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).

• Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

  PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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  ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

  presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous

• Genome informatics: taming the avalanche of genomic data.

  PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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  Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

  genes arabidopsis genome vertebrate comparative conservation whole-genome

• Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae.

  PMID 15983137 · PMC1160521 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  A codon usage similarity statistic (ε, based on squared/absolute differences of codon frequencies with an optimized amino acid usage factor) was developed to compare ORFs against a set of 80 reference genomes.

  influenzae novel reference codon phylogenetic comparative

• 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

  Many strains currently classified as L. casei or L. paracasei are taxonomically misclassified; reclassifying them to their closest type strain improves functional predictive power

  novel casei genomes selected whole-genome maximum-likelihood pairwise

• Genetic diversity among five T4-like bacteriophages.

  PMID 16716236 · PMC1524935 · Virology journal · 2006 · 8 claims · 8 setups

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  A core set of 82 conserved genes (T4-like genes) is present in all five genomes analyzed, clustered in large collinear blocks.

  bacteriophages five conserved aeh1 genome orf trna

• Comparative genomics.

  PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups

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  Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences

  caenorhabditis yeast mammalian vertebrate whole-genome comparative interspecies-similarity-informed

• Microbial metagenomics.

  PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups

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  Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides

  gastrointestinal acid ocean group metagenomic shotgun comparative

• SARS--beginning to understand a new virus.

  PMID 15035025 · PMC7097337 · Nature reviews. Microbiology · 2003 · 8 claims · 8 setups

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  A previously unknown coronavirus (SARS-CoV) was isolated from FRhK-4 and Vero E6 cells inoculated with clinical specimens from SARS patients and identified as the causative agent of SARS

  frhk-4 macaques sars-cov coronavirus virus infection whole-genome

• Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.

  PMID 17916580 · PMC2533590 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 7 claims · 7 setups

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  Adult and weaned-children gut microbiota show high functional (gene-content) uniformity despite taxonomic differences, while unweaned infant microbiota show high inter-individual variation in both taxonomic and gene composition.

  fecal assembled predicted gut whole-genome gene reciprocal

• The DNA sequence and analysis of human chromosome 13.

  PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

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  95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

  chromosome rpci-11 genomic comparative fluorescence

• Genomics, proteomics and bioinformatics: all in the same boat.

  PMID 12374575 · PMC244909 · Genome biology · 2002 · 8 claims · 8 setups

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  Microarray sensitivity has improved enough to analyze clinical samples as small as 10-50 nanograms, and many early microarray experiments may need to be repeated due to data quality issues

  clinical oligonucleotide-immobilized dendritic blood microarray chip combined

• MitoVariome: a variome database of human mitochondrial DNA.

  PMID 19958475 · PMC2788364 · BMC genomics · 2009 · 8 claims · 5 setups

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  MitoVariome is a web-based, integrated variome database for human mitochondrial DNA that unifies sequence variation, haplogroup, and disease annotation information not jointly available in prior databases (MITOMAP, mtDB, Mitome, MitoRes).

  mitochondrial korean sequence short restriction

• Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

  PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

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  Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

  parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr

• Population genomics: diversity and virulence in the Neisseria.

  PMID 18822386 · PMC2612085 · Current opinion in microbiology · 2008 · 8 claims · 8 setups

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  Horizontal genetic exchange (recombination) plays a central role in shaping bacterial speciation and population structure in Neisseria

  neisseria meningitidis meningococcal multi-locus microarray genome

• Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

  PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

  brassica r500 rapa genomic bulk reference-based snp

• Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

  PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 51

  Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects

  pbmcs eight pbmc monocytes scrna-seq genetic cis-eqtl

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr