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).
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Has reproduction · 74
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups
ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.
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miRGen 2.0: a database of microRNA genomic information and regulation.
PMID 19850714 · PMC2808909 · Nucleic acids research · 2010 · 7 claims · 6 setups
miRGen 2.0 is a database providing comprehensive information about the genomic position of human and mouse microRNA coding transcripts and their regulation by transcription factors
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In silico meets in vivo.
PMID 18304380 · PMC2374716 · Genome biology · 2008 · 8 claims · 8 setups
About 10% of positions in multiple sequence alignments of the human genome with other vertebrate genomes are likely incorrect.
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Genomic views of distant-acting enhancers.
PMID 19741700 · PMC2923221 · Nature · 2009 · 8 claims · 8 setups
Meta-analysis of ~1200 top GWAS SNPs found that in 40% of cases (472/1170) no known exons overlap the linked SNP or its haplotype block, implying noncoding variation causally contributes to many traits.
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Full-text index only
DNA methylation of cancer genome.
PMID 19960550 · PMC2940836 · Birth defects research. Part C, Embryo today : reviews · 2009 · 8 claims · 7 setups
Cancer epigenome alterations fall into two main categories: hypermethylation of tumor suppressor genes and hypomethylation of oncogenes or heterochromatin.