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).

• Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.

  PMID 15784611 · PMC1069129 · Nucleic acids research · 2005 · 7 claims · 8 setups

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  Position-specific phylogenetic features describing evolutionary conservation at a site (e.g. SIFT score, normalized site entropy, residue frequency change) are the best individual discriminators of disease-causing versus neutral GPCR mutations.

  dbsnp gpcr transmembrane sequence six-frame sift logistic

• Comprehensive splice-site analysis using comparative genomics.

  PMID 16914448 · PMC1557818 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  Over half a million splice sites were collected from five species (H. sapiens, M. musculus, D. melanogaster, C. elegans, A. thaliana) and classified into four main subtypes: U2-type GT-AG and GC-AG, and U12-type GT-AG and AT-AC.

  refseq u2-type genes comparative information phylogenetic

• ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

  PMID 16845048 · PMC1538778 · Nucleic acids research · 2006 · 6 claims · 4 setups

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  ProMiR II improves on the original ProMiR by integrating free energy, G/C ratio, conservation score and entropy for more controllable miRNA prediction

  genome cytomegalovirus six probabilistic 5-fold directional

• Two previously proposed P1/P2-differentiating and nine novel polymorphisms at the A4GALT (Pk) locus do not correlate with the presence of the P1 blood group antigen.

  PMID 16212661 · PMC1282566 · BMC genetics · 2005 · 8 claims · 4 setups

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  The previously proposed P2-specific markers -551_-550insC and -160A>G do not correlate with P1/P2 phenotype, since they occur homozygously in many P1 individuals too

  genomic erythrocytes direct pcr pcr-asp

• Prevalence of von Hippel-Lindau gene mutations in sporadic renal cell carcinoma: results from The Netherlands cohort study.

  PMID 15932632 · PMC1177929 · BMC cancer · 2005 · 7 claims · 4 setups

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  VHL mutations were detected in 61% (114/187) of sporadic clear-cell RCC patients

  archival subset flanking paraffin-embedded pcr-sscp feasibility histopathological

• Ab initio identification of human microRNAs based on structure motifs.

  PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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  MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

  genome mirna hairpins chromosome secondary linear five-fold

• Does distance matter? Variations in alternative 3' splicing regulation.

  PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

  intronic human-mouse same comparative polypyrimidine branch

• Analysis of recent segmental duplications in the bovine genome.

  PMID 19951423 · PMC2796684 · BMC genomics · 2009 · 8 claims · 6 setups

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  Recently duplicated sequence (≥1 kb, ≥90% identity) comprises 3.11% (94.4 Mb) of the bovine genome assembly (Btau_4.0)

  bos bovine genes cattle genome fluorescent repeat

• Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.

  PMID 15817567 · PMC1074747 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  966 pseudogenes derived from the four human Y (hY) RNAs were characterized in the human genome

  genome chimpanzee pseudogenes genomic megablast blat sequence

• Widespread ultraconservation divergence in primates.

  PMID 18492662 · PMC2464743 · Molecular biology and evolution · 2008 · 8 claims · 4 setups

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  The number of UCEs has decreased throughout primate evolution, from ~1,000 in ancestral primates to 635 in modern humans.

  hg18 genome genes computed comparative snp gene

• Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

  PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups

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  A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys

  personal genomic pcr-validated unrelated short-read pcr sanger

• Molecular characterization of retinitis pigmentosa in Saudi Arabia.

  PMID 19956407 · PMC2786884 · Molecular vision · 2009 · 8 claims · 7 setups

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  The causative mutation was identified in 51 of 52 (94%/98%) Saudi RP patients, including seven novel mutations.

  blood-derived families pcr-amplified ethnically genome-wide linkage bidirectional

• Variants in the ATM gene associated with a reduced risk of contralateral breast cancer.

  PMID 18701470 · PMC2562548 · Cancer research · 2008 · 7 claims · 4 setups

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  Carriers of common ATM variants (>=1% frequency) have a statistically significant reduction in risk of contralateral breast cancer (CBC)

  peripheral wecare atm mutation case-control variant

• Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

  PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

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  The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

  genome seven genes computational cage comparative

• Sequence context affects the rate of short insertions and deletions in flies and primates.

  PMID 18291026 · PMC2374710 · Genome biology · 2008 · 8 claims · 6 setups

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  The rate of insertion or deletion of specific lengths can vary by more than 100-fold depending on the surrounding sequence context

  chimpanzee simulans chimp primate comparative direct nucleotide

• Positive selection for the male functionality of a co-retroposed gene in the hominoids.

  PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups

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  PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives

  african chimpanzee orangutan reconstructed population hka comparative

• Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.

  PMID 36864379 · PMC9979506 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups

  Has reproduction · 100

  French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population.

  boars lwd lws pig whole-genome genetic genome-wide

• Exon deletions and intragenic insertions are not rare in ataxia with oculomotor apraxia 2.

  PMID 19744353 · PMC2749023 · BMC medical genetics · 2009 · 8 claims · 6 setups

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  Gross mutations (exon deletions and intragenic insertions) are a frequent, not rare, cause of AOA2

  genomic peripheral setx sanger dosage long-range