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).

• HLA-A gene polymorphism defined by high-resolution sequence-based typing in 161 Northern Chinese Han people.

  PMID 15629059 · PMC5172246 · Genomics, proteomics & bioinformatics · 2003 · 7 claims · 5 setups

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  HLA-A gene shows high polymorphism in the Northern Chinese Han population, with 74 gene types and 36 alleles detected in 161 individuals

  genomic ihwg peripheral allele sequence-based pcr sbt

• RotaC: a web-based tool for the complete genome classification of group A rotaviruses.

  PMID 19930627 · PMC2785824 · BMC microbiology · 2009 · 7 claims · 4 setups

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  RotaC is a freely available web-based tool for complete genome classification of group A rotaviruses across all 11 gene segments.

  group rotavirus neighbor-joining profile pairwise

• Does excitatory fronto-extracerebral tDCS lead to improved working memory performance?

  PMID 24555105 · PMC3869492 · F1000Research · 2013 · 8 claims · 4 setups

  Has reproduction · 61

  Active anodal left DLPFC tDCS with a contralateral cheek reference did not significantly enhance 3-back working memory performance over sham across the two-day experiment (no main effect of group, no group x time interaction).

  healthy 3-back linear

• Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes.

  PMID 16091150 · PMC1208870 · BMC cancer · 2005 · 7 claims · 5 setups

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  Three of the five DNA repair genes (MRE11A, RAD50, XRCC4) do not conform to a contiguous haplotype block structure; instead SNPs in high LD can be non-contiguous, fitting a more flexible LD group paradigm

  unrelated same haplotype caucasian snp haplotype group

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• 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

• MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

  PMID 19906735 · PMC2808943 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  MBGD allows users to create ortholog groups using a specified subgroup of organisms, distinguishing it from other comparative genomics resources

  complete user-submitted ortholog mbgd hierarchical automated phylogenetic

• TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.

  PMID 34197621 · PMC8464036 · Nucleic acids research · 2021 · 8 claims · 8 setups

  Has reproduction · 60

  TRAPID 2.0 is a web application performing global characterization of de novo transcriptomes via structural, functional, and taxonomic annotation in an initial processing phase, followed by an exploratory phase of downstream analyses.

  mmetsp query putative ciliate taxonomic similarity non-coding

• Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

  PMID 18687142 · PMC2546438 · Retrovirology · 2008 · 7 claims · 6 setups

  Full-text index only

  Integrase displays significantly less inter- and intra-subtype amino acid diversity and lower Shannon's entropy than protease or RT.

  genbank hiv-1 protease integrase blastp phylogenetic amino

• A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.

  PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 7 setups

  Has reproduction · 83

  The DSS phenotype-by-time interaction defines parsimonious temporal (dynamic) expression and splicing signatures of acute and chronic colitis distinct from time-specific differential expression.

  intestine colon dss distal bulk phenotypic h&e

• Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.

  PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups

  Has reproduction · 63

  The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.

  balb cl-sl donovani experimental transgenic genome

• Examination of FMR1 transcript and protein levels among 74 premutation carriers.

  PMID 19927162 · PMC4122982 · Journal of human genetics · 2010 · 7 claims · 4 setups

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  FMR1 premutation carriers (55-199 CGG repeats) show increased FMR1 transcript levels alongside decreased FMRP levels compared to normal individuals.

  peripheral subset real-time western cgg

• Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame.

  PMID 30648934 · PMC6412060 · Microbial genomics · 2019 · 7 claims · 7 setups

  Has reproduction · 100

  The S. Adjame outbreak produced a heterogeneous phylogeny with multiple temporally/geographically linked sub-clusters, atypical of a point-source Salmonella outbreak and consistent with contamination from an endemic mixed-strain source (imported South Asian herbs/spices).

  salmonella adjame outbreak commonly genome reference-based cgmlst

• ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

  PMID 14617382 · PMC305365 · BMC genetics · 2003 · 8 claims · 7 setups

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  A novel O1v-A2 hybrid allele, containing four missense mutations, causes the A weak B phenotype in five individuals of African descent

  genomic red computational abo sequencing blood

• Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum.

  PMID 41212030 · PMC12691615 · mBio · 2025 · 8 claims · 8 setups

  Has reproduction · 86

  Of the four most frequent plasmid types, types II and III have more stable size, larger core genomes, and track the chromosomal phylogeny (more vertical transmission), while types I and IV (pSym) vary in size and gene content with phylogenies consistent with frequent horizontal transmission.

  clover-associated plasmids plasmidome replicons long-read k-mer genome

• Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

  PMID 16925841 · PMC1810556 · Genome biology · 2006 · 8 claims · 5 setups

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  Exogean is a framework using directed acyclic coloured multigraphs (DACMs) to represent biological objects (mRNA, ESTs, protein alignments, exons) and iteratively combine them into complex protein-coding transcript models.

  genome sequences automatic manual sequence

• MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

  PMID 19758471 · PMC2745589 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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  MtSNPscore, a weighted scoring pipeline combining literature evidence, in silico predictions, and case/control frequency, can prioritize likely pathogenic mtDNA variations

  sporadic mitochondrial reported ataxia mitochondrial functional compensatory

• Global genetic diversity of human metapneumovirus fusion gene.

  PMID 15207075 · PMC3323143 · Emerging infectious diseases · 2004 · 8 claims · 6 setups

  Full-text index only

  Phylogenetic analysis of the HMPV F gene identifies two main groups (A and B, 93%-96% amino acid identity) further divided into four subgroups (A1, A2, B1, B2)

  hmpv llc-mk2 clinical rt-pcr sequence phylogenetic

• OPTIC: orthologous and paralogous transcripts in clades.

  PMID 17933761 · PMC2238935 · Nucleic acids research · 2008 · 6 claims · 7 setups

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  OPTIC is a database providing gene predictions and orthology assignments for three clades: amniotes (human, dog, mouse, opossum, platypus, chicken), 12 Drosophila species, and 4 Caenorhabditis nematodes.

  drosophila translated gene orthologous homology-based all-against-all tree-based

• Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis.

  PMID 18307777 · PMC2268939 · BMC microbiology · 2008 · 8 claims · 7 setups

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  MLST of 26 C. trachomatis strains reveals three non-overlapping clonal complexes (groups I, II, III)

  trachomatis pneumoniae chlamydiales mlst eburst upgma