional multi-modal variational autoencoder integrating paired scRNAseq and scTCRseq data, predicts T cell clonality and transcriptional states at unmeasured tissue sites/timepoints.

hnscc colorectal pan-cancer tcr paired umap convolutional
Retentive Network promotes efficient RNA language modeling of long sequences.

PMID 41814064 · PMC13111708 · Communications biology · 2026 · 8 claims · 6 setups

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RNAret, a RetNet-based RNA language model with O(n) complexity, achieves training parallelism and low computational overhead while processing long RNA sequences

million rnacentral mirtarraw rnastralign self-supervised t-sne mirna-mrna
Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings.

PMID 39039281 · PMC11319204 · Nature genetics · 2024 · 6 claims · 5 setups

Has reproduction · 87

A structured multidisciplinary exome sequencing framework established molecular genetic diagnoses in 32% of patients with suspected ultrarare disorders, comprising 370 distinct molecular causes.

patients exome deep computer-assisted

Experiments

Improving genomic prediction accuracy for methane emission and feed efficiency in sheep: integrating rumen microbial PCA with host genomic variation using neural network GBLUP (NN-GBLUP).

Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.

scArchon: a scalable benchmarking framework for assessing single-cell perturbation models.

Machine learning-predicted chromatin organization landscape across pediatric tumors.

scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy.

Retentive Network promotes efficient RNA language modeling of long sequences.

Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings.