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).

• miRge 2.0 for comprehensive analysis of microRNA sequencing data.

  PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups

  Has reproduction · 89

  miRge 2.0 introduces a novel SVM-based miRNA detection method using both hairpin structure and isomiR composition, yielding higher specificity for miRNA identification

  pooled colon datasets small a-to-i novel

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript

• Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

  PMID 12783626 · PMC161800 · BMC genomics · 2003 · 8 claims · 5 setups

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  A comparative genomics approach using hamster testis cDNA sequencing can identify genes not previously annotated in the human, mouse, rat and Fugu genomes

  hamster testis predicted cdna northern comparative

• GENCODE: producing a reference annotation for ENCODE.

  PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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  GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

  tissues encode rt-pcr comparative automated

• Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.

  PMID 15447792 · PMC523852 · BMC medical genetics · 2004 · 8 claims · 8 setups

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  TMPRSS3 mutations were identified in four additional Pakistani families with recessive, nonsyndromic congenital deafness co-segregating with DFNB8/B10 haplotypes

  pakistani affected retina tissues linkage sanger race

• 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

  Full-text index only

  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

  whole-genome genome computational gene northern

• Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.

  PMID 18719945 · PMC2716558 · Human genetics · 2008 · 8 claims · 6 setups

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  PCDH15 has an updated gene structure with four additional exons beyond the previously reported 35, producing isoforms in four classes with three alternative cytoplasmic domains (CD1, CD2, CD3).

  genomic retina cdna protocadherin str pcr rt-pcr