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).

• Deconvoluting the 'omics' for organ transplantation.

  PMID 19644370 · PMC2993238 · Current opinion in organ transplantation · 2009 · 8 claims · 5 setups

  Full-text index only

  High-throughput 'omic' technologies (genomics, proteomics, metabolomics, antibiomics) can uncover novel biomarkers for acute rejection, chronic rejection, and operational tolerance without a priori pathway bias

  kidney sera peripheral microarray non-parametric antibiomics

• Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

  PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups

  Has reproduction · 71

  TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.

  blood cynomolgus external gene differential principal

• 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

• FEM: mining biological meaning from cell level in single-cell RNA sequencing data.

  PMID 34909283 · PMC8641482 · PeerJ · 2021 · 7 claims · 5 setups

  Has reproduction · 75

  The FEM algorithm converts each cell's gene expression matrix (GEM) into a functional expression matrix by applying Fisher's exact test enrichment per cell and per gene set, then encoding adjusted p-values as information content.

  peripheral pancreas liver pbmc scrna-seq differential dimensionality

• Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.

  PMID 19903332 · PMC3091321 · Genome biology · 2009 · 6 claims · 5 setups

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  A candidate 37-transcript diagnostic signature distinguishes septicemic melioidosis from sepsis caused by other organisms with 100% accuracy in the training set and 78%/80% accuracy in two independent validation sets

  blood whole-genome unsupervised class

• 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

• 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

• Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

  PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups

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  277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow

  umbilical ucb zebrafish microarray fluorescence-activated quantitative

• Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

  PMID 26538066 · PMC4634735 · BMC medical genomics · 2015 · 8 claims · 5 setups

  Has reproduction · 83

  A multigene peripheral-blood gene-expression biomarker accurately classifies which women from high-risk families develop familial breast cancer.

  peripheral pbmcs blood normal gene-expression lymphocyte gene

• Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.

  PMID 28583124 · PMC5458481 · Environmental health : a global access science source · 2017 · 7 claims · 6 setups

  Has reproduction · 71

  Gestational PM2.5 exposure is associated with sex-specific gene expression changes in newborn cord blood, with major differences between boys and girls.

  cord maternal genes significant genome pm2.5 isolation

• Nimbus: a design-driven analyses suite for amplicon-based NGS data.

  PMID 29538618 · PMC6084620 · Bioinformatics (Oxford, England) · 2018 · 7 claims · 4 setups

  Has reproduction · 64

  Nimbus is an end-to-end software suite for amplicon-based NGS data that tracks source amplicons through alignment and variant calling, with tools for trimming, alignment, SNP/InDel calling, QC and visualization.

  blood twin na15510 haloplex snp whole-exome

• Blood RNA signature RISK4LEP predicts leprosy years before clinical onset.

  PMID 34090257 · PMC8182229 · EBioMedicine · 2021 · 7 claims · 5 setups

  Has reproduction · 53

  A 4-gene blood RNA signature (RISK4LEP: MT-ND2, REX1BD, TPGS1, UBC) predicts leprosy development 4–61 months before clinical diagnosis

  blood rna-seq paxgene bulk rt-qpcr random

• Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data.

  PMID 19733729 · PMC2748225 · Analytica chimica acta · 2009 · 8 claims · 4 setups

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  ACA-based wavelet coefficient feature selection can achieve up to 100% classification accuracy on training, validating, and independent testing sets using only 5 selected features.

  blood baseline-corrected 953-dimensional training seldi-tof wavelet ant

• Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

  PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 8 setups

  Has reproduction · 100

  A network-based meta-analysis across studies identifies a common 45-gene signature specific to active TB disease that accounts for cohort/population heterogeneity

  n×m common independent viral blood gene random

• A blood-based DNA damage signature in patients with Parkinson's disease is associated with disease progression.

  PMID 40913219 · PMC12443628 · Nature aging · 2025 · 8 claims · 2 setups

  Has reproduction · 69

  A blood-based DNA damage signature is present in PD patients and is associated with disease progression.

  blood gwas bulk genetic

• Improved epigenetic age prediction models by combining sex chromosome and autosomal markers.

  PMID 40665390 · PMC12261677 · Epigenetics & chromatin · 2025 · 7 claims · 5 setups

  Has reproduction · 48

  Combining sex chromosomal DNAm markers with autosomal age-informative markers can produce a high-accuracy age prediction model competitive with autosomal-only models

  blood buffy methylation random spearman

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

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

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  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

• Trans-ethnic association study of blood pressure determinants in over 750,000 individuals.

  PMID 30578418 · PMC6365102 · Nature genetics · 2019 · 8 claims · 8 setups

  Has reproduction

  Discovery and replication GWAS of SBP, DBP and pulse pressure in up to 776,078 individuals identified 208 novel common blood pressure SNPs and 53 rare variants.

  mvp tissues kidney gwas genome-wide transcriptome-wide

• Novel mutations in the BRCA1 and BRCA2 genes in Iranian women with early-onset breast cancer.

  PMID 12100744 · PMC116720 · Breast cancer research : BCR · 2002 · 8 claims · 4 setups

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  Germline BRCA1 and BRCA2 mutations are present in Iranian women with early-onset breast cancer, including four novel frameshift mutations

  genomic pcr-amplified pcr truncation single-strand heteroduplex

• A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.

  PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 7 setups

  Has reproduction · 83

  The DSS phenotype-by-time interaction defines parsimonious temporal (dynamic) expression and splicing signatures of acute and chronic colitis distinct from time-specific differential expression.

  intestine colon dss distal bulk phenotypic h&e