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).

• Technical Brief: a novel strategy for enrichment of trabecular meshwork protease proteome.

  PMID 18490959 · PMC2386506 · Molecular vision · 2008 · 7 claims · 6 setups

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  A novel affinity-enrichment strategy using UV cross-linked protease inhibitor peptides on Protein A/G columns improves capture of the TM protease proteome compared to SDS-PAGE fractionation alone

  cytosolic affinity-eluted porcine affinity-enriched affinity western sds-page

• Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.

  PMID 24782521 · PMC4066758 · Nucleic acids research · 2014 · 8 claims · 5 setups

  Has reproduction · 79

  EDD is a new algorithm that detects broad (megabase-size) enrichment domains from ChIP-seq data of widely distributed chromatin proteins such as A- and B-type lamins.

  normal dermal analysis set chip-seq chip-qpcr rna-seq

• Single-cell analysis reveals multi-faceted features of B cell development, together with age-associated B cell subpopulations.

  PMID 41520091 · PMC12905261 · Communications biology · 2026 · 8 claims · 8 setups

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  18 B cell subpopulations were identified spanning the full developmental continuum from early progenitors to plasma cells, including 4 previously unappreciated minor subpopulations (FTLhi, S100A8hi immature; FOShi, HSPA1Ahi naïve).

  in-house enriched tonsil peripheral scrna-seq scvdj-seq velocity

• Aurka-Bhlhe41 axis prevents premature aging-like microglial dysfunction and promotes remyelination.

  PMID 41896238 · PMC13260908 · Nature communications · 2026 · 8 claims · 8 setups

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  Bhlhe41 is microglia-enriched in the CNS and is negatively autoregulated (self-repressed) at its own promoter.

  yolk microglia cerebral enriched sequencing flow western

• An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.

  PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups

  Has reproduction · 74

  An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead

  ipsc-derived same top differentially bulk principal hierarchical

• Identification of intrinsic genes across general hypertension, hypertension with left ventricular remodeling, and uncontrolled hypertension.

  PMID 36277786 · PMC9582241 · Frontiers in cardiovascular medicine · 2022 · 7 claims · 8 setups

  Has reproduction · 73

  FBXW4 and 13 other genes are uniquely enriched in the general hypertension group

  peripheral white four gse75360 microarray gene weighted

• Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.

  PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups

  Has reproduction · 66

  Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.

  blood transcriptomic postmortem saliva gsea machine differential

• WebGestalt: an integrated system for exploring gene sets in various biological contexts.

  PMID 15980575 · PMC1160236 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  WebGestalt is an integrated web-based system composed of four modules: gene set management, information retrieval, organization/visualization, and statistics.

  genes gene est-based enrichment kegg

• Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

  PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

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  Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

  luad demtdmrgs gse131907 wgcna kegg univariate

• Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis.

  PMID 38879692 · PMC11180211 · Communications biology · 2024 · 7 claims · 7 setups

  Has reproduction · 69

  Epithelial cell populations are significantly reduced during acute DSS colitis, reflecting tissue damage, with partial recovery in chronic colitis

  colon gut single-cell 16s western

• Integrated Analysis of Multiple Microarrays Based on Raw Data Identified Novel Gene Signatures in Recurrent Implantation Failure.

  PMID 35197930 · PMC8859149 · Frontiers in endocrinology · 2022 · 6 claims · 7 setups

  Has reproduction · 85

  Robust Rank Aggregation (RRA) can integrate DEG lists from multiple independent RIF microarray datasets to identify robust DEGs.

  endometrium integrated robust ppi microarray robust gene

• Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.

  PMID 38650649 · PMC11034498 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 83

  188 differentially expressed genes (DEGs) between IS and control blood samples were identified and enriched in immune-related biological pathways

  blood degs peripheral hub microarray kegg cibersort

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 50

  A 186-gene signature predictive of nCRT response was derived from integrating six GEO transcriptomic datasets using machine learning.

  pre-treatment combined larc 186-gene differential machine molecular

• Pathway analysis of kidney cancer using proteomics and metabolic profiling.

  PMID 17123452 · PMC1665458 · Molecular cancer · 2006 · 8 claims · 8 setups

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  31 proteins are differentially expressed with high statistical significance (p<0.05) in ccRCC tumor tissue compared to adjacent non-malignant kidney tissue

  ccrcc rcc computational random gel immunoblotting immunohistochemistry

• PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells.

  PMID 41565684 · PMC12881479 · Nature communications · 2026 · 8 claims · 8 setups

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  PURE-seq integrates FACS sorting directly into PIP-seq barcoding reaction tubes, minimizing manual handling and cell loss for rare-cell single-cell sequencing.

  hek293t pbmcs melanoma bone single-cell infercnv gene

• TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining.

  PMID 33705981 · PMC9403021 · Genomics, proteomics & bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction · 79

  TSUNAMI is a freely accessible web-based tool suite that mines gene co-expression network (GCN) modules from public (GEO, TCGA) or user-uploaded numerical omics data and performs downstream gene set enrichment analysis.

  gse17537 36th first gene circos survival

• STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.

  PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 8 claims · 6 setups

  Has reproduction · 66

  Low STAT3 expression in primary PCa is associated with increased OXPHOS and ribosomal biosynthesis at the transcriptomic level

  prostate bulk weighted reverse

• Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.

  PMID 34680427 · PMC8533098 · Biomedicines · 2021 · 8 claims · 7 setups

  Has reproduction · 75

  AD and PD patients can be stratified by transcriptomic clustering into three subclasses with distinct gene expression and metabolic profiles

  post-mortem brain zebrafish bulk single-cell unsupervised

• Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.

  PMID 35457273 · PMC9026532 · International journal of molecular sciences · 2022 · 7 claims · 6 setups

  Has reproduction · 88

  Meta-analysis of five transcriptomic experiments identified 1151 differentially expressed genes that compose a coordinated gene network responding to high light stress

  arabidopsis deg promoter selected meta-analysis transcription hexamer

• Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.

  PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  WGCNA-derived gene coexpression modules from breast cancer cell line RNA-seq data correlate significantly with specific cell-shape features

  breast same gene identified bulk high-content regulon