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).

• ScLRTC: imputation for single-cell RNA-seq data via low-rank tensor completion.

  PMID 34844559 · PMC8628418 · BMC genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  scLRTC imputes dropout entries closest to the original expression values on simulated datasets, outperforming other state-of-the-art methods by SSE and PCC.

  usoskin pollen zeisel yan scrna-seq umap masking

• Evaluating imputation methods for accurate estimation of cell population fractions in single-cell RNA sequencing.

  PMID 41503159 · PMC12770975 · NAR genomics and bioinformatics · 2026 · 8 claims · 6 setups

  Full-text index only

  Eight prominent imputation methods (MAGIC, SAVER, scVI, DCA, scBiG, kNN-smoothing, scImpute, ALRA) were systematically evaluated for their ability to recover the true non-zero expression fraction using simulated and real-world scRNA-seq data

  basal tracheal airway k562 simulated scrna-seq imputation

• scGACL: a generative adversarial network with multi-scale contrastive learning for accurate single-cell RNA sequencing imputation.

  PMID 41632596 · PMC12866930 · Briefings in bioinformatics · 2026 · 8 claims · 6 setups

  Full-text index only

  scGACL, a GAN integrated with multi-scale contrastive learning, is proposed to overcome the over-smoothing problem in scRNA-seq imputation

  simulated real-world scrna-seq scrna-seq clustering gene

• ICE: robust detection of cellular senescence from weak single-cell signatures using imputation-based marker refinement.

  PMID 41668152 · PMC12990438 · Genome biology · 2026 · 8 claims · 7 setups

  Full-text index only

  Senescence-associated marker genes show weak, non-specific expression across human tissues and cell types compared to canonical tissue/cell-type markers

  tissues pancreas pancreatic brain bulk scrna-seq train

• Bridging unpaired single-cell multimodal data for integrative analyses with SuperMap.

  PMID 41650244 · PMC12890892 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 7 setups

  Full-text index only

  SuperMap learns cross-modal feature mappings directly from unpaired multimodal data without requiring paired training data

  pbmc bone skin embryos scrna-seq scnmt-seq asap-seq

• Neural network-assisted RNA velocity imputation for empowering transcript dynamics-based analyses.

  PMID 41736867 · PMC12927306 · iScience · 2026 · 8 claims · 8 setups

  Full-text index only

  NARVI, a deep neural network trained on expression-velocity relationships of passed genes, can impute RNA velocity for dropped genes that conventional tools (e.g., scVelo, UniTVelo) fail to calculate

  hematopoietic lung erythroid bone scrna-seq cross-validation

• Spatial information matters: are traditional imputation methods effective for spatial transcriptomics data?

  PMID 41627342 · PMC12862982 · Briefings in bioinformatics · 2026 · 7 claims · 3 setups

  Has reproduction · 89

  No single existing SOTA imputation method consistently performs well across newer SRT platforms/datasets

  datasets srt same computational proposed

• Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits.

  PMID 33461502 · PMC7812657 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 5 setups

  Has reproduction · 90

  Gene expression, exon expression, and intron excision ratio (splicing) molecular phenotypes are significantly heritable in sheep liver and muscle

  liver sheep sequencing snp heritability

• Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.

  PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 6 claims · 8 setups

  Has reproduction · 78

  CIBERSORTx can combine scRNA-seq-derived signature matrices with bulk RNA-seq data to estimate proportions of 11 TIL subsets in HCC tumor and normal tissue

  tcga degs cd4-gzma prognostic scrna-seq cibersortx differential

• Leveraging RNA-seq deconvolution to improve complex in vitro model characterization.

  PMID 40701251 · PMC12391696 · The Journal of biological chemistry · 2025 · 8 claims · 6 setups

  Has reproduction · 67

  RNA-seq deconvolution can predict cell type proportions from bulk RNA-seq using scRNA-seq references, offering a useful characterization tool for CIVMs where single-cell methods are impractical

  intestine rodent duodenal neonatal bulk scrna-seq marker

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

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

  Full-text index only

  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

• COVID-19 vaccination atlas using an integrative systems vaccinology approach.

  PMID 40456760 · PMC12130191 · NPJ vaccines · 2025 · 8 claims · 6 setups

  Has reproduction · 69

  mRNA vaccines induce transient but strong immune responses after booster doses

  pbmcs immune pbmc bulk gene principal

• Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

  PMID 41029822 · PMC12486589 · Journal of translational medicine · 2025 · 8 claims · 6 setups

  Has reproduction · 67

  The negative binomial distribution best fits fRNA-seq transcript counts, with little evidence supporting zero-inflated extensions

  compendium ffpe simulated frna-seq statistical bulk integrity

• VISTA uncovers missing gene expression and spatial-induced information for spatial transcriptomic data analysis.

  PMID 41507434 · PMC12891734 · Communications biology · 2026 · 8 claims · 6 setups

  Full-text index only

  VISTA predicts unmeasured gene expression in subcellular spatial transcriptomic data by integrating scRNA-seq and SST through variational inference and geometric deep learning with built-in uncertainty quantification

  brain breast embryo muscle imaging-based sequencing spot-based