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).

• Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.

  PMID 38504986 · PMC10950096 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.

  fresh tcga gbm bulk rna-seq consensus

• A P4HA2 hypoxia signature derived from single cell atlas stratifies conserved subtypes with prognostic significance in cervical squamous cell carcinoma.

  PMID 41559646 · PMC12910786 · BMC cancer · 2026 · 6 claims · 8 setups

  Full-text index only

  A tumor cell metaprogram (MP7) identified from scRNA-seq of CSCC shows elevated hypoxia, invasion, metastasis, proliferation, and angiogenesis scores compared to other metaprograms.

  cscc tcga-cscc mp7 siha single-cell bulk gene

• A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.

  PMID 38157249 · PMC10781479 · Aging · 2023 · 7 claims · 8 setups

  Has reproduction · 85

  Consensus clustering of 74 oxidative stress-related genes identifies three distinct HNSCC molecular subgroups (Cluster1-3) with significantly different overall survival and tumor stage distribution

  tcga-hnscc gse41613 gse103322 prjeb23709 bulk single-cell immunohistochemistry

• 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

• scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.

  PMID 40501071 · PMC12159290 · Briefings in bioinformatics · 2025 · 8 claims · 6 setups

  Has reproduction · 62

  scATD enables high-throughput single-cell drug sensitivity prediction for new patients without model parameter retraining via bidirectional Bi-AdaIN style transfer

  panglaodb cancer geo gse137829 single-cell bulk

• Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.

  PMID 39779736 · PMC11711664 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 74

  540 DEGs overlap across breast, colorectal, and lung cancers out of 11,384 DEGs analyzed

  breast colorectal lung common microarray kegg protein-protein

• The complement system contributes to the immunosuppressive microenvironment of uveal melanoma.

  PMID 41803879 · PMC13130498 · Journal of translational medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  Primary UM (pUM) preferentially expresses early complement pathway components over terminal membrane attack complex elements, with early factors showing prognostic significance.

  short-term metastatic normal pum bulk label-free single-cell

• Betacoronavirus-specific alternate splicing.

  PMID 35074468 · PMC8782732 · Genomics · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  Genes differentially spliced during SARS-CoV-2 infection show a similar functional (GO) profile to those differentially spliced in SARS-CoV and MERS infection, affecting a diverse set of genes tied to virus biology.

  mrc5 calu-3 nasal lung bulk

• TiRank prioritizes phenotypic niches in tumor microenvironment for clinical biomarker discovery.

  PMID 41689080 · PMC12910759 · Genome medicine · 2026 · 7 claims · 4 setups

  Full-text index only

  TiRank is a framework that integrates scRNA-seq, ST, and bulk transcriptomes using an REO-transformation module and multitask transfer learning to align data into a unified embedding space for prioritizing clinically relevant spatial niches

  benchmark pan-cancer gastric independent scrna-seq bulk spatial

• MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.

  PMID 29901703 · PMC6025204 · GigaScience · 2018 · 8 claims · 7 setups

  Has reproduction · 95

  The MetaMap pipeline recapitulates known infection agents in bona fide dual RNA-seq validation studies (Salmonella, HPV, HSV, rhinovirus)

  hela tumor lymphoblast rna-seq dual blastn-based

• Ionizing Radiation Enhances Prognostically Significant Cellular Immunity Programs in the Brain Metastasis Microenvironment.

  PMID 41817317 · PMC13223553 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2026 · 8 claims · 7 setups

  Full-text index only

  High-grade histopathologic TIL infiltration is associated with significantly prolonged overall survival in breast and lung cancer BM.

  breast lung histopathologic sequencing tcr

• PRDM1+ Malignant Cells Mediate an Immunosuppressive Landscape and Resistance to Neoadjuvant Chemoradiotherapy and Immunotherapy in Esophageal Squamous Cell Carcinoma.

  PMID 41556358 · PMC13042517 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  A PRDM1+ malignant epithelial cell subcluster (Epi_C4) is enriched in NMPR patients and is associated with nICRT treatment resistance

  locally escc pd-1 kyse-30 single-arm scrna-seq bulk

• Intra-Tissue Bacteriome and Cellular Profiles in Periodontal Granulation Tissue From Osseous Defects and Extraction Sockets.

  PMID 41732956 · PMC13086548 · Journal of clinical periodontology · 2026 · 7 claims · 6 setups

  Full-text index only

  Osseous defect granulation tissue (GT) and inflamed gingival tissue (PT) exhibit periodontal health-associated, commensal-enriched bacteriome profiles, while root (RT) and socket (ST) granulation tissues show periodontopathogen enrichment and commensal depletion

  periodontal 16s subjects 16s single-cell histology

• RNA Editing Alterations Define Disease Manifestations in the Progression of Experimental Autoimmune Encephalomyelitis (EAE).

  PMID 36429012 · PMC9688714 · Cells · 2022 · 7 claims · 7 setups

  Has reproduction · 37

  RNA-editing events mediated by APOBEC and ADAR deaminases are significantly reduced throughout the course of EAE disease progression

  brain rna-edited brain-isolated naïve rna-seq pathway pcr

• Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.

  PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 61

  Twelve HIA-related genes were identified that are transcriptionally activated by HIF1A/HIF2A and functionally implicated in angiogenesis in CRC

  hct116 crc tumor chip-seq bulk single

• Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.

  PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 78

  A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors

  hcc-associated hcc malignant cd8+ single-cell bulk metabolomics

• The past and future of tuberculosis research.

  PMID 19855821 · PMC2745564 · PLoS pathogens · 2009 · 8 claims · 6 setups

  Full-text index only

  Integrating systems biology with epidemiology ('systems epidemiology') will be required to better predict TB's trajectory and eliminate the disease

  clinical mycobacterium mtbc patients fingerprinting whole-genome microarray

• Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline.

  PMID 42166739 · PMC13242923 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

  Full-text index only

  SAMI is a UMI-aware, Singularity-contained Nextflow pipeline that detects splicing events diverging from transcript annotations directly from raw FASTQ files.

  seraseq simulated small processed targeted simulated computation

• Discovery and Evaluation of Biomarkers for Triple-Negative Breast Cancer Subtypes Uncovers Patient Stratification and Targeted Therapeutic Strategies.

  PMID 41671401 · PMC13176827 · Cancer research · 2026 · 7 claims · 8 setups

  Full-text index only

  A set of basal identity genes (SMA/ACTA2, TAGLN, TPM2) defined by scRNA-seq analysis enables subclassification of TNBC into a subgroup termed true basal TNBC (tB-TNBC)

  healthy ffpe tcga i-spy2 scrna-seq immunohistochemistry bulk

• 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