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).

• Contribution of retrotransposition to developmental disorders.

  PMID 31604926 · PMC6789007 · Nature communications · 2019 · 8 claims · 6 setups

  Has reproduction · 79

  De novo retrotransposition events cause a small but detectable fraction of severe developmental disorders, with 4 of 9 de novo MEIs deemed likely causative (~0.04%).

  ddd overlapping proband ppg whole-exome processed matched

• Neoadjuvant sintilimab plus chemotherapy in EGFR-mutant NSCLC: Phase 2 trial interim results (NEOTIDE/CTONG2104).

  PMID 38897205 · PMC11293361 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

  Has reproduction · 72

  Neoadjuvant sintilimab plus carboplatin/nab-paclitaxel is clinically feasible and tolerable in resectable EGFR-mutant NSCLC, with all 18 patients completing treatment and undergoing radical surgery.

  pre resected tumor serial whole-exome bulk single-cell

• Genomics Define Malignant Transformation in Myeloma Precursor Conditions.

  PMID 41061199 · PMC12614327 · Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2026 · 7 claims · 5 setups

  Has reproduction · 78

  Genomic profiling can identify malignant transformation in MGUS/SMM patients, distinguishing 'genomic MM' from 'genomic MGUS' despite identical clinical/morphologic presentation

  cd138+ mgus whole-exome whole-genome copy-number

• Bacillus Calmette-Guérin Treatment Changes the Tumor Microenvironment of Non-Muscle-Invasive Bladder Cancer.

  PMID 35311085 · PMC8930202 · Frontiers in oncology · 2022 · 8 claims · 8 setups

  Has reproduction · 30

  BCG therapy has bidirectional effects on tumor evolution and immune checkpoint landscape, with a significant reduction in neoantigen burden percentage in relapsed tumors

  tur matched nmibc relapsed whole-exome sequencing immune

• hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.

  PMID 36498841 · PMC9738810 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 63

  hgtseq is a fully automated, portable, and scalable Nextflow/nf-core pipeline for detecting horizontal gene transfer signatures from unmapped sequencing reads.

  copd chikv bos canis exome taxonomic reference

• Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.

  PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 7 claims · 8 setups

  Has reproduction

  Tabular ML classifiers (TabNet, XGBoost, LightGBM) trained on tumor-only-derived features achieve state-of-the-art somatic vs germline classification, with AUC>94% on TCGA holdout and AUC>85% on metastatic melanoma.

  tcga metastatic tumor-only whole-exome wes copy-number

• Next-generation sequencing.

  PMID 20030863 · PMC2797692 · Breast cancer research : BCR · 2009 · 8 claims · 7 setups

  Full-text index only

  Massively parallel sequencing can simultaneously capture base-pair mutations, copy number aberrations and somatic rearrangements of a cancer genome in a single experiment

  individuals metastatic acute oestrogen whole-exome whole-genome large-scale

• An AP4B1 frameshift mutation in siblings with intellectual disability and spastic tetraplegia further delineates the AP-4 deficiency syndrome.

  PMID 24781758 · PMC4297901 · European journal of human genetics : EJHG · 2015 · 5 claims · 2 setups

  Has reproduction · 83

  A novel homozygous 2-bp deletion c.1160_1161delCA (p.(Thr387Argfs*30)) in AP4B1 was identified in two siblings with severe ID, absent speech, microcephaly, growth retardation, and progressive spastic tetraplegia

  affected family whole-exome sanger

• Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.

  PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 7 claims · 5 setups

  Has reproduction · 53

  A computational framework integrating independently measured CNV (DNA sequencing) and single-cell RNA-seq from the same patients identifies recurrent concordant copy number gain and gene upregulation (CNG-UP) events and functional modules at the single-cell level.

  metastatic top breast tnbc single-cell functional mutational

• TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples.

  PMID 36699358 · PMC9710689 · Bioinformatics advances · 2022 · 6 claims · 2 setups

  Has reproduction · 50

  TOSCA is the first automated, open-source, end-to-end tumor-only somatic calling workflow for WES and targeted panel sequencing data.

  t-cell hcc1395 targeted whole-exome

• Single duplex DNA sequencing with CODEC detects mutations with high sensitivity.

  PMID 37106072 · PMC10181940 · Nature genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 78

  CODEC concatenates both strands of an original DNA duplex into a single NGS read pair via an adapter quadruplex and strand-displacing extension, enabling single-duplex resolution

  cfdna na12878 genomic sperm targeted whole-genome whole-exome

• DNA demethylation is associated with malignant progression of lower-grade gliomas.

  PMID 30760837 · PMC6374451 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction

  Nearly half of IDH-mutant glioblastomas that progressed from lower-grade gliomas show characteristic partial DNA demethylation in previously methylated (G-CIMP) genomic regions of their initial tumor.

  gliomas neural analysis tcga methylation whole-exome sequencing

• Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.

  PMID 37954334 · PMC10637964 · Heliyon · 2023 · 8 claims · 8 setups

  Has reproduction · 88

  APOBEC family genes are differentially expressed across cancer types and tissues, with APOBEC3B being the most aberrantly upregulated gene in most cancers including LUAD

  tcga tcga-luad beas-2b rna-seq somatic gene

• Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

  PMID 40993300 · PMC12460824 · NPJ digital medicine · 2025 · 8 claims · 8 setups

  Has reproduction

  Metabolic status is closely tied to tumor differentiation state, with distinct metabolic reprogramming occurring during thyroid cancer dedifferentiation

  thyroid fuscc gse193581 aggregated untargeted whole-exome transcriptomics

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• IRSN-23 gene diagnosis enhances breast cancer subtype classification and predicts response to neoadjuvant chemotherapy: new validation analyses.

  PMID 40128415 · PMC11993443 · Breast cancer (Tokyo, Japan) · 2025 · 8 claims · 8 setups

  Has reproduction · 71

  IRSN-23 Gp-R patients have significantly higher pCR rates than Gp-NR patients without anti-HER2 therapy, across the OUH cohort and multiple independent public datasets

  breast microarray rna-seq exome

• Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

  PMID 35028613 · PMC8714941 · Cell reports. Medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 75

  Stage-stratified molecular subclassification (analyzing Ta and T1 separately) is more biologically and clinically informative than subtypes derived from all NMIBC combined, especially for T1 tumors.

  stage combined patients copy genome-wide targeted

• Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs.

  PMID 38781959 · PMC11228554 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

  Has reproduction · 76

  DSRCT tumor cells cluster into consistent subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs across patients and samples

  fresh matched archived dsrct scrna-seq single-nucleus bulk

• Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma.

  PMID 40961944 · PMC12629791 · Cell reports. Medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 88

  CD39+CD8+ TILs constitute a terminally exhausted, tumor-antigen-specific subset of CD8+ T cells

  memory sorted caix-specific cd39+pd-1bright scrna-seq bulk mhc