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).

• The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.

  PMID 19911046 · PMC2768904 · PLoS computational biology · 2009 · 8 claims · 3 setups

  Full-text index only

  The replication rate of the strain that initiates an infection has a strong effect on the fitness of the infection at the between-host level, even though the virus evolves rapidly within the host.

  computational same simulation stochastic parameter-sweep multivariate

• Topological approximate Bayesian computation for parameter inference of an angiogenesis model.

  PMID 35191485 · PMC9048691 · Bioinformatics (Oxford, England) · 2022 · 7 claims · 3 setups

  Has reproduction · 100

  TDA summary statistics can be combined with ABC to infer parameters (ρ, χ) of the Anderson–Chaplain angiogenesis model

  square simplicial simulated computational persistent approximate

• Computing Ka and Ks with a consideration of unequal transitional substitutions.

  PMID 16740169 · PMC1552089 · BMC evolutionary biology · 2006 · 7 claims · 7 setups

  Full-text index only

  MYN, a modified version of the Yang-Nielsen (YN) algorithm based on the Tamura-Nei Model, allows unequal transitional substitution rates between purines (κR) and pyrimidines (κY) plus codon frequency bias

  simulated pairs human-mouse human-dog computer comparative

• On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve.

  PMID 18076765 · PMC2211327 · BMC bioinformatics · 2007 · 8 claims · 4 setups

  Full-text index only

  The TGDR-AUC algorithm regularizes the empirical AUC by replacing the non-differentiable 0-1 loss with a smooth sigmoid surrogate function and applies constrained threshold gradient descent regularization

  simulated serum preprocessed simulation mass high-resolution

• Stability analysis of mixtures of mutagenetic trees.

  PMID 18366778 · PMC2335279 · BMC bioinformatics · 2008 · 7 claims · 5 setups

  Full-text index only

  Mutagenetic trees mixture models capture multiple alternative pathways of ordered accumulation of genetic events (e.g., HIV resistance mutations, cancer chromosomal aberrations).

  simulated hiv-1 hiv timed simulation genotypic mutagenetic

• A note on generalized Genome Scan Meta-Analysis statistics.

  PMID 15717930 · PMC551600 · BMC bioinformatics · 2005 · 7 claims · 3 setups

  Full-text index only

  An Edgeworth series approximation to the null distribution of the weighted GSMA statistic provides a more accurate representation than the normal approximation, especially in the tails

  simulated schizophrenia monte genome numerical

• NETISCE: a network-based tool for cell fate reprogramming.

  PMID 35725577 · PMC9209484 · NPJ systems biology and applications · 2022 · 8 claims · 4 setups

  Has reproduction · 85

  NETISCE predicts cell fate reprogramming targets in static (GRN/signaling) networks without needing full kinetic parameterization of a dynamical model.

  ascidian pluripotent drosophila signal fvs-finding sfa

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

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

  Full-text index only

  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

• Software JimenaE allows efficient dynamic simulations of Boolean networks, centrality and system state analysis.

  PMID 36725967 · PMC9892028 · Scientific reports · 2023 · 8 claims · 4 setups

  Has reproduction · 74

  JimenaE simulates Boolean networks dynamically and systematically calculates all system states rather than heuristically as SQUAD does.

  mesenchymal arabidopsis dendritic network boolean dynamic immune

• 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

• The origins of lactase persistence in Europe.

  PMID 19714206 · PMC2722739 · PLoS computational biology · 2009 · 8 claims · 5 setups

  Full-text index only

  The −13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly linked to the Linearbandkeramik culture.

  simulated simulation 910*t farming demic approximate comparison

• PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.

  PMID 18620604 · PMC2483288 · BMC bioinformatics · 2008 · 8 claims · 4 setups

  Full-text index only

  PRESTO is an order of magnitude faster than other existing permutation testing software for genetic association studies.

  case-control same wtccc genome-wide benchmark stratified

• Population history and natural selection shape patterns of genetic variation in 132 genes.

  PMID 15361935 · PMC515367 · PLoS biology · 2004 · 7 claims · 5 setups

  Full-text index only

  Developed a rigorous computational approach that corrects for multiple hypothesis testing and models population demographic history to test for natural selection

  genomic empirical snps chromosome comprehensive coalescent fst

• Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.

  PMID 17158152 · PMC1802574 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  GLR is a novel maximum-likelihood measure of gene loss rate that probabilistically weighs all possible ancestral phyletic patterns rather than relying on a single parsimonious reconstruction.

  synthetic eukaryotic simulated 16-species analytical comparative simulation

• pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS).

  PMID 31035919 · PMC6489300 · BMC bioinformatics · 2019 · 7 claims · 8 setups

  Has reproduction · 88

  pwrEWAS is a user-friendly tool (R package and Shiny web interface) for comprehensive power estimation in two-group EWAS using Illumina HumanMethylation BeadChip technology.

  saliva blood cord-blood pbmc illumina simulation

• The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation.

  PMID 39549198 · PMC11979089 · GeroScience · 2025 · 9 claims · 2 setups

  Has reproduction · 54

  The Multi-State Epigenetic Pacemaker (MSEPM) can accurately model multiple methylation-associated factors (e.g., age, sex, cell-type) simultaneously.

  blood simulated methylation simulation

• A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noise.

  PMID 18615428 · PMC2855839 · Proteomics · 2008 · 6 claims · 4 setups

  Full-text index only

  Noise in SELDI-TOF/MALDI-TOF mass spectrometry data is heteroscedastic across the m/z range, with larger variance at lower m/z values, contrary to the homogeneous noise assumption of existing wavelet denoising methods.

  serum raw denoised simulated seldi-tof wavelet-based peak

• Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

  PMID 18270580 · PMC2217631 · PloS one · 2008 · 8 claims · 6 setups

  Full-text index only

  Pairs of unlinked SNPs showing excess genetic differentiation (LD in mouse RILs, Fst in human populations) beyond what simulations/coalescent models predict by chance represent candidate functionally interacting (epistatic) gene pairs.

  bxd simulated subset populations genome-wide simulation genotype-phenotype

• Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

  PMID 37853325 · PMC10583454 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 6 setups

  Has reproduction

  Selective linkage disequilibrium pruning (SLDP) refines whole-genome SNP sets using GWAS prior information to improve genomic prediction accuracy.

  duroc 1000-individual real low-coverage genome-wide genomic

• Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals.

  PMID 39418301 · PMC11521246 · PLoS computational biology · 2024 · 7 claims · 4 setups

  Has reproduction · 23

  COPD GWAS loci are more spatially clustered across the genome than expected by chance, with significant enrichment on chromosome 4q.

  lung sakornsakolpat string bulk microarray gwas