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).

• Bayesian survival analysis in genetic association studies.

  PMID 18617538 · PMC2530885 · Bioinformatics (Oxford, England) · 2008 · 7 claims · 5 setups

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  A novel Bayesian method (BETA-Surv) extends prior case-control haplotype-clustering work to censored survival outcomes by clustering haplotypes via gene tree/perfect phylogeny topology and relative mutation age.

  simulated same sanad bayesian univariate partial

• Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays.

  PMID 16549007 · PMC1544357 · BMC bioinformatics · 2006 · 7 claims · 2 setups

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  A methodology combining Cox proportional hazards models with a compound covariate, cross-validated log partial likelihood (ACVL) for predictive accuracy, and permutation-based significance testing can identify an optimal subset of significant genes for survival prediction

  simulated diffuse simulation cdna

• HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD).

  PMID 37907883 · PMC10619225 · BMC medical genomics · 2023 · 6 claims · 5 setups

  Has reproduction · 67

  HASCAD, a DNN-based cell composition deconvolution model, predicts the fractions of up to 15 immune cell types from bulk RNA-seq.

  pbmc bulk tcga-lihc harmony-symphony scrna-seq simulated bulk

• A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles.

  PMID 32111252 · PMC7049190 · Genome medicine · 2020 · 8 claims · 8 setups

  Has reproduction · 91

  DeClust is a reference profile-free deconvolution method that simultaneously deconvolves bulk tumor expression into cancer, immune, and stromal compartments and clusters samples into cancer cell-intrinsic molecular subtypes, outputting subtype-specific reference profiles for the cohort rather than for individuals.

  solid muscle-invasive ccrcc for bulk single-cell scrna-seq

• The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers.

  PMID 15743497 · PMC1064126 · Breast cancer research : BCR · 2005 · 7 claims · 5 setups

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  The AR CAG repeat polymorphism does not modify breast cancer risk in BRCA1 mutation carriers

  peripheral brca1 same simulated fluorescent cox weighted

• Statistical challenges in preprocessing in microarray experiments in cancer.

  PMID 18829474 · PMC3529914 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 7 setups

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  Choice of pre-processing method materially changes which features are found significantly associated with survival in the Beer et al. lung cancer microarray dataset

  lung beer individual outlier expression rank-covariance quality-control

• Heterogeneity and Differentiation Trajectories of Infiltrating CD8+ T Cells in Lung Adenocarcinoma.

  PMID 36358600 · PMC9658355 · Cancers · 2022 · 7 claims · 8 setups

  Has reproduction · 67

  Infiltrating CD8+ T cells in LUAD can be divided into ten transcriptionally distinct subsets: eight cytotoxic (CTL) subsets, one naive-like (NTL) subset, and one exhausted (ETL) subset.

  luad tcga cd8+ degs single-cell cibersort survival

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• Early life-stage thermal resilience is determined by climate-linked regulatory variation.

  PMID 41505517 · PMC12799179 · Proceedings of the National Academy of Sciences of the United States of America · 2026 · 8 claims · 8 setups

  Has reproduction · 64

  Embryonic heat tolerance in D. melanogaster is determined by climate-linked regulatory genetic variation at loci on chromosomes 2R and X

  melanogaster simulated synthetic wild-collected heat-shock pool-seq drift-only

• Identification of genomic regions contributing to etoposide-induced cytotoxicity.

  PMID 19089452 · PMC2714550 · Human genetics · 2009 · 7 claims · 6 setups

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  Etoposide-induced cytotoxicity in CEPH lymphoblastoid cell lines is heritable, with genetics explaining 17-25% of variation

  ceph subset hapmap simulated growth heritability non-parametric

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc

• Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

  PMID 18505588 · PMC2430713 · BMC genomics · 2008 · 8 claims · 8 setups

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  Comparative genomics of B. longum DJO10A (minimally cultured) and NCC2705 (culture collection strain) reveals 17 unique DNA regions in DJO10A and 6 in NCC2705 despite otherwise high genome collinearity and identity

  bifidobacterium longum xbai-digested whole-genome base codon