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).

• 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

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  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

• Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.

  PMID 41507908 · PMC12879358 · Lipids in health and disease · 2026 · 8 claims · 8 setups

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  Early hepatocyte-specific APA remodeling, characterized by 3' UTR lengthening of metabolism-related genes (especially LPGAT1), occurs in MASLD and is established before fibrosis progression

  liver hepg2 293t serum bulk single-cell oil

• EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

  PMID 41527854 · PMC12796812 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  EpiXFormer achieves high accuracy (mean AUROC ~0.99) predicting binding sites of both TFs and non-sequence-specific DBPs across 199 DBP-cell type pairs

  dbps tfs common ctcf deep comparative feature-ablation

• Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

  PMID 24830797 · PMC4022483 · PLoS computational biology · 2014 · 8 claims · 8 setups

  Has reproduction · 75

  A convolved Gaussian process model of pol-II occupancy across gene segments captures the transcription wave and yields estimates of transcription speed and promoter-proximal pol-II activity.

  mcf7 promoter gene signals pol-ii clustering transcription

• Single-immunocyte transcriptomics reveal the role of natural killer cell-dependent exogenous antigen presentation in ankylosing spondylitis severity.

  PMID 41593306 · PMC12868835 · Experimental & molecular medicine · 2026 · 8 claims · 8 setups

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  Innate antibacterial defense functions are generally enhanced in most cell types at AS onset and are negatively associated with AS severity

  pbmcs gwas pbmc-derived cd4+ single-cell bulk mendelian

• Oxidative stress-associated genes TPPP3 and VEGFA in COPD revealed by bulk and single-cell sequencing analysis.

  PMID 41620539 · PMC12916760 · Scientific reports · 2026 · 8 claims · 9 setups

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  76 overlapping genes were identified between COPD-associated DEGs and oxidative stress-related genes.

  lung genecards differentially bronchial bulk database functional

• Development and validation of an oxidative phosphorylation based prognostic model revealing tumor progression and immune microenvironment in lung adenocarcinoma.

  PMID 41670771 · PMC12996521 · Discover oncology · 2026 · 8 claims · 8 setups

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  OXPHOS activity is significantly elevated in LUAD tumor tissue compared to adjacent normal tissue

  tcga-luad geo lung single-cell bulk ssgsea cibersort

• HRCHY-CytoCommunity identifies hierarchical tissue organization in cell-type spatial maps.

  PMID 41764165 · PMC13065825 · Nature communications · 2026 · 8 claims · 5 setups

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  HRCHY-CytoCommunity is an end-to-end graph neural network framework that jointly identifies multi-level (coarse tissue compartment and fine cellular neighborhood) tissue structures from cell-type spatial maps using differentiable graph pooling, adaptive edge pruning, and consistency/balance regularization.

  healthy colorectal simulated breast codex visium merfish

• Computational identification of transcriptional regulatory elements in DNA sequence.

  PMID 16855295 · PMC1524905 · Nucleic acids research · 2006 · 8 claims · 3 setups

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  Weight matrix (PWM/PSSM) models of TF binding sites are grounded in biophysical theory of protein-DNA interactions, with position weights corresponding to log-odds contributions to binding free energy

  saccharomyces generic pwm-based pwm

• Immersive virtual environment technology: a promising tool for future social and behavioral genomics research and practice.

  PMID 20183376 · PMC2829714 · Health communication · 2009 · 8 claims · 4 setups

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  IVET allows researchers to simultaneously maintain high experimental control and high mundane realism, unlike traditional research settings where these trade off against each other.

  participants students ivet virtual ivet cybersickness

• Using multiple alignments to improve seeded local alignment algorithms.

  PMID 16100379 · PMC1185574 · Nucleic acids research · 2005 · 8 claims · 2 setups

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  Using information implicit in a multiple alignment to dynamically build a spaced-seed index weighted toward promising regions increases sensitivity of local alignment search compared to indexing a sequence alone

  alignment query leave-one-species-out seeded

• TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.

  PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups

  Has reproduction · 89

  TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency

  melanogaster simulated long-read whole-genome genome

• SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis.

  PMID 15980517 · PMC1160189 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  SNPAnalyzer is an integrated web-based workbench that performs four statistical SNP analyses (Hardy-Weinberg equilibrium, haplotype estimation, linkage disequilibrium, and QTL analysis) in one common computational environment.

  african simulated hardy-weinberg haplotype linkage

• Regulation of P2X2 receptors by the neuronal calcium sensor VILIP1.

  PMID 18922787 · PMC3523710 · Science signaling · 2008 · 8 claims · 8 setups

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  VILIP1 was identified via a proteomic (GST pull-down) approach as a protein interacting with the P2X2 receptor C-terminal tail

  brain hek gst co-immunoprecipitation immunocytochemistry

• Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

  PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

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  ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

  paralogous human-mouse duplicated comparative ortholog binomial