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).

• A small-cell lung cancer genome with complex signatures of tobacco exposure.

  PMID 20016488 · PMC2880489 · Nature · 2010 · 8 claims · 7 setups

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  22,910 somatic substitutions, including 132 in coding exons, were identified genome-wide in the NCI-H209 SCLC genome.

  nci-h209 sclc lu-135 massively pcr multiplex

• stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images.

  PMID 41692960 · PMC12960910 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 5 setups

  Has reproduction · 75

  stDyer-image is an end-to-end deep learning framework that directly associates image features with predicted cluster labels to improve clustering of SRT and SRP data with images.

  non-small-cell breast brain intestine spatially image

• The cancer secretome: a reservoir of biomarkers.

  PMID 18796163 · PMC2562990 · Journal of translational medicine · 2008 · 8 claims · 8 setups

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  Cancer secretome analysis is a promising reservoir for identifying novel, non-invasive cancer biomarkers, addressing limitations of whole blood/serum proteomics

  a549 m-be sw480 neoplastic 2-de dige icat

• Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

  PMID 18438408 · PMC2705838 · Nature genetics · 2008 · 8 claims · 8 setups

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  Massively parallel paired-end sequencing can characterize somatic and germline structural rearrangements to base-pair resolution across a whole cancer genome

  nci-h2171 nci-h1770 massively genomic rt-pcr

• miRGen 2.0: a database of microRNA genomic information and regulation.

  PMID 19850714 · PMC2808909 · Nucleic acids research · 2010 · 7 claims · 6 setups

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  miRGen 2.0 is a database providing comprehensive information about the genomic position of human and mouse microRNA coding transcripts and their regulation by transcription factors

  lung organ malme embryonic polii small nucleosome

• Detection of ras gene mutations in human lung cancer: comparison of two screening assays based on the polymerase chain reaction.

  PMID 1486847 · PMC1519635 · Environmental health perspectives · 1992 · 8 claims · 3 setups

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  Somatic K-ras mutations were found in one-third of lung carcinomas studied, but no N-ras mutations were detected.

  lung plasmid pcr-based denaturing

• A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.

  PMID 35047825 · PMC8759566 · NAR cancer · 2022 · 7 claims · 7 setups

  Has reproduction · 100

  Five miRNAs (Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p [miR-141-3p], Mir-1307_5p, Mir-155_5p) are up-regulated at multiple metastatic sites in colorectal cancer.

  pcrc mli mirna-seq mirna mirna qpcr differential

• miRge 2.0 for comprehensive analysis of microRNA sequencing data.

  PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups

  Has reproduction · 89

  miRge 2.0 introduces a novel SVM-based miRNA detection method using both hairpin structure and isomiR composition, yielding higher specificity for miRNA identification

  pooled colon datasets small a-to-i novel

• Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity.

  PMID 35418127 · PMC9008010 · Scientific data · 2022 · 6 claims · 5 setups

  Has reproduction · 87

  This dataset is the most comprehensive public-facing dataset of ultra-deep ctDNA sequencing data generated to date

  contrived enzymatically extracted targeted

• Patterns of somatic mutation in human cancer genomes.

  PMID 17344846 · PMC2712719 · Nature · 2007 · 8 claims · 5 setups

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  Systematic resequencing of a large gene family (protein kinases) across diverse cancers reveals a larger repertoire of cancer genes than previously anticipated

  cancers additional computational combined targeted follow-up statistical

• The field of tissue injury in the lung and airway.

  PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

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  Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

  bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific

• Molecular genetic analysis of the cytochrome P450-debrisoquine hydroxylase locus and association with cancer susceptibility.

  PMID 1486838 · PMC1519624 · Environmental health perspectives · 1992 · 7 claims · 8 setups

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  A PCR-RFLP DNA-based assay targeting the intron 3/exon 4 G-to-A transition can identify approximately 70-80% of CYP2D6 poor metabolizers (PMs) without drug phenotyping.

  blood pcr-rflp

• Interpretable and integrative analysis of single-cell multiomics with scMKL.

  PMID 40770488 · PMC12328712 · Communications biology · 2025 · 8 claims · 7 setups

  Has reproduction · 65

  scMKL combines multiple kernel learning with random Fourier features and group Lasso to jointly model transcriptomic and epigenomic single-cell data interpretably

  mcf-7 t-47d small prostate 10x scrna-seq sciatac-seq

• Rapid detection, cloning and molecular cytogenetic characterisation of sequences from an MRP-encoding amplicon by chromosome microdissection.

  PMID 8018546 · PMC2033297 · British journal of cancer · 1994 · 7 claims · 6 setups

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  Chromosome microdissection can be used to rapidly detect, clone and cytogenetically characterise amplified sequences from hsrs/dmins in drug-resistant cells

  ht1080 normal h69ar hsr micro-fish chromosome southern

• Mutational analysis of oncogenic AKT E17K mutation in common solid cancers and acute leukaemias.

  PMID 18392055 · PMC2391109 · British journal of cancer · 2008 · 7 claims · 8 setups

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  AKT1 E17K mutation occurs in breast cancers at a low frequency (4/93, 4.3%)

  breast colorectal gastric hepatocellular pcr-sscp capillary

• Graph Random Forest: A Graph Embedded Algorithm for Identifying Highly Connected Important Features.

  PMID 37509188 · PMC10377046 · Biomolecules · 2023 · 8 claims · 3 setups

  Has reproduction · 89

  Graph Random Forest (GRF) embeds graph/network information directly into the decision-tree building process by splitting on features in the k-hop neighborhood of a data-driven head-splitting node.

  scale-free non-small embryonic simulation rna-seq

• Social and ethical implications of genomics, race, ethnicity, and health inequities.

  PMID 19000599 · PMC2892396 · Seminars in oncology nursing · 2008 · 8 claims · 5 setups

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  Race and ethnicity are increasingly viewed as genetic surrogates for predicting disease risk and treatment response, though directly assessing genomic and environmental factors is more accurate.

  population prostate non-small-cell breast genome-wide gene somatic

• Candidate target genes for loss of heterozygosity on human chromosome 17q21.

  PMID 15187990 · PMC2409524 · British journal of cancer · 2004 · 8 claims · 5 setups

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  JUP (plakoglobin) is the only identified gene physically located between the D17S746 and D17S846 markers that define the smallest common region of LOH on chromosome 17q21

  genomic normal breast p1-phage nucleotide rt-pcr cold

• GENCODE: producing a reference annotation for ENCODE.

  PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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  GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

  tissues encode rt-pcr comparative automated

• spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

  PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 6 setups

  Has reproduction · 53

  spliceJAC quantifies multivariate mRNA splicing from unspliced/spliced count matrices to construct cell state-specific gene-gene (Jacobian) interaction matrices.

  two-gene three-gene emt circuit simulation grn scrna-seq