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).

• Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

  PMID 35012625 · PMC8743438 · Genome biology · 2022 · 8 claims · 9 setups

  Has reproduction · 68

  GENEVA (Gene Expression Variance Analysis) is a semi-automated framework that mines large-scale public RNA-seq datasets to identify conditions associated with a gene's expression variance

  gtex genetic lncap heart rna-seq meta-analysis electronic

• Evaluating the Utilities of Foundation Models in Single-Cell Data Analysis.

  PMID 41869863 · PMC13170260 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  Among ten/eleven evaluated single-cell FMs, scGPT, Geneformer, and CellFM are the top models considering both performance and user accessibility

  scrna-seq unpaired single-cell scgpt batch multi-omic cell-type

• ASTROREPOMICS: A curated transcriptomic database for reproductive biology in space.

  PMID 41940322 · PMC13049440 · iScience · 2026 · 8 claims · 6 setups

  Full-text index only

  ASTROREPOMICS integrates 17 rigorously normalized and batch-corrected transcriptomic datasets spanning multiple species and reproductive tissues

  pooled mus rattus pca-based combat differential

• Integrating and mapping single-cell transcriptomics across the entire gene expression space.

  PMID 42059480 · PMC13130072 · Briefings in bioinformatics · 2026 · 8 claims · 1 setups

  Full-text index only

  scGES is a deep learning framework that corrects batch effects across the entire gene expression space by leveraging information from both HVGs and LVGs

  real scrna-seq

• Embeddings from language models are good learners for single-cell data analysis.

  PMID 41726097 · PMC12921509 · Patterns (New York, N.Y.) · 2026 · 8 claims · 8 setups

  Full-text index only

  scELMo combines LLM-derived embeddings of gene and cell metadata with raw single-cell expression data via matrix operations to generate cell embeddings without pretraining a new model

  scrna-seq multi-batch diseased perturbation clustering batch cell-type

• MUUMI: an R package for statistical and network-based meta-analysis for multi-omics data integration.

  PMID 41634555 · PMC12955011 · BMC bioinformatics · 2026 · 8 claims · 5 setups

  Full-text index only

  MUUMI unifies statistical meta-analysis and network-based omics data integration within a single analytical R package framework

  lung integrated ranked thp-1 sequencing microarray statistical

• scDecorr: feature decorrelation based representation learning enables self-supervised alignment of multiple single-cell experiments.

  PMID 42056283 · PMC13128840 · Scientific reports · 2026 · 7 claims · 1 setups

  Full-text index only

  scDecorr learns robust cell representations of unlabelled single-cell experiments in a negative-sample-free self-supervised fashion using feature decorrelation

  datasets scrna-seq

• Indirect genomic effects on survival from gene expression data.

  PMID 18358079 · PMC2397510 · Genome biology · 2008 · 7 claims · 6 setups

  Full-text index only

  A novel methodology (dynamic path analysis combined with additive hazard survival regression) can detect and quantify indirect effects of gene expression on survival mediated through transcription factor target genes.

  dutch uppsala dlbcl gene gene literature permutation

• Size matters: just how big is BIG?: Quantifying realistic sample size requirements for human genome epidemiology.

  PMID 18676414 · PMC2639365 · International journal of epidemiology · 2009 · 7 claims · 2 setups

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  Conventional power calculations for case-control studies disregard analytic complexity (e.g. clinical assessment errors, unmeasured aetiological determinants) and can seriously underestimate true sample size requirements

  simulated simulation-based simulated

• Curation of over 10 000 transcriptomic studies to enable data reuse.

  PMID 33599246 · PMC7904053 · Database : the journal of biological databases and curation · 2021 · 8 claims · 6 setups

  Has reproduction · 80

  Gemma is a curated database and bioinformatics system that addresses metadata, probe annotation, and expression data inconsistencies in GEO to enable transcriptomic data reuse

  microarray curated geo microarray rna-sequencing probe-to-gene

• An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.

  PMID 36352408 · PMC9648005 · BMC biology · 2022 · 7 claims · 5 setups

  Has reproduction · 84

  A signal transduction/gene regulatory network model of the articular chondrocyte was built combining knowledge-based curation and data-driven (machine learning) network inference

  osteoarthritic articular chondrocyte microarray computational high-throughput

• RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations.

  PMID 41222189 · PMC12857227 · GigaScience · 2026 · 8 claims · 8 setups

  Full-text index only

  RNA-SeqEZPZ is the first open-source tool offering a point-and-click interface with interactive plots, spanning raw FASTQ reads through differential gene and pathway analysis.

  generic paired-end aligned gene bulk adapter read

• DHODH links mitochondrial bioenergetics, one-carbon metabolism, and DNA repair to sustain aggressive prostate adenocarcinoma.

  PMID 41612476 · PMC12930642 · Cell communication and signaling : CCS · 2026 · 8 claims · 8 setups

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  DHODH is markedly overexpressed in malignant prostate epithelial cells and abundant in tumors

  tcga-prad gse141445 22rv1 bulk single-cell lentiviral

• RADAR: differential analysis of MeRIP-seq data with a random effect model.

  PMID 31870409 · PMC6927177 · Genome biology · 2019 · 8 claims · 6 setups

  Has reproduction · 10

  RADAR is a novel analytical tool for differential methylation analysis of MeRIP-seq data combining gene-level INPUT normalization with a Poisson random effect model.

  simulated fallopian pancreatic liver merip-seq m6a-merip-seq pca

• Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder.

  PMID 32825264 · PMC7563725 · Biomolecules · 2020 · 6 claims · 7 setups

  Has reproduction · 80

  Combining WGCNA hub genes and VAE 10-dimensional representation as features for an SVM classifier achieves high accuracy in predicting CRC

  colorectal same combined meturquoise microarray differential batch

• Comprehensive comparison of gene expression diversity among a variety of human stem cells.

  PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 71

  Tissue origin has a stronger influence on gene expression in iPSCs than in other stem cell types

  escs stem batch-corrected degs bulk batch dimensionality

• F-SNP: computationally predicted functional SNPs for disease association studies.

  PMID 17986460 · PMC2238878 · Nucleic acids research · 2008 · 6 claims · 8 setups

  Full-text index only

  F-SNP is a database integrating functional effect predictions for SNPs from 16 bioinformatics tools/databases across four categories: splicing, transcription, translation, and post-translation

  genome protein-coding genomic genome-wide non-synonymous exonic nonsense

• Combining evidence of preferential gene-tissue relationships from multiple sources.

  PMID 23950964 · PMC3741196 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 53

  A high-level integration approach combining three methods across four human microarray datasets, merged by consensus voting and a rule-based inner/total score, predicts preferentially expressed genes while reducing method- and study-specific bias.

  normal four microarray genes microarray computational bayes

• Context-specific regulatory genetic variation in MTOR dampens neutrophil-T cell crosstalk in pneumonia-associated sepsis.

  PMID 41741465 · PMC13057173 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  The MTOR eQTL variant rs4845987 has context-specific, opposite effects on MTOR expression: decreasing it in activated T cells and increasing it in neutrophils.

  blood bulk eqtl sepsis bulk cell-type colocalisation

• Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.

  PMID 34654806 · PMC8519947 · Nature communications · 2021 · 6 claims · 8 setups

  Has reproduction · 100

  A pathway-based super signature from on-treatment samples (PASS-ON) predicts anti-PD1 response with high accuracy (validation AUC 0.85-0.89, combined AUC 0.88) and outperforms existing signatures across all four datasets.

  metastatic pathway bulk gene elastic-net