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).

• Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma.

  PMID 33086062 · PMC7649750 · Cell reports · 2020 · 8 claims · 8 setups

  Has reproduction · 59

  KMT2D is a potent tumor suppressor in melanoma

  hmel-brafv600e tyr-creert2 tma kmt2d pooled xenograft genetically

• Antigen and checkpoint receptor engagement recalibrates T cell receptor signal strength.

  PMID 34534438 · PMC8585507 · Immunity · 2021 · 8 claims · 6 setups

  Has reproduction · 37

  TCR signal strength drives dynamic and time-dependent transcriptional changes in CD4+ T cells in vivo

  tg4 splenic sorted flow bulk checkpoint

• Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses.

  PMID 32542016 · PMC7295234 · PloS one · 2020 · 7 claims · 8 setups

  Has reproduction · 51

  Five tyrosine catabolic enzymes (TAT, HPD, HGD, GSTZ1, FAH) are downregulated in HCC compared to normal liver at mRNA and/or protein level

  oncomine tcga-lihc gse89377 hcc pan-cancer bulk microarray

• TGF-β-dependent reprogramming of amino acid metabolism induces epithelial-mesenchymal transition in non-small cell lung cancers.

  PMID 34168290 · PMC8225889 · Communications biology · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  TGF-β induces reprogramming of intracellular amino acid metabolism that is necessary to promote EMT in NSCLC cells

  a549 metabolomics real-time western

• Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

  PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups

  Has reproduction · 91

  SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes

  deep co-assembled surf_17 surf_5 whole-genome novo 16s

• 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

• Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease.

  PMID 38566100 · PMC10985960 · Cell communication and signaling : CCS · 2024 · 8 claims · 8 setups

  Has reproduction · 55

  Microglia, endothelial cells, and pericytes exhibit the highest IFN-I activity among PD midbrain cell types, with microglia and endothelial cells showing significantly elevated high-IFN-I-scoring proportions in PD versus controls

  midbrain single microglia substantia single-cell scenic monocle

• Refining breast cancer biomarker discovery and drug targeting through an advanced data-driven approach.

  PMID 38253993 · PMC10810249 · BMC bioinformatics · 2024 · 8 claims · 8 setups

  Has reproduction · 59

  The BGWO_SA_Ens algorithm (hybrid BGWO + simulated annealing with an ensemble classifier objective function) selects predictive breast cancer biomarker genes with high classification performance

  merged gse45827 superior differential feature comparative

• ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout.

  PMID 35100964 · PMC8805291 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 9 setups

  Has reproduction · 87

  Italian brown trout populations are genetically differentiated but show strong admixture from stocking practices, especially with the Atlantic lineage.

  brown snp subset salmo ddrad-seq admixture newhybrids

• GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses.

  PMID 33758032 · PMC8547006 · mSystems · 2021 · 8 claims · 7 setups

  Has reproduction · 70

  GAUGE automatically annotates GEO microbial transcriptomic data sets (microarray and RNA-seq), increasing the proportion of annotatable studies from 4% to 33%

  microarray rna-seq aeruginosa mantel manual anova

• Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer.

  PMID 33986754 · PMC8110914 · Frontiers in immunology · 2021 · 7 claims · 8 setups

  Has reproduction · 51

  A higher immune infiltration-related risk score (IRS) indicates worse prognosis and lower sensitivity to immunotherapy in breast cancer patients

  tcga candidate cancer univariate weighted lasso

• 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

• Integrating multi-omics data reveals the antitumor role and clinical benefits of gamma-delta T cells in triple-negative breast cancer.

  PMID 40197136 · PMC11974128 · BMC cancer · 2025 · 8 claims · 8 setups

  Has reproduction · 59

  High γδT cell infiltration is associated with favorable prognosis in TNBC but not in HR-positive or HER2-positive breast cancer

  tnbc tcga-brca metabric single-cell bulk immunohistochemistry

• 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

• Inflammatory Bone Marrow Mesenchymal Stem Cells in Multiple Myeloma: Transcriptional Signature and In Vitro Modeling.

  PMID 37958322 · PMC10650304 · Cancers · 2023 · 8 claims · 8 setups

  Has reproduction · 50

  A 279-gene 'iMSC signature' is upregulated in BM MSCs from MM patients compared to healthy donors, identified by reanalysis of single-cell RNA-seq data.

  facs-isolated expanded bm-mscs mscs single-cell bulk gene

• 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

• Differentiation status determines the effects of IFNγ on the expression of PD-L1 and immunomodulatory genes in melanoma.

  PMID 39736644 · PMC11687009 · Cell communication and signaling : CCS · 2024 · 8 claims · 8 setups

  Has reproduction · 61

  Dedifferentiation via MITF knockdown renders 624Mel melanoma cells hypersensitive to IFNγ, producing non-additive (synergistic) upregulation of IFNγ-induced genes.

  624mel yumm1.7 patient-derived qpcr sequencing luminex

• Downregulation of Splicing Factor PTBP1 Curtails FBXO5 Expression to Promote Cellular Senescence in Lung Adenocarcinoma.

  PMID 39057099 · PMC11276454 · Current issues in molecular biology · 2024 · 8 claims · 8 setups

  Has reproduction · 59

  PTBP1 is significantly upregulated across multiple cancer types including LUAD, and higher PTBP1 levels are associated with worse LUAD patient survival

  cancer luad fibroblast a549 pan-cancer differential replicative

• High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma.

  PMID 37388735 · PMC10303802 · Frontiers in immunology · 2023 · 8 claims · 8 setups

  Has reproduction · 76

  Almost 90% of TCGA EC tumors exhibit DNA methylation age deceleration (DNAmad) relative to patient chronological age as assessed by the Horvath clock

  tumors metastatic methylation bulk kegg

• Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

  PMID 38254989 · PMC10815467 · Genes · 2024 · 7 claims · 8 setups

  Has reproduction · 85

  High expression of transcription factors FOXA1 and EZH2 in malignant cells at the invasive front plays a key role in driving tumor progression

  breast er+ epithelial malignant scrna-seq spatial copy