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).

• The global landscape of sequence diversity.

  PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups

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  Eukaryotic sequence datasets show substantially greater genetic diversity (higher sequence/gene family discovery rates) than bacterial datasets, likely related to differences in modes of genetic inheritance.

  fully eukaryotic complete gene blast-based est gene

• Comparative proteomic analysis of cell lines and scrapings of the human intestinal epithelium.

  PMID 17407598 · PMC1852558 · BMC genomics · 2007 · 8 claims · 7 setups

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  Global protein expression profiles of cultured intestinal epithelial cell lines differ from those of intestinal epithelial scrapings in vivo

  caco-2 ht-29 hep muscle 2-d 2-de principal

• Daily temperature cycles promote alternative splicing of RNAs encoding SR45a, a splicing regulator in maize.

  PMID 33705553 · PMC8195531 · Plant physiology · 2021 · 8 claims · 4 setups

  Has reproduction · 76

  Increasing maximum daily temperature (MDT) globally elevates the frequency of alternative splicing in maize, particularly intron retention and exon skipping.

  maize bulk gene enrichment

• Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

  PMID 17062162 · PMC1635044 · Virology journal · 2006 · 8 claims · 6 setups

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  VACV-DUKE is most similar to VACV-ACAM2000 and VACV-CLONE3, confirming it as a Dryvax-derived isolate

  vacv-duke whole-genome phylogenetic comparative

• Mice and more.

  PMID 14519193 · PMC328447 · Genome biology · 2003 · 8 claims · 7 setups

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  A multispecies weighted conservation score, which accounts for each species' divergence rate, can identify conserved non-coding sequences (multispecies conserved sequences, MCSs) likely to be biologically significant

  cftr ciona embryonic chromosome comparative genome bac-based

• 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

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

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

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  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

• Evolutionary origins of human apoptosis and genome-stability gene networks.

  PMID 18832373 · PMC2577361 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  The entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2.

  apoptosis fully same orthologous protein-protein comparative orthology

• A mouse plasma peptide atlas as a resource for disease proteomics.

  PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups

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  A publicly available, high-quality mouse plasma peptide/protein repository (mouse PeptideAtlas) was built from 568 LC-MS/MS runs on four reference plasma pools.

  plasma peptides fully tissues lc-ms anion database

• FeatureScan: revealing property-dependent similarity of nucleotide sequences.

  PMID 16845077 · PMC1538849 · Nucleic acids research · 2006 · 6 claims · 5 setups

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  FeatureScan transforms nucleotide sequences into numerical signals of physico-chemical/conformational properties and compares them via a convolution/correlation (Fourier transform) method rather than comparing letters

  randomly fully same chimpanzee signal-theoretic featurescan blast

• Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

  PMID 20161474 · PMC2794050 · Nature chemistry · 2009 · 8 claims · 7 setups

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  A parallel combinatorial one-pot multi-step protecting-group procedure (Lewis acid catalyzed, up to seven steps) can transform tetra-O-TMS glucopyranosides into differentially protected monosaccharide building blocks without intermittent work-up/purification

  library database oligovalent b-cells glycan bioinformatics one-pot

• BRCA1 and BRCA2 mutations in Turkish breast/ovarian families and young breast cancer patients.

  PMID 10952777 · PMC2363542 · British journal of cancer · 2000 · 7 claims · 4 setups

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  11 mutations (9 BRCA1, 2 BRCA2) were identified across 105 Turkish patients using combined PTT, sequencing, and heteroduplex analysis.

  peripheral genomic truncation direct heteroduplex

• Genetic diversity of vaccine candidate antigens in Plasmodium falciparum isolates from the Amazon basin of Peru.

  PMID 18505558 · PMC2432069 · Malaria journal · 2008 · 8 claims · 7 setups

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  CSP (Th2R/Th3R region) is polymorphic in Peruvian isolates, with four distinct alleles identified, none identical to the 3D7 vaccine strain

  pfcsp pfmsp-1 pfama-1 pflsa-1 pcr polymorphism multilocus

• Evaluating native-like structures of RNA-protein complexes through the deep learning method.

  PMID 36828844 · PMC9958188 · Nature communications · 2023 · 8 claims · 7 setups

  Has reproduction · 67

  DRPScore identifies native-like RNA-protein structures with higher success rates than ITScore-PR, DARS-RNP, and 3dRPC across bound and unbound testing sets.

  bound-bound unbound-bound unbound-unbound bacillus structure interface secondary

• Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

  PMID 23979935 · PMC3789805 · G3 (Bethesda, Md.) · 2013 · 8 claims · 8 setups

  Has reproduction · 91

  An index of 23,859,893 (~24 million) homoeo-SNPs distinguishing A-genome from D-genome cotton was constructed at a density of one SNP per 32.3 bases of the D5 reference.

  gossypium longicalyx nine diploids whole-genome wgs read

• Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

  PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups

  Has reproduction · 93

  24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).

  jatropha geo bulk semi-quantitative quantitative