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 the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.

  PMID 18803882 · PMC2566316 · BMC genomics · 2008 · 8 claims · 5 setups

  Full-text index only

  About 20% of the 909,622 SNPs on the SNP Array 6.0 are monomorphic in the Japanese population

  genomic japanese reference snp concentration agarose

• HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD).

  PMID 37907883 · PMC10619225 · BMC medical genomics · 2023 · 6 claims · 4 setups

  Has reproduction · 67

  Removal of batch effects in reference scRNA-seq datasets (via Harmony-Symphony) benefits the task of cell composition deconvolution

  pbmc derived tcga-lihc scrna-seq simulated bulk

• Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

  PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 8 setups

  Has reproduction · 75

  CLAD exhibits specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages

  clad covid-19 million formalin-fixed single-cell single-nucleus integrated

• Cataloging coding sequence variations in human genome databases.

  PMID 18974781 · PMC2570488 · PloS one · 2008 · 8 claims · 7 setups

  Full-text index only

  A significant proportion of CVs overlap between HGMD and dbSNP (4.36% of HGMD CVs registered in dbSNP; 8.11% of dbSNP CVs registered in HGMD), warranting caution when interpreting phenotypic relevance of concurrent CVs.

  coding hapmap concurrent nssnps database hapmap amino

• VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data.

  PMID 37180100 · PMC10172660 · Frontiers in immunology · 2023 · 7 claims · 7 setups

  Has reproduction · 64

  VIGET is a web portal that lets users select vaccines/ImmPort studies, run differential gene expression analysis, and perform Reactome-based pathway enrichment and functional interaction network construction

  blood lists differentially individual differential pathway functional

• A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen.

  PMID 41505094 · PMC12781895 · Nucleic acids research · 2026 · 7 claims · 6 setups

  Has reproduction · 78

  MERLIN-P-TFA network inference on 18 curated public RNA-seq datasets produced a genome-wide GRN resource for A. fumigatus called GRAsp.

  aspergillus fumigatus bulk computational chip-seq-based

• Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.

  PMID 34675242 · PMC8531356 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 69

  Only 8 of 20 previously published COVID-19 scRNA-seq findings were reproducible across all relevant datasets in a standardized meta-analysis

  pbmc bronchoalveolar nasopharyngeal combined scrna-seq tcr bcr

• Tracing human genetic histories and natural selection with precise local ancestry inference.

  PMID 40379651 · PMC12084304 · Nature communications · 2025 · 7 claims · 7 setups

  Has reproduction · 76

  Orchestra, a two-stage LAI method combining a recombination-distance base layer with a deep learning (convolutional + attention) smoothing module, outperforms RFmix, FLARE and Gnomix in precision and recall across simulated admixture generations.

  1kgp-16pops independent simulated 1kgp simulated population-level local

• A four-gene signature from blood to exclude bacterial etiology of lower respiratory tract infection in adults.

  PMID 41285807 · PMC12644739 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 94

  A 4-gene signature (ITGB4, ITGA7, IFI27, FAM20A) derived from whole blood RNA-seq discriminates any bacterial from nonbacterial ARI with cross-validated AUC = 0.90

  hospitalized adults pediatric blood bulk rna-seq microarray

• Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

  PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 92

  Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.

  skeletal merged myogenic muscle scrnaseq batch-correction differential

• GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data.

  PMID 31110304 · PMC6527554 · Scientific reports · 2019 · 8 claims · 7 setups

  Has reproduction · 73

  GREIN is a web application providing user-friendly interfaces to manipulate, visualize, and analyze GEO RNA-seq data.

  mcf10a nde&dt hypoxia bulk correlation 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

• The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.

  PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 50

  Only two of seven published sepsis gene signatures (derived from adult/pediatric/geriatric cohorts) showed good concordance (>80% accuracy) when applied to infant sepsis, showing limited generalizability of non-infant signatures.

  blood merged deg microarray coconut pseudotime

• Celline: a flexible tool for one-step retrieval and integrative analysis of public single-cell RNA sequencing data.

  PMID 41458999 · PMC12738925 · Frontiers in bioinformatics · 2025 · 8 claims · 6 setups

  Has reproduction · 64

  Celline is a Python package that automates the full scRNA-seq workflow (retrieval, metadata extraction, preprocessing, cell-type annotation, batch correction, trajectory inference) via single-line commands.

  c57bl embryonic scrna-seq quality cell-type

• Exploring Gene Expression Patterns in Alzheimer's Disease Using a Human Microarray Data Meta-Analysis.

  PMID 41744654 · PMC12938635 · Biology · 2026 · 7 claims · 7 setups

  Has reproduction · 100

  A meta-analysis of eight microarray studies (10 sub-studies) produced a combined list of 4218 statistically significant DEGs between AD and healthy brain at an adjP cut-off of 0.001

  post-mortem combined sub-studies down-regulated microarray differential statistical

• Statistical challenges in preprocessing in microarray experiments in cancer.

  PMID 18829474 · PMC3529914 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 7 setups

  Full-text index only

  Choice of pre-processing method materially changes which features are found significantly associated with survival in the Beer et al. lung cancer microarray dataset

  lung beer individual outlier expression rank-covariance quality-control

• High-throughput crystallography for structural genomics.

  PMID 19765976 · PMC2764548 · Current opinion in structural biology · 2009 · 8 claims · 8 setups

  Full-text index only

  SG programs use genomic sequence data to select structurally novel protein targets, avoiding proteins with known structural homologues

  recombinant recalcitrant hundred family hydrogen situ site-directed