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).

• Better smelling through genetics: mammalian odor perception.

  PMID 18938244 · PMC2590501 · Current opinion in neurobiology · 2008 · 8 claims · 8 setups

  Full-text index only

  Odorant receptor (OR) gene repertoire size and pseudogene fraction vary dramatically across mammalian species

  mammals subjects v1r trpc2 comparative genetic targeted

• Analysis of sequence conservation at nucleotide resolution.

  PMID 18166073 · PMC2230682 · PLoS computational biology · 2007 · 8 claims · 4 setups

  Full-text index only

  SCONE (Sequence CONservation Evaluation) is a novel method that estimates evolutionary rate and a neutrality p-value for individual nucleotide positions in a multiple sequence alignment.

  encode population comparative snp functional

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

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

  Full-text index only

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

  panel brain chicken flna comparative rt-pcr homology

• Long-range regulation is a major driving force in maintaining genome integrity.

  PMID 19682388 · PMC2741452 · BMC evolutionary biology · 2009 · 7 claims · 5 setups

  Full-text index only

  Long-range transcriptional regulation is a major driving force in maintaining genome integrity by constraining where chromosomal breakpoints can become fixed.

  opossum genome comparative identification statistical

• Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

  PMID 17052348 · PMC1624830 · BMC genomics · 2006 · 8 claims · 8 setups

  Full-text index only

  Phyletic retention (ortholog presence across organisms) is the single most predictive feature of gene essentiality in both E. coli and S. cerevisiae.

  coli cerevisiae comparative machine single-gene

• From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism.

  PMID 17983265 · PMC2062474 · PLoS computational biology · 2007 · 8 claims · 7 setups

  Full-text index only

  There has been a large turnover of the mitochondrial proteome during evolution: cell envelope synthesis proteins virtually disappeared, and replication, transcription, cell division, transport, regulation, and signal transduction proteins were replaced by eukaryotic proteins

  alpha-proteobacterial reclinomonas reconstructed yeast comparative phylogenomic cog

• H-DBAS: human-transcriptome database for alternative splicing: update 2010.

  PMID 19969536 · PMC2808982 · Nucleic acids research · 2010 · 8 claims · 4 setups

  Full-text index only

  RNA-Seq tags from the polysome fraction identify AS exons that are very likely used for protein synthesis

  dld-1 rna-seq western real-time

• From microarrays to genome duplications.

  PMID 12914655 · PMC193639 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Gene3D shows that most genes across sequenced genomes can be assigned to known structural domain families, many of which are shared across kingdoms of life

  tumor cancer plated saccharomyces comparative nonsense-mediated cell-based

• MODBASE: a database of annotated comparative protein structure models and associated resources.

  PMID 16381869 · PMC1347422 · Nucleic acids research · 2006 · 8 claims · 7 setups

  Full-text index only

  MODBASE is a database of automatically calculated comparative protein structure models covering all UniProt sequences matchable to a known structure

  uniprot non-redundant complexes saccharomyces comparative pairwise domain-domain

• Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry.

  PMID 18939861 · PMC2669493 · Journal of proteome research · 2008 · 8 claims · 5 setups

  Full-text index only

  IEF provides superior reproducibility and resolution of peptide fractionation compared to SCX, for both large (100 µg) and small (10 µg) protein inputs

  rko rectal bovine shotgun comparative ief

• Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs.

  PMID 18450818 · PMC2425492 · Nucleic acids research · 2008 · 8 claims · 5 setups

  Full-text index only

  Pyknons (recurrent, genome-specific, ≥16nt motifs with ≥30 intact intergenic/intronic copies and ≥1 exonic copy) span a substantial fraction of previously uncharacterized intronic space (7.4% human, 4.4% mouse)

  pyknon computational comparative term

• 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

• Getting positive about selection.

  PMID 12914654 · PMC193638 · Genome biology · 2003 · 8 claims · 4 setups

  Full-text index only

  Purifying selection is the predominant form of molecular evolution, preserving fitness by eliminating deleterious mutations, while positive selection is rare but critical for adaptation.

  genome chimpanzee human-chimpanzee humans whole-genome ratio maximum-likelihood

• DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

  PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

  Full-text index only

  Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

  aml tumor novo additional genome snp comparative

• Proteomics identifies multipotent and low oncogenic risk stem cells of the spleen.

  PMID 20005973 · PMC2891339 · The international journal of biochemistry & cell biology · 2010 · 8 claims · 5 setups

  Full-text index only

  CD45- splenic stem cell-specific proteins are identical to core iPS/ES markers OCT3/4, SOX2, KLF4, c-MYC and NANOG.

  spleen cd45 hox11+ lc-ms rt-pcr immunofluorescence

• A novel approach to tag and identify geranylgeranylated proteins.

  PMID 19784953 · PMC2855049 · Electrophoresis · 2009 · 7 claims · 7 setups

  Full-text index only

  Metabolic incorporation of azido-GG alcohol followed by Cu(I)-catalyzed click reaction with TAMRA-alkyne selectively labels geranylgeranylated proteins for fluorescence detection

  jurkat cos-7 mcf-7 embryonic metabolic comparative fractionation

• Evolutionary cores of domain co-occurrence networks.

  PMID 15788102 · PMC1079808 · BMC evolutionary biology · 2005 · 8 claims · 4 setups

  Full-text index only

  The innermost (globally central) cores of protein domain co-occurrence networks gradually grow in size with increasing evolutionary/developmental complexity of the organism.

  cerevisiae domain weighted comparative

• EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

  PMID 16381980 · PMC1347508 · Nucleic acids research · 2006 · 7 claims · 4 setups

  Full-text index only

  EPD is an annotated, non-redundant collection of experimentally defined eukaryotic POL II promoters accessed via genome position pointers.

  rice preliminary primer sequence quality

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

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

  Full-text index only

  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

• 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