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).

• Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

  PMID 19329065 · PMC5054122 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 8 setups

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  Nucleotide preference at CpG flanking sites transitions from 5' T (invertebrates) to 5' A (vertebrates) at the invertebrate-vertebrate boundary

  genomes same pufferfish elegans nucleotide genome-wide kruskal-wallis

• BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

  PMID 16417652 · PMC1413985 · Breast cancer research : BCR · 2006 · 8 claims · 7 setups

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  BOADICEA predicts accurately the number of BRCA1 and BRCA2 mutations across family groups and discriminates well between carriers and noncarriers

  french-canadian families brca1-positive same targeted full-length multiplex

• Recurring genomic breaks in independent lineages support genomic fragility.

  PMID 17090315 · PMC1636669 · BMC evolutionary biology · 2006 · 6 claims · 6 setups

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  The propensity of a chromosomal region to break is significantly correlated among independent lineages, even after accounting for covariates like region length and functional class.

  hg17 genome computationally comparative marker segmental

• Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms.

  PMID 16916449 · PMC1559705 · BMC genomics · 2006 · 8 claims · 5 setups

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  Genome-wide, both intronic SNPs (iSNPs) and FFD SNPs show a significant excess of A→G over complementary T→C substitutions, confirming prior transcription-coupled repair (TCR) findings from a single chromosome 7 region.

  autosomal intronic chimpanzee genes comparative human-chimpanzee background

• Intronic alternative splicing regulators identified by comparative genomics in nematodes.

  PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

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  Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

  elegans database transgenic comparative est cross-species

• Bias of selection on human copy-number variants.

  PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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  Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

  genome human-mouse cnv-encompassed inbred comparative randomization molecular

• Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

  PMID 18086709 · PMC2241899 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Preferred nucleotide sequences around the initiation codon are diverse among eukaryote species, but differences roughly reflect evolutionary relationships between species

  eukaryote genes hexanucleotide saccharomyces comparative cluster hexanucleotide

• Prevalence and penetrance of BRCA1 and BRCA2 mutations in a population-based series of breast cancer cases. Anglian Breast Cancer Study Group.

  PMID 11044354 · PMC2408797 · British journal of cancer · 2000 · 6 claims · 4 setups

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  BRCA1 and BRCA2 mutations are rare in the general population and account for only a small fraction of all breast cancer in the UK

  genomic pedigrees first-degree study pcr pedigree-based age

• Detecting transcriptionally active regions using genomic tiling arrays.

  PMID 16859498 · PMC1779562 · Genome biology · 2006 · 8 claims · 4 setups

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  A non-parametric method (TranscriptionDetector) integrates single-channel p-values from multiple replicate arrays into a multi-channel p-value (MCPV) to identify transcribed probed loci without assumptions about intensity distributions.

  anopheles chromosomes simulated genomic high-density sequence-based

• Polymorphisms in COL4A3 and COL4A4 genes associated with keratoconus.

  PMID 20029656 · PMC2796875 · Molecular vision · 2009 · 6 claims · 5 setups

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  No disease-causing mutations in COL4A3 or COL4A4 were found to be related to KC.

  genomic patients pcr sequencing genetic

• Involvement of the modifier gene of a human Mendelian disorder in a negative selection process.

  PMID 19888326 · PMC2765618 · PloS one · 2009 · 7 claims · 4 setups

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  The frequency of SAA1 alpha/alpha homozygotes is much higher among Armenian FMF patients (24%) than Karabakhian FMF patients (4%)

  genomic population simulated pcr pearson monte

• Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

  PMID 16417627 · PMC1382246 · BMC genetics · 2006 · 8 claims · 7 setups

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  Heterozygous truncating BRCA2 mutations occur in 47% (7/15) of gastrointestinal MSI cancer cell lines/xenografts, a higher rate than previously reported

  gastrointestinal ls174t pl3 msi gene rt-pcr rad51

• On the holobiont 'predictome' of immunocompetence in pigs.

  PMID 37127575 · PMC10150480 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 8 setups

  Has reproduction · 40

  Holobiont (combined genotype + microbiome) models performed better than partial models (genotype-only or microbiome-only) overall

  duroc fecal plasma serum snp 16s immunoglobulin

• A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

  PMID 16626494 · PMC1459863 · Malaria journal · 2006 · 8 claims · 5 setups

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  Pyrosequencing, after adjustment to a standard curve, provides accurate and precise estimates of allele frequencies in mixed MSP-1_19 infections

  falciparum cloned pyrosequencing pcr

• Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

  PMID 18418848 · PMC6668724 · Genes, chromosomes & cancer · 2008 · 6 claims · 5 setups

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  Emulsion PCR combined with picotiter plate pyrosequencing (454 sequencing) enables high-resolution, high-throughput detection of low-frequency sequence variants among the many individual copies of an amplified gene.

  erbb2-amplified erbb2-positive plasmid cos-7 emulsion serial immune-complex

• Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.

  PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.

  calanus sinicus genomic rna-seq novo sequence