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).

• EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

  PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

  sequences homologous proteins coding pairwise single sequence

• Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

  PMID 15790396 · PMC1087472 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  Paircomp, FamilyRelationsII, and Cartwheel together form an integrated system for comparing, viewing, and managing analyses of BAC-sized (~100 kb) genomic sequence pairs.

  otx sea elegans endo16 windowed reporter comparative

• Bayesian estimates of linkage disequilibrium.

  PMID 17592642 · PMC1924864 · BMC genetics · 2007 · 8 claims · 3 setups

  Full-text index only

  The MLE of D' is biased toward disequilibrium, with the bias particularly severe in small samples (<100 subjects) and rare alleles (MAF<0.05)

  simulated genotype pairwise computer genotype bayesian

• Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'.

  PMID 17980034 · PMC2180187 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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  CubeX, a Python program/web tool, computes the exact algebraic (Cardan/Nickalls) solution(s) of Hill's cubic equation to estimate pairwise haplotype frequencies, D', r2 and chi-square for each solution

  simulated real apoe igf2 cubic pairwise haplotype

• Optimized mixed Markov models for motif identification.

  PMID 16749929 · PMC1534070 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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  OMiMa can incorporate more than NNSplice's pairwise dependencies

  simulated regulatory splice biological motif pairwise

• Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.

  PMID 34462475 · PMC8405622 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction

  SDSD constitutes a distinct taxonomic entity within S. dysgalactiae, with a mean intra-subspecies average nucleotide identity of 99%.

  dysgalactiae sdse sdsd isolates genome multilocus pangenome

• Benchmarking tools for the alignment of functional noncoding DNA.

  PMID 14736341 · PMC344529 · BMC bioinformatics · 2004 · 8 claims · 4 setups

  Full-text index only

  Global alignment tools (Avid, ClustalW, Lagan, Needle, DiAlign-G) typically have higher sensitivity over entire noncoding sequences and within constrained blocks than local tools

  simulated melanogaster sapiens sequence pairwise genome

• 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

• TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.

  PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups

  Has reproduction · 89

  TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency

  melanogaster simulated long-read whole-genome genome

• Modeling the amplification dynamics of human Alu retrotransposons.

  PMID 16201008 · PMC1239904 · PLoS computational biology · 2005 · 8 claims · 4 setups

  Full-text index only

  Combining sequence diversity (π) and insertion polymorphism level (IPL) statistics can statistically exclude implausible Alu amplification scenarios and narrow the range of plausible ones for individual subfamilies.

  simulated genome population computer comparative population

• The Proteomic Code: a molecular recognition code for proteins.

  PMID 17999762 · PMC2206014 · Theoretical biology & medical modelling · 2007 · 8 claims · 8 setups

  Full-text index only

  The Proteomic Code is a set of rules by which genetic information is transferred into the physico-chemical properties of amino acids, determining protein-protein interactions and folding; it is part of the redundant Genetic Code.

  anti-peptide sequence exon smooth radioimmunoassay pairwise genome-wide

• Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats.

  PMID 29590198 · PMC5874073 · PloS one · 2018 · 8 claims · 8 setups

  Has reproduction · 99

  Verrucomicrobia is highly prevalent in north-temperate freshwater lakes, on average the 4th most abundant phylum (range 1.7–41.7%).

  southeastern lake muskegon lake-type 16s within-phylum phylogenetic

• The formation of avian montane diversity across barriers and along elevational gradients.

  PMID 35022441 · PMC8755808 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 75

  Genetic differentiation is generally greater across the oceanic barrier separating Buru and Seram than across the lowland barrier separating New Guinea mountain ranges.

  forest population individuals single whole-genome f_st principal

• Power analysis for genome-wide association studies.

  PMID 17725844 · PMC2042984 · BMC genetics · 2007 · 8 claims · 6 setups

  Full-text index only

  Developed a method to compute genome-wide association study power using tag SNPs and representative population genotype data (HapMap), equivalent to the cumulative r2-adjusted power of Jorgenson and Witte.

  hapmap power pairwise tag

• Genome-wide diversity and selective pressure in the human rhinovirus.

  PMID 17477878 · PMC1892812 · Virology journal · 2007 · 7 claims · 6 setups

  Full-text index only

  Whole genome and subgenomic phylogenies of HRV are essentially identical at every locus, indicating consistent phylogenetic patterns across the genome.

  diverse hrv fully hrva genome phylogenetic pairwise

• Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

  PMID 18471294 · PMC2397415 · BMC genomics · 2008 · 7 claims · 7 setups

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  The complete genome of HAdV-37 was sequenced and annotated (35,213 bp, 56.6% GC content, 35 predicted coding sequences plus 8 hypothetical ORFs)

  hadv-37 predicted select genome cpg global

• Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

  PMID 30476109 · PMC6320677 · Genome biology and evolution · 2019 · 8 claims · 8 setups

  Has reproduction · 87

  Subgenus Houzingenia originated via transoceanic dispersal from Africa ~6.6 Ma, with most biodiversity arising from rapid mid-Pleistocene (0.5–2.0 Ma) diversification plus multiple long-distance dispersals.

  gossypium d-genome houzingenia orthologous whole-genome novo reference

• Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.

  PMID 40258987 · PMC12012037 · Communications biology · 2025 · 8 claims · 9 setups

  Has reproduction · 68

  200 years of quasi-isolation and the 1962 epizootic caused a two-fold increase in inbreeding and an excess of highly deleterious mutations in Crater lions relative to other Greater Serengeti populations

  african lion crater simulated genome principal admixture

• Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.

  PMID 30993001 · PMC6459838 · NPJ systems biology and applications · 2019 · 8 claims · 7 setups

  Has reproduction · 71

  Retaining only the top ~3 most correlated edges per gene (EPG3) combined with FastUnfold clustering (termed PGCNA) produces gene co-expression modules with significantly better separation and enrichment of known biology than using all edges or other clustering methods.

  breast colorectal brca representative gene comparative multi-omic

• PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies.

  PMID 35338232 · PMC8956664 · Communications biology · 2022 · 8 claims · 8 setups

  Has reproduction · 85

  Two computational approaches (sub-sampling and phenotype-simulation) can be implemented to perform power calculations for bacterial GWAS using existing genome collections, packaged as the PowerBacGWAS pipeline

  enterococcus klebsiella mycobacterium faecium pan-genome burden variant