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).

• 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

• Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.

  PMID 38548265 · PMC11954816 · Journal of advanced research · 2025 · 8 claims · 8 setups

  Has reproduction · 79

  Meta-analysis confirmed a positive association between DED and DEP occurrence

  patients taiwan biobank twb meta-analysis genome-wide score

• Genomic views of distant-acting enhancers.

  PMID 19741700 · PMC2923221 · Nature · 2009 · 8 claims · 8 setups

  Full-text index only

  Meta-analysis of ~1200 top GWAS SNPs found that in 40% of cases (472/1170) no known exons overlap the linked SNP or its haplotype block, implying noncoding variation causally contributes to many traits.

  genome patients embryos ret gwas targeted transgenic

• Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.

  PMID 31980607 · PMC6981202 · Nature communications · 2020 · 8 claims · 8 setups

  Has reproduction · 52

  MetaMEx integrates transcriptomic data from 66 published human skeletal muscle studies (>1100 individuals) into an online meta-analysis resource (www.metamex.eu)

  skeletal pooled transcriptomic principal qpcr

• Molecular subtype of recurrent implantation failure reveals distinct endometrial etiology of female infertility.

  PMID 40660214 · PMC12257665 · Journal of translational medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 68

  RIF endometrial samples segregate into two reproducible molecular subtypes: an immune-driven subtype (RIF-I) and a metabolic-driven subtype (RIF-M)

  endometrial in-house bulk rif-degs meta-analysis sequencing immune

• The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.

  PMID 37036103 · PMC10084500 · GigaScience · 2022 · 8 claims · 8 setups

  Full-text index only

  GEN-ERA is a unified, publicly available toolbox of 13 Nextflow workflows supported by 14 Singularity containers for reproducible microbial genomic/phylogenomic analyses in both bacteria and small eukaryotes.

  gloeobacterales gloeobacteraceae publicly ncbi-deposited phylogenomics ssu genome

• Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance.

  PMID 39009986 · PMC11247842 · Genetics, selection, evolution : GSE · 2024 · 5 claims · 8 setups

  Has reproduction · 69

  Meta-analysis of GWAS across six dairy cattle breeds identifies 58 lead markers associated with clinical mastitis and somatic cell score

  six combined per-breed genome-wide sequence-based trans-ethnic fixed-effect

• Integrative Transcriptomic and Evolutionary Analysis of Drought and Heat Stress Responses in Solanum tuberosum and Solanum lycopersicum.

  PMID 41470732 · PMC12736803 · Plants (Basel, Switzerland) · 2025 · 7 claims · 8 setups

  Has reproduction · 84

  Drought and heat stress induce coordinated transcriptional reprogramming in potato and tomato: induction of molecular chaperone activity, oxidative stress responses, and immune signaling, with repression of photosynthetic and primary metabolic pathways reflecting energy reallocation.

  solanum bulk term novo

• Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

  PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups

  Full-text index only

  A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.

  liver simulated conserved nearly gene simulation kolmogorov-smirnov

• CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

  PMID 17202170 · PMC1899094 · Nucleic acids research · 2007 · 7 claims · 4 setups

  Full-text index only

  Cyclonet is a web-based integrated database combining 'omics' and chemoinformatics data on mammalian cell cycle regulation in normal and pathological (cancer) states, built on a systems biology approach.

  breast commercial vertebrate genes cdna activity computational

• Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.

  PMID 36855106 · PMC9976425 · BMC medical genomics · 2023 · 8 claims · 7 setups

  Has reproduction · 86

  RNA-seq of peripheral blood from 23 sepsis patients and 10 healthy controls identifies 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs.

  peripheral demrnas blood thp-1 rna-seq annotation wgcna

• Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

  PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

  Full-text index only

  HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

  tcga-luad best brain advanced bulk kaplan-meier pearson

• 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

• Pharokka: a fast scalable bacteriophage annotation tool.

  PMID 36453861 · PMC9805569 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 5 setups

  Has reproduction · 84

  Pharokka is a one-line, fast, scalable bacteriophage annotation tool producing standards-compliant outputs, installable via a two-line bioconda command

  enterobacteria staphylococcus crass-like predicted genome large-scale homology

• A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.

  PMID 41501133 · PMC12886967 · NPJ precision oncology · 2026 · 8 claims · 8 setups

  Full-text index only

  CSRGPS is a robust, machine-learning-derived prognostic signature that outperforms existing glioma prognostic models across multiple cohorts

  tcga-gbm glioma meta consensus wgcna machine

• Proneural-mesenchymal antagonism dominates the patterns of phenotypic heterogeneity in glioblastoma.

  PMID 38433919 · PMC10905000 · iScience · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  The four proposed GBM molecular subtypes (Proneural, Neural, Classical, Mesenchymal / NPC-like, OPC-like, AC-like, MES-like) are not mutually exclusive or independent of one another

  scrna-seq tcga-gbm gse131928 tumor gene pairwise principal

• Shared and unique phosphoproteomics responses in skeletal muscle from exercise models and in hyperammonemic myotubes.

  PMID 36345342 · PMC9636548 · iScience · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  Comparative phosphoproteomics of hyperammonemic myotubes and exercise-model muscle identifies shared enriched pathways: PKA, calcium signaling, MAPK signaling, and protein homeostasis.

  c2c12 hyperammonemic phosphoproteomics immunoblot comparative

• Cardiovascular genomics, personalized medicine, and the National Heart, Lung, and Blood Institute: part I: the beginning of an era.

  PMID 20031542 · PMC3097376 · Circulation. Cardiovascular genetics · 2008 · 7 claims · 8 setups

  Full-text index only

  Rare Mendelian mutations (e.g., in sarcomere genes, ion channels, FBN1, LMNA) cause specific rare cardiovascular conditions (hypertrophic/dilated cardiomyopathy, long-QT syndrome, thoracic aortic aneurysm, progeria) but explain little of common CVD risk.

  community-based subjects dallas mice exon community-based gene

• A genome-wide association analysis identifies 16 novel susceptibility loci for carpal tunnel syndrome.

  PMID 30833571 · PMC6399342 · Nature communications · 2019 · 6 claims · 8 setups

  Has reproduction · 90

  A GWAS of 12,312 CTS cases and 389,344 controls in UK Biobank identifies 16 novel genome-wide significant susceptibility loci for CTS

  biobank surgically gwas transformed genome-wide sequencing gene-based

• Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.

  PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups

  Has reproduction · 73

  Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.

  peripheral overlapping geo pbmcs bulk kegg protein-protein