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).

• Direct maximum parsimony phylogeny reconstruction from genotype data.

  PMID 18053244 · PMC2222657 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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  The paper presents the first practical method for computing maximum parsimony phylogenies directly from genotype data, using integer linear programming.

  simulated mitochondrial lipoprotein coalescent maximum sliding-window

• A human genome-wide library of local phylogeny predictions for whole-genome inference problems.

  PMID 18710563 · PMC2556685 · BMC genomics · 2008 · 7 claims · 5 setups

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  A genome-wide library of nearly 16 million local maximum parsimony phylogenies was constructed from HapMap CEU and YRI SNP data across all human autosomes

  hapmap 5-snp genome-wide first maximum mutual pearson

• Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

  PMID 17931731 · PMC7114232 · Virus research · 2008 · 7 claims · 5 setups

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  8 amino acid sites in the extracellular domain of hMPV lineage 1a show a higher rate of nonsynonymous than synonymous substitutions (posterior probability >0.95), indicating positive selection.

  unique hmpv sequence neighbor-joining codon

• Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.

  PMID 19922637 · PMC2784780 · Virology journal · 2009 · 7 claims · 6 setups

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  A new intragenotypic recombinant HCV strain (1b/1a), named H23, was detected in 1 of 10 hemophiliac patients studied

  hcv 5'ncr serum maximum sequence recombination

• A computational screen for type I polyketide synthases in metagenomics shotgun data.

  PMID 18953415 · PMC2568958 · PloS one · 2008 · 8 claims · 6 setups

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  Combining HMM domain searches with maximum-likelihood phylogenetic trees can discriminate true PKS I sequences from evolutionarily related but functionally different enzymes (e.g., FAS I) in metagenomic data.

  predicted hmm-identified reference hmm hmm maximum-likelihood robinson-foulds

• Assessing the impacts of COVID-19 vaccination programme's timing and speed on health benefits, cost-effectiveness, and relative affordability in 27 African countries.

  PMID 36882868 · PMC9991879 · BMC medicine · 2023 · 8 claims · 6 setups

  Has reproduction · 89

  Vaccination programmes with earlier start dates yield the most health benefits and lowest ICERs compared to late-starting programmes

  population-level age-structured same ethiopia dynamic epidemiological daly

• Mucospheres produced by a mixotrophic protist impact ocean carbon cycling.

  PMID 35288549 · PMC8921327 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 58

  P. cf. balticum constructs carbon-rich mucospheres that attract, capture and immobilise microbial prey to facilitate phago-heterotrophic consumption

  tara four xenic balticum 18s its toxin

• Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.

  PMID 33138772 · PMC7607865 · BMC genomics · 2020 · 8 claims · 6 setups

  Has reproduction · 83

  scPPIN integrates scRNA-seq-derived p-values with PPINs to detect maximum-weight connected subgraphs (active/functional modules) via an exact Steiner-tree approach

  liver hepatocyte detected adipose single-cell differential protein-protein

• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.

  PMID 36088548 · PMC9487593 · Briefings in bioinformatics · 2022 · 8 claims · 6 setups

  Has reproduction · 94

  Well-established, hierarchically organized pathway annotation systems (e.g. GO, Reactome, KEGG) yield the best overall enrichment performance despite covering much of the human genome only in general terms.

  user-submitted string pubmed protein-coding gene hierarchical text-mining

• Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

  PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.

  hiv-1 four simulated population-based maximum bayesian

• The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

  PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

  putative nonredundant homo genes computational pssm semantic

• Genome-wide survey for biologically functional pseudogenes.

  PMID 16680195 · PMC1456316 · PLoS computational biology · 2006 · 8 claims · 6 setups

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  A subset of ancient, cross-species-conserved pseudogenes (30 of 1,453 candidate quartets) show evidence consistent with retained biological function

  human-mouse chimpanzee cross-species maximum-likelihood synteny

• The human phylome.

  PMID 17567924 · PMC2394744 · Genome biology · 2007 · 6 claims · 5 setups

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  Reconstruction of the human phylome: evolutionary trees for all human proteins and their homologs among 39 fully sequenced eukaryotic genomes, using a pipeline combining alignment trimming, NJ, ML (PhyML) and Bayesian (MrBayes) methods.

  proteome proteins neighbor-joining maximum bayesian

• Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

  PMID 28845461 · PMC5566788 · mSystems · 2017 · 8 claims · 8 setups

  Has reproduction · 94

  The L. casei group resolves into three distinct clades (A, B, C) supported by phylogeny, GC content, ANI, and TETRA, and many strains are misclassified relative to their nearest type strain.

  casei orthogroups unclassified selected whole-genome comparative pairwise

• Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

  PMID 18820744 · PMC2553485 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

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  Positive selection has played an important role in the molecular evolution of putative virulence factors of P. brasiliensis

  brasiliensis gp43 ratio codon-based mutational

• Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

  PMID 19759830 · PMC2736399 · PloS one · 2009 · 8 claims · 7 setups

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  Statistical evidence of genetic compartmentalization between lung and blood HIV-1 env sequences was found in 10 of 18 subjects.

  paired lung tissue-pair pooled hiv-1 maximum statistical

• Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates.

  PMID 18541024 · PMC2446394 · BMC evolutionary biology · 2008 · 8 claims · 3 setups

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  Extant bony vertebrates (osteichthyans) retain only Lbx1- and Lbx2-type genes; no distinct Lbx3/Lbx4 proteins exist.

  osteichthyan aligned genome blast maximum comparative

• VGEA: an RNA viral assembly toolkit.

  PMID 34567846 · PMC8428259 · PeerJ · 2021 · 8 claims · 5 setups

  Has reproduction · 80

  VGEA is a Snakemake workflow that chains existing tools (fastp, BWA, SAMtools, IVA, shiver, SeqKit, QUAST, MultiQC) into an all-in-one RNA viral genome assembly pipeline

  sars-cov-2 lassa hiv-1 ngs-based computational comparative

• Genotyping, Orientalis-like Yersinia pestis, and plague pandemics.

  PMID 15498160 · PMC3320270 · Emerging infectious diseases · 2004 · 6 claims · 6 setups

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  Multiple spacer typing (MST), based on intergenic spacer sequencing, differentiates the three Y. pestis biovars

  pestis combined dental contemporary spacer phylogenetic pcr

• Evolutionary sequence analysis of complete eukaryote genomes.

  PMID 15762985 · PMC1274250 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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  A conservative genome-comparison method (MIA) identifies panorthologs — strict single-copy 1:1 orthologs containing only species divergences, no paralogy — to minimize errors from gene duplication in evolutionary sequence analysis.

  complete panortholog concatenated individual reciprocal sequence neighbor-joining