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).

• Uncertainty in the mating strategy of honeybees causes bias and unreliability in the estimates of genetic parameters.

  PMID 38632535 · PMC11022492 · Genetics, selection, evolution : GSE · 2024 · 7 claims · 3 setups

  Has reproduction · 98

  The most precise estimates of genetic parameters and genetic trends are obtained when breeding queens are mated with drones of a single DPQ that is correctly assigned in the pedigree (SS mating).

  simulated simulation sensitivity

• DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data.

  PMID 38950178 · PMC11236288 · Bioinformatics (Oxford, England) · 2024 · 8 claims · 2 setups

  Has reproduction · 40

  DeepGSEA is an explainable deep gene set enrichment analysis method built on interpretable, prototype-based neural networks.

  simulated real-world simulation scrna-seq-based

• Testing whether genetic variation explains correlation of quantitative measures of gene expression, and application to genetic network analysis.

  PMID 18444230 · PMC2729096 · Statistics in medicine · 2008 · 8 claims · 3 setups

  Full-text index only

  A statistical test (delta method and Steiger-Browne optimal linear composites) is developed to test equality of the marginal correlation and the partial correlation of two gene expression traits conditional on a set of covariates.

  simulated real analytical simulation application

• Bayesian transcriptome assembly.

  PMID 25367074 · PMC4397945 · Genome biology · 2014 · 8 claims · 8 setups

  Has reproduction · 68

  Bayesembler, a probabilistic transcriptome assembler built on a Bayesian model of the RNA sequencing process with Gibbs sampling over expressed candidates, abundances and read assignments, is introduced.

  k562 embryonic dendritic rna-seq simulated paired-end long-read

• An empirical study of choosing efficient discriminative seeds for oligonucleotide design.

  PMID 19958494 · PMC2788383 · BMC genomics · 2009 · 8 claims · 3 setups

  Full-text index only

  The spaced seed is the most efficient discriminative seed for oligonucleotide design among the five algorithms tested.

  simulated pmoa nirs seed

• RNA modifications detection by comparative Nanopore direct RNA sequencing.

  PMID 34893601 · PMC8664944 · Nature communications · 2021 · 7 claims · 5 setups

  Has reproduction · 50

  Nanocompore is a model-free comparative method that uses a 2-component Gaussian mixture model (GMM) and univariate statistical tests on signal intensity/dwell time to detect RNA modifications in Nanopore direct RNA sequencing data without needing a training set

  simulated synthetic escherichia saccharomyces nanopore computational

• Tracing human genetic histories and natural selection with precise local ancestry inference.

  PMID 40379651 · PMC12084304 · Nature communications · 2025 · 7 claims · 7 setups

  Has reproduction · 76

  Orchestra, a two-stage LAI method combining a recombination-distance base layer with a deep learning (convolutional + attention) smoothing module, outperforms RFmix, FLARE and Gnomix in precision and recall across simulated admixture generations.

  1kgp-16pops independent simulated 1kgp simulated population-level local

• Optimality driven nearest centroid classification from genomic data.

  PMID 17912341 · PMC1991588 · PloS one · 2007 · 7 claims · 5 setups

  Full-text index only

  A theoretical result determines the subset of features of a given size that minimizes the misclassification rate for a nearest-centroid (LDA) classifier, based on equation (4).

  artificial simulated previously-published simulated simulation clinical

• Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

  PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

  Full-text index only

  Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

  normalized individuals subset same affymetrix fluorescent snp

• Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

  PMID 19761607 · PMC2759961 · BMC bioinformatics · 2009 · 8 claims · 5 setups

  Full-text index only

  2LOmb performs an omnibus permutation test on ensembles of two-locus analyses via a four-step algorithm (two-locus analysis, permutation test, global p-value determination, progressive ensemble search)

  simulated same snp type two-locus 2lomb benchmark

• Optimisation of the core subset for the APY approximation of genomic relationships.

  PMID 36418945 · PMC9682752 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 3 setups

  Has reproduction · 85

  APY approximates the full genomic relationship matrix by splitting genotyped animals into a core subset (fully dependent, direct inverse) and a non-core subset (conditionally independent given core), reducing inversion cost.

  simulated real genotyped gblup population

• 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

• Importance sampling for the infinite sites model.

  PMID 18976228 · PMC2832804 · Statistical applications in genetics and molecular biology · 2008 · 7 claims · 2 setups

  Full-text index only

  A new importance sampling proposal distribution for the ISM, derived from a new result on exact sampling from a single segregating site, generally shows greater efficiency than the GT and SD proposals.

  simulated empirical computational reanalysis

• TEMP: a computational method for analyzing transposable element polymorphism in populations.

  PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

  drosophila five four melanogaster simulated comparative whole-genome

• Inferring human colonization history using a copying model.

  PMID 18497854 · PMC2367454 · PLoS genetics · 2008 · 8 claims · 6 setups

  Full-text index only

  A copying-model approach using SNP haplotype sharing can infer both the order of population founding and the donor populations contributing ancestry to each new population.

  simulated populations coalescent snp ascertainment

• Calculating expected DNA remnants from ancient founding events in human population genetics.

  PMID 18928554 · PMC2588638 · BMC genetics · 2008 · 8 claims · 3 setups

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  Genetic parameters (native/migrant population size, mutation rate, generations since admixture) strongly determine the final frequency of migrant alleles detectable today.

  simulated forward-based size

• binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

  PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 67

  binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)

  cami real-world metagenomic binned genome binning mag

• Evolutionary distance estimation and fidelity of pair wise sequence alignment.

  PMID 15840174 · PMC1087827 · BMC bioinformatics · 2005 · 8 claims · 8 setups

  Full-text index only

  Evolutionary distance estimation is relatively unaffected by alignment error as long as 50% or more of homologous sites remain identical between sequences

  simulated simulated sequence indel

• 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

• Assessing the gene space in draft genomes.

  PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

  Full-text index only

  The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

  caenorhabditis toxoplasma homo briggsae cegma blast tblastn