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).

• CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

  PMID 19854943 · PMC2800233 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Functional ('bona fide') CGIs show distinct average/cumulative mutual information (AMI/CMI) distributions of neighboring CpG distances compared to non-functional CGIs and random genome segments

  genome random cd4+ six average mutual chip-seq

• Epigenetics and phenotypic variation in mammals.

  PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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  Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

  mammalian mhc chromosomes embryonic methylation high-throughput chip

• The gene guessing game.

  PMID 11025532 · PMC2448377 · Yeast (Chichester, England) · 2000 · 8 claims · 6 setups

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  Published methods for estimating human gene number diverge widely, from ~30,000 to over 140,000 genes.

  genomic ests tetraodon genome cpg est comparative

• A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.

  PMID 24204593 · PMC3810253 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 71

  MBD-Fc bound to Protein A paramagnetic beads selectively binds methylated (vertebrate host) DNA, depleting it from mixed samples

  3h-labeled imr-90 lambda saliva scintillation genome restriction

• In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

  PMID 17603907 · PMC1934366 · BMC genomics · 2007 · 8 claims · 8 setups

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  Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π GABA A receptor subunit genes

  subunit mammalian α1-β2-γ2-α6 cross-species promoter transcription

• Analysis of sequence conservation at nucleotide resolution.

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

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  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

• Evolution of motif variants and positional bias of the cyclic-AMP response element.

  PMID 17288573 · PMC1796609 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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  Canonical CRE positional bias toward the -1 to -150 bp TSS region is present in vertebrates (human, mouse, rat, chicken, frog, zebrafish) but absent in sea squirt, fruit fly and worm.

  tss-spanning cres genome known genome-wide comparative cpg