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).

• Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

  PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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  1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

  genome rhesus vega-annotated tpas transcript-to-genome same synteny

• Visualization-based discovery and analysis of genomic aberrations in microarray data.

  PMID 15953389 · PMC1181623 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  ChARMView integrates dynamic visualization with automated statistical analysis (EM-based breakpoint detection, one-sample sign test, permutation mean test) to discover chromosomal aberrations from array CGH and gene expression data

  saccharomyces breast yeast array gene

• A note on generalized Genome Scan Meta-Analysis statistics.

  PMID 15717930 · PMC551600 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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  An Edgeworth series approximation to the null distribution of the weighted GSMA statistic provides a more accurate representation than the normal approximation, especially in the tails

  simulated schizophrenia monte genome numerical

• The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements.

  PMID 18699995 · PMC2542386 · BMC genomics · 2008 · 8 claims · 5 setups

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  Some relatively recent (young) SDs accumulate in regions homologous to chromosomal inversions that occurred in the sister lineage

  genome sds chimpanzee colinear comparative interspecific genomic

• Recurrent DNA copy number changes in 1q, 4q, 6q, 9p, 13q, 14q and 22q detected by comparative genomic hybridization in malignant mesothelioma.

  PMID 9052404 · PMC2063309 · British journal of cancer · 1997 · 7 claims · 2 setups

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  This is the first genome-wide screening for DNA sequence gains and losses using CGH in malignant pleural mesothelioma tumours.

  pleural cgh comparative statistical

• GPCR genes are preferentially retained after whole genome duplication.

  PMID 18382678 · PMC2270905 · PloS one · 2008 · 8 claims · 6 setups

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  WGD-derived nGPCR duplicates in Tetraodon nigroviridis are retained at a significantly higher rate (23.5%) than the genome-wide average (15%)

  vertebrate ngpcr nigroviridis syntenic phylogenetic chromosomal

• High-density single nucleotide polymorphism genome-wide linkage scan for susceptibility genes for diabetic nephropathy in type 1 diabetes: discordant sibpair approach.

  PMID 18559660 · PMC2518505 · Diabetes · 2008 · 8 claims · 3 setups

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  Primary linkage finding for diabetic nephropathy is on chromosome 19q

  sibpairs genotype patients genome-wide statistical urinary

• Genome screen to detect linkage to common susceptibility genes for intracranial and aortic aneurysms.

  PMID 18948608 · PMC2629798 · Stroke · 2009 · 8 claims · 4 setups

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  Genomewide linkage analysis in 26 multiplex IA families with AA-affected members identified LOD peaks on chromosome 11 (LOD=3.0) and chromosome 6 (LOD=2.3) using a broad IA/AA-combined phenotype

  multiplex individuals fia subjects genomewide snp medical

• Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

  PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

  Has reproduction · 98

  Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

  clinical dnaa isogenic h37rv genome-wide structural deep-sequencing

• Genome-wide analysis of the human Alu Yb-lineage.

  PMID 15588477 · PMC3525081 · Human genomics · 2004 · 8 claims · 6 setups

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  1,733 Alu Yb-lineage elements are present on human autosomal chromosomes

  genome genomic non-human yb7 computational pcr-based pcr

• Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

  PMID 17000641 · PMC1636412 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  An anonymous SHyP oligonucleotide microarray can capture genomic signatures of DNA sequence variation from any organism, including a previously unsequenced species

  genomic gonystylus subset restriction-digested custom self-self blast

• EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

  PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

  sequences homologous proteins coding pairwise single sequence

• Bacteriophage Mu integration in yeast and mammalian genomes.

  PMID 18953026 · PMC2602771 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  In vitro-assembled Mu transpososomes, delivered by electroporation, efficiently integrate marker genes into yeast, mouse ES, human HeLa, and human ES cell genomes

  cerevisiae ab2.2 hela fes29 electroporation southern transposition