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).

• 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

• 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

• 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

• 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

• 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

• 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

• Compression of structured high-throughput sequencing data.

  PMID 24260313 · PMC3832420 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 43

  Leveraging an explicit data schema (separate field encoding, field modeling, template compression, domain modeling) enables stronger compression of HTS alignment data than general-purpose compression of serialized bytes.

  benchmark ten rna-seq exome genome

• CDKL1 variants affecting ciliary formation predispose to thoracic aortic aneurysm and dissection.

  PMID 41056017 · PMC12646653 · The Journal of clinical investigation · 2025 · 8 claims · 8 setups

  Has reproduction · 67

  Heterozygous CDKL1 missense variants (Cys143Arg, Ser206Leu, Thr135Met) were identified in 6 patients from 3 families with TAAD spectrum disorders

  patients cohort cdkl1 aortic exome gene structural

• 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 are a terminally exhausted, tumor-antigen-specific subset of CD8+ T cells within ccRCC tumors

  ccrcc tumor-reactive cd39 caix-specific single-cell bulk co-culture

• Targeted capture and massively parallel sequencing of 12 human exomes.

  PMID 19684571 · PMC2844771 · Nature · 2009 · 8 claims · 8 setups

  Full-text index only

  Targeted exome capture combined with massively parallel sequencing sensitively and specifically identifies rare and common variants across >300 Mb of coding sequence

  hapmap unrelated na18507 randomly targeted array-based molecular

• 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

• Personalized genomic medicine with a patchwork, partially owned genome.

  PMID 18449389 · PMC2347364 · The Yale journal of biology and medicine · 2007 · 8 claims · 6 setups

  Full-text index only

  Structural variants (CNVs) cover as much as 20 percent of the human genome length and are present in phenotypically normal individuals without apparent negative consequences.

  phenotypically single genome chimpanzee molecular diploid encode

• 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