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).

• Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

  PMID 25057820 · PMC4109851 · PLoS genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 78

  In vivo gene expression is generally not correlated with a gene's importance for fitness, with the exception of metabolic genes, for which differential expression is more predictive of fitness.

  aeruginosa differentially paired rna-seq tn-seq computational

• BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

  PMID 19919682 · PMC3091323 · Genome biology · 2009 · 8 claims · 4 setups

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  BioGPS aggregates distributed, third-party gene annotation resources into a single customizable portal for human, mouse, and rat genes.

  biogps diverse tissues specified web reference exon

• 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

  PMID 19917133 · PMC2781828 · BMC genomics · 2009 · 8 claims · 4 setups

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  3' tag DGE transcript profiles are highly reproducible between technical and biological replicates, across libraries made at different labs, and across two generations of Illumina Genome Analyzers (GA I and GA II).

  brain hbrr topo-cloned tag microarray quantitative

• Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

  PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups

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  Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.

  lung gene differentially significantly laser histology principal

• Delineation of a gene network underlying the pulmonary response to oxidative stress in asthma.

  PMID 19730131 · PMC3328512 · Journal of investigative medicine : the official publication of the American Federation for Clinical Research · 2009 · 8 claims · 6 setups

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  Integration of multiple public microarray datasets via a four-way Venn diagram identifies genes commonly expressed in asthma- and cigarette smoke-exposed lung

  respiratory lung a549 gene affymetrix network

• Utilization of genomic signatures to identify phenotype-specific drugs.

  PMID 19714244 · PMC2729377 · PloS one · 2009 · 8 claims · 8 setups

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  A RAS pathway gene expression signature applied to NCI-60 cells identifies compounds selectively active against RAS-activated cells, including the MEK inhibitor Hypothemycin

  nci-60 breast mda-mb-231 signature-drug gene signature

• Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

  PMID 19706770 · PMC2745517 · Cancer research · 2009 · 8 claims · 8 setups

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  Genome-wide DNA copy number analysis of 161 primary breast tumors identified six novel focally amplified genes: POLD3, IRAK4, IRX2, TBL1XR1, ASPH, and BRD4

  breast mcf10a mcf10ca1h snp quantitative rt-qpcr

• Exploration of effective biomarkers for venous thrombosis embolism in Behçet's disease based on comprehensive bioinformatics analysis.

  PMID 38987624 · PMC11236978 · Scientific reports · 2024 · 6 claims · 8 setups

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  Four hub genes (E2F1, GATA3, HDAC5, MSH2) serve as diagnostic biomarkers for VTE in BD with high accuracy (AUC 0.816)

  peripheral degs candidate microarray weighted protein–protein

• 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

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  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 a pediatric acute hypoxemic respiratory failure signature in peripheral blood leukocytes at 24 hours post-ICU admission with machine learning.

  PMID 37009294 · PMC10063855 · Frontiers in pediatrics · 2023 · 7 claims · 5 setups

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  A machine learning stability selection approach (bootstrapped logistic regression, 100 simulations) can identify genes associated with PaO2/FiO2 < 200 vs ≥200 when standard differential expression with FDR correction shows no overlap between cohorts.

  pediatric combined top-ranked whole-blood machine pathway

• CRESCENT, a comprehensive RNA-Seq expression, splicing, and coding/non-coding element network tool.

  PMID 41566196 · PMC12895761 · BMC bioinformatics · 2026 · 6 claims · 6 setups

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  CRESCENT is a Snakemake workflow performing fully automated, comprehensive RNA-Seq analysis integrating differential expression, differential alternative splicing (DAS), differential transcript usage (DTU), and GO enrichment

  arabidopsis bulk rna-seq-based rna-seq

• Resource Availability Modulates Gene Expression Across Life Stages in a Migratory Butterfly.

  PMID 41797265 · PMC12968515 · Molecular ecology · 2026 · 7 claims · 6 setups

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  Adult female exposure to host plants for egg-laying is associated with differential expression of ecdysteroid and juvenile-hormone pathway genes, consistent with endocrine regulation of reproductive readiness and the oogenesis–flight syndrome

  vanessa bulk gene kegg

• Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

  PMID 41832957 · PMC13137218 · Cell reports · 2026 · 8 claims · 8 setups

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  Generated a single-nucleus multiome (snATAC + gene expression) dataset from 357 human dorsolateral prefrontal cortex samples (ages 15-100, European and African admixed ancestry), yielding over 1.5 million cells as a public resource.

  postmortem million+ pfc each single-nucleus umap pseudobulk

• Validation of bronchial airway gene expression associated with bronchiectasis in nasal epithelium.

  PMID 42094231 · PMC13139922 · ERJ open research · 2026 · 7 claims · 6 setups

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  No genes were significantly differentially expressed in nasal epithelium between participants with and without widespread radiologic BE (FDR<0.1)

  nasal bronchial bulk gene cell-type

• MicroRNA Enrichment and Docking-Based Evaluation of Ilomastat Targeting of MMP-2 in Esophageal Squamous Cell Carcinoma: Insights from a South African Cohort.

  PMID 42158110 · PMC13181172 · Computational and structural biotechnology journal · 2026 · 7 claims · 5 setups

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  The miR-29 family inhibits MMP-2 and represents a key regulatory axis in tumor invasion

  paired deg mmp-2 escc bulk pathway molecular

• A stem and progenitor cell-derived gene expression signature is prognostic for survival in myelofibrosis.

  PMID 41481381 · PMC13155955 · Blood · 2026 · 8 claims · 4 setups

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  A 24-gene HSPC-derived weighted-sum expression score (MPN24) is prognostic for overall survival in myelofibrosis

  peripheral lin-cd34+ pb-mncs pm-c1 bulk single-cell nanostring

• Deep-learning prediction of gene expression from personal genomes.

  PMID 41495833 · PMC12869966 · Genome biology · 2026 · 8 claims · 8 setups

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  Fine-tuning Enformer on paired personal WGS and RNA-seq data (Variformer) corrects Enformer's failure to predict inter-individual gene expression differences across held-out people.

  gtex rosmap same monocyte paired mutagenesis chromhmm

• CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

  PMID 41498638 · PMC12948241 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  CellPolaris is a unified computational framework performing TF-centered GRN construction, master TF identification, and TF perturbation simulation

  bulk previously round paired transfer-learning cross-species

• VISTA uncovers missing gene expression and spatial-induced information for spatial transcriptomic data analysis.

  PMID 41507434 · PMC12891734 · Communications biology · 2026 · 8 claims · 6 setups

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  VISTA predicts unmeasured gene expression in subcellular spatial transcriptomic data by integrating scRNA-seq and SST through variational inference and geometric deep learning with built-in uncertainty quantification

  brain breast embryo muscle imaging-based sequencing spot-based

• sCellST predicts single-cell gene expression from H& E images.

  PMID 41513659 · PMC12858858 · Nature communications · 2026 · 7 claims · 6 setups

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  sCellST is a weakly supervised (Multiple Instance Learning) deep learning framework that predicts single-cell gene expression from H&E images alone, trained using paired spatial transcriptomics (Visium) and H&E slides

  ovarian kidney prostate breast simulation spot-level nucleus