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).

• Therapy effect of either paclitaxel or cyclophosphamide combination treatment in patients with epithelial ovarian cancer and relation to TP53 gene status.

  PMID 9703286 · PMC2063030 · British journal of cancer · 1998 · 6 claims · 4 setups

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  Paclitaxel/cisplatin therapy produces a higher positive response rate than cyclophosphamide/cisplatin therapy in advanced ovarian cancer

  patients frozen genomic clinically randomized rt-pcr temporal

• Getting it right: being smarter about clinical trials.

  PMID 16608383 · PMC1435786 · PLoS medicine · 2006 · 9 claims · 8 setups

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  Bias and confounding in observational studies can produce misleading associations that are overturned by randomized trials (e.g., HRT).

  postmenopausal general patients men randomized population-based large

• Future possibilities in the prevention of breast cancer: intervention strategies in BRCA1 and BRCA2 mutation carriers.

  PMID 11250722 · PMC138789 · Breast cancer research : BCR · 2000 · 8 claims · 8 setups

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  BRCA1 and BRCA2 mutations confer an 80-85% lifetime risk (by age 80) of female breast cancer

  normal affected women brca1 clonogenic germline mammographic

• Identification and analysis of co-occurrence networks with NetCutter.

  PMID 18781200 · PMC2526157 · PloS one · 2008 · 8 claims · 4 setups

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  Random sampling from a complete permutation set of the bipartite graph permits co-occurrence analysis with optimal stringency, and the edge-swapping (ES) model closely approximates this and is the preferred null-model among six tested.

  publime bipartite randomized co-occurrence null-model signal-to-noise

• A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.

  PMID 37963558 · PMC10645512 · Journal of the Royal Society, Interface · 2023 · 8 claims · 7 setups

  Has reproduction · 95

  RKIP and BACH1 are negatively correlated with each other across most cancer types in TCGA

  tcga er+ ccle computational spearman correlation gene

• Indirect genomic effects on survival from gene expression data.

  PMID 18358079 · PMC2397510 · Genome biology · 2008 · 7 claims · 6 setups

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  A novel methodology (dynamic path analysis combined with additive hazard survival regression) can detect and quantify indirect effects of gene expression on survival mediated through transcription factor target genes.

  dutch uppsala dlbcl gene gene literature permutation

• 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

• Human synthetic lethal inference as potential anti-cancer target gene detection.

  PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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  Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

  saccharomyces sapiens ihsln genes database phylogenetic gene

• Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

  PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups

  Has reproduction · 78

  Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely

  gene racipe clinical tcga racipe influence principal

• A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.

  PMID 19087293 · PMC2636810 · BMC bioinformatics · 2008 · 6 claims · 6 setups

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  A theoretical exon-exon junction protein database accounting for all in-phase (frame-preserving) exon combinations can be built from the Ensembl Core Database using Perl/Bioperl/MySQL/Ensembl API.

  ensembl liver candidate same database tandem decoy

• Highlights of international conference of immunogenomics and immunomics, October 8-12, 2006 Budapest, Hungary.

  PMID 17470366 · PMC7130317 · Cellular immunology · 2006 · 8 claims · 8 setups

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  An 'immunological constant of rejection' involving interferon-stimulated genes (ISGs) and innate immune effector functions (IEF) underlies diverse immune-mediated tissue destruction processes (allograft rejection, cancer rejection, autoimmunity, infection)

  hla-b44 plasma macrophages complement proteomics shotgun cap

• Nutritional genomics, polyphenols, diets, and their impact on dietetics.

  PMID 18954579 · PMC2692306 · Journal of the American Dietetic Association · 2008 · 8 claims · 8 setups

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  Nutrient-gene interactions, exemplified by the MTHFR C677T polymorphism, modulate individual metabolic responses (e.g., homocysteine metabolism) and can be offset by adjusting nutrient intake such as folate

  mammary embryonic subjects rats gene histone carcinogen-induced