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).

• Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.

  PMID 41826827 · PMC13202766 · BMC microbiology · 2026 · 8 claims · 8 setups

  Has reproduction · 71

  R. artemisiae harbors six prokaryotic taxa: two plant pathogens ('Ca. P. solani', 'Ca. A. phytopathogenicus') and four insect endosymbionts ('Ca. Vidania', 'Ca. Purcelliella', 'Ca. Karelsulcia', and Wolbachia).

  individual long endosymbiont artemisiae pcr-free pcr nucleic

• Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a.

  PMID 18613968 · PMC2483966 · Virology journal · 2008 · 7 claims · 7 setups

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  Quasispecies complexity and diversity within HVR1 are lower in the SVR group than in the TF group

  serum hvr1 svr rt-pcr shannon hamming

• Characterizing natural variation using next-generation sequencing technologies.

  PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups

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  Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.

  pichia individuals saccharomyces individual whole-genome partial comparative

• Evolutionarily conserved human targets of adenosine to inosine RNA editing.

  PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

  panel brain chicken flna comparative rt-pcr homology

• Reconstruction of pathways associated with amino acid metabolism in human mitochondria.

  PMID 18267298 · PMC5054205 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 5 setups

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  Out of 20 amino acids, the metabolic pathways of 17 utilize mitochondrial enzymes, and dysfunction of these enzymes causes over 40 known human mitochondrial diseases/disorders

  mitoproteome orthologous liver mitochondrial sequence-based computational literature

• One-pot shotgun quantitative mass spectrometry characterization of histones.

  PMID 19764812 · PMC2798817 · Journal of proteome research · 2009 · 8 claims · 8 setups

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  One-pot propionylation and trypsin digestion of unfractionated bulk histones enables quantitative Bottom Up MS characterization of histone PTMs without prior off-line HPLC or SDS-PAGE purification

  hela wild-type set2δ yeast bottom rp-hplc one-pot

• Increasing the number of SNP loci does not necessarily improve prediction power at least in the comparison of MTHFR SNP and haplotypes.

  PMID 19075497 · PMC4771609 · Journal of epidemiology · 2008 · 7 claims · 6 setups

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  Increasing the number of typed SNP loci does not necessarily improve prediction power, at least for the MTHFR gene

  healthy genomic genotype trial randomized snp haplotype

• In silico segmentations of lentivirus envelope sequences.

  PMID 17376229 · PMC1847453 · BMC bioinformatics · 2007 · 8 claims · 8 setups

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  C and V regions of lentivirus SU sequences have distinct statistical (oligonucleotide/amino-acid) compositions that HMMs can learn and use to delimit them.

  eiav hiv hmm-based hmm artificial

• Genetic determinants of virulence in pathogenic lineage 2 West Nile virus strains.

  PMID 18258114 · PMC2600181 · Emerging infectious diseases · 2008 · 8 claims · 7 setups

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  The nonstructural genes, especially NS5, are the most variable regions between highly and less neuroinvasive lineage 2 WNV strains

  lineage mice patients complete phylogenetic nucleotide

• Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

  PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 82

  An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

  exemplar paired-end cleaned assembled transcriptome read novo

• Geographic distribution and genetic diversity of the Ehrlichia sp. from Panola Mountain in Amblyomma americanum.

  PMID 18433500 · PMC2394526 · BMC infectious diseases · 2008 · 8 claims · 6 setups

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  PME was not recently introduced to the United States, given its extensive geographic distribution, multi-year persistence at sites, and genetic variability

  amblyomma pme-positive map1 nested pcr sanger

• Scapuloperoneal spinal muscular atrophy and CMT2C are allelic disorders caused by alterations in TRPV4.

  PMID 20037587 · PMC3786192 · Nature genetics · 2010 · 8 claims · 6 setups

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  SPSMA and CMT2C are allelic disorders caused by mutations in TRPV4

  spsma spsma-affected hek293 candidate histopathology confocal

• Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.

  PMID 19851457 · PMC2760143 · PLoS pathogens · 2009 · 8 claims · 4 setups

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  Genetically distinct RV clades of the same G/P-type (G3P[8]) can co-circulate within a single epidemic season and cause disease

  g3p[8] rv-positive concatenated deduced rt-pcr pcr-elisa phylogenetic

• Cataloging coding sequence variations in human genome databases.

  PMID 18974781 · PMC2570488 · PloS one · 2008 · 8 claims · 7 setups

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  A significant proportion of CVs overlap between HGMD and dbSNP (4.36% of HGMD CVs registered in dbSNP; 8.11% of dbSNP CVs registered in HGMD), warranting caution when interpreting phenotypic relevance of concurrent CVs.

  coding hapmap concurrent nssnps database hapmap amino

• Isoforms of U1-70k control subunit dynamics in the human spliceosomal U1 snRNP.

  PMID 19784376 · PMC2747018 · PloS one · 2009 · 8 claims · 8 setups

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  Native human U1 snRNP shows differential incorporation of four protein isoforms (U1-70k isoforms 1/2, Sm-B/B')

  native snrna intact denatured proteomic denaturing nucleic

• A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

  PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

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  A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

  domestic red same white partial comparative pcr

• Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

  PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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  Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

  hgmd refseq aligned svm svm reciprocal inter-species

• Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

  PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups

  Has reproduction · 58

  Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.

  dissected concatenated yakuba reference whole-transcriptome novo read

• Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation.

  PMID 19812689 · PMC2753653 · PloS one · 2009 · 7 claims · 5 setups

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  Natural CTL immunodominance toward variable proteome regions increases epitope mismatch with challenge strains and recapitulates the escape-driven CTL failure seen in natural infection, contributing to HIV vaccine failure

  hiv-1 polyclonally shannon cross-clade ctl

• The development of an integrated platform to identify breast cancer glycoproteome changes in human serum.

  PMID 19782370 · PMC4142217 · Journal of chromatography. A · 2010 · 8 claims · 6 setups

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  M-LAC (multi-lectin affinity chromatography combining Con A, WGA and Jacalin) provides comprehensive capture of glycoproteins from biological fluids based on differing glycan specificities

  pooled m-lac excised individual high-performance sds-page lectin