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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miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.
PMID 18029362 · PMC2238982 · Nucleic acids research · 2008 · 8 claims · 6 setups
miRNAMap 2.0 is a resource collecting experimentally verified miRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes
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In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.
PMID 17201911 · PMC1774567 · BMC genomics · 2007 · 8 claims · 5 setups
A computational EST-based pipeline can identify UTR-SNPs that are statistically over-represented in cancerous versus normal tissue libraries
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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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Genomic organization of zebrafish microRNAs.
PMID 18510755 · PMC2427041 · BMC genomics · 2008 · 8 claims · 6 setups
Using sequence conservation and prediction algorithms, 35 new zebrafish miRNAs were identified, bringing the total to 415.
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Identification of novel homologous microRNA genes in the rhesus macaque genome.
PMID 18186931 · PMC2254598 · BMC genomics · 2008 · 8 claims · 2 setups
454 rhesus miRNA genes were identified in total, including 383 novel genes in addition to 71 previously reported
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In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.
PMID 15871745 · PMC1156887 · BMC genomics · 2005 · 7 claims · 6 setups
Only 14±2% of canine transcripts were detected by U133A probe sets versus 49±6% of human transcripts when hybridized to the same chip
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The 10 sea urchin receptor for egg jelly proteins (SpREJ) are members of the polycystic kidney disease-1 (PKD1) family.
PMID 17629917 · PMC1934368 · BMC genomics · 2007 · 8 claims · 5 setups
Sea urchins possess 10 SpREJ (PKD1 family) genes, compared to five in humans, all defined by possession of a ~600 residue REJ domain
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The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.
PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups
The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.
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Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.
PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups
Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase
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Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.
PMID 17175533 · PMC1802619 · Nucleic acids research · 2007 · 8 claims · 6 setups
202 novel box H/ACA RNA-related sequences were identified in the human genome
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snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.
PMID 16990247 · PMC1636440 · Nucleic acids research · 2006 · 8 claims · 5 setups
snoSeeker (comprising CDseeker and ACAseeker) is a computational package that can screen for both guide and orphan snoRNA genes, unlike prior programs limited to guide snoRNAs
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CD70 (TNFSF7) is expressed at high prevalence in renal cell carcinomas and is rapidly internalised on antibody binding.
PMID 16892042 · PMC2360640 · British journal of cancer · 2006 · 6 claims · 6 setups
CD70 was identified by proteomic analysis of plasma membrane preparations as highly expressed in A498 and SW839 RCC-derived cell lines
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Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.
PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups
Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.
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The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.
PMID 18948287 · PMC2686472 · Nucleic acids research · 2009 · 8 claims · 5 setups
fRNAdb 3.0 is a completely rebuilt sequence database hosting a much larger collection of known/predicted non-coding RNA sequences with improved search functionality
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Non-EST based prediction of exon skipping and intron retention events using Pfam information.
PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups
A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.
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miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.
PMID 16381831 · PMC1347497 · Nucleic acids research · 2006 · 6 claims · 6 setups
miRNAMap integrates known miRNA genes from miRBase, literature-curated validated targets, and computationally predicted miRNA genes and targets for human, mouse, rat and dog.