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).

• Finding signals that regulate alternative splicing in the post-genomic era.

  PMID 12429065 · PMC244920 · Genome biology · 2002 · 8 claims · 8 setups

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  Alternative splicing generates protein and regulatory diversity from a limited number of genes and modulates isoform levels in a cell-context-specific manner

  intron-containing genome brain-specific cell-free computational comparative selex

• Intronic alternative splicing regulators identified by comparative genomics in nematodes.

  PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

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  Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

  elegans database transgenic comparative est cross-species

• Context dependent function of APPb enhancer identified using enhancer trap-containing BACs as transgenes in zebrafish.

  PMID 18832376 · PMC2577333 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  A novel enhancer trap method retrofitting BACs with Tn10-based transposons enables nontargeted, functional mapping of noncontiguous cis-regulatory elements as zebrafish transgenes.

  zebrafish bac genomic transgenic field bac

• Mutation analysis of SLC26A4 in mainland Chinese patients with enlarged vestibular aqueduct.

  PMID 19786220 · PMC3309400 · Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery · 2009 · 7 claims · 5 setups

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  SLC26A4 mutations are highly prevalent in Chinese patients with SNHL and EVA, with mutations found in 100% (32/32) of subjects.

  blood-derived subjects mutation pure high-resolution

• Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

  PMID 18187510 · PMC2275096 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  G-richness downstream of the TSS is strand-biased, concentrated on the nontemplate strand, with a peak at +200 to +300 bp

  refseq chicken random genome-wide quadparser regulatory

• A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.

  PMID 16237125 · PMC1258171 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  A genome-wide computational survey identifies 245 genes in mammals (264 across six species) that produce RREO events in expressed sequences

  expressed representative random genes computational orf statistical

• Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

  PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

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  Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

  genomic pnmt promoter pcr population haplotype

• Target SNP selection in complex disease association studies.

  PMID 15248903 · PMC487897 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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  A computational pipeline can retrieve gene sequence, collect SNP variation data, and annotate SNPs falling in functional motifs (promoter, exon-intron structure, AU-rich elements, TF binding sites, splice sites) with expression in target tissue

  genes pooled primer computational maldi-tof blast

• CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity.

  PMID 15507145 · PMC526769 · BMC medical genetics · 2004 · 8 claims · 7 setups

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  PCR amplification and sequencing of CLC-2 revealed 1 SNP in the promoter, 4 SNPs in intron 1, and none in exon 20

  nasal genomic ib3-1 western pcr fisher's

• A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

  PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

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  Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

  unigene shuffled real genomes genome-wide alignment gene

• Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases.

  PMID 19063745 · PMC2613935 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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  Gene Prospector is a Web-based application that selects and prioritizes potential disease-related genes using a curated, updated literature database of genetic association studies

  huge pdgene snps3d dbsnp curated comparative snp

• Identification of five novel mutations in the long isoform of the USH2A gene in Chinese families with Usher syndrome type II.

  PMID 19023448 · PMC2584772 · Molecular vision · 2008 · 8 claims · 7 setups

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  Mutations in USH2A are responsible for most cases of USH2

  genomic family probands ush2a direct restriction single

• Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.

  PMID 18410676 · PMC2375447 · BMC genomics · 2008 · 8 claims · 7 setups

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  Chicken and turkey genomes differ by only two inter-chromosomal rearrangements (GGA2 orthologous to MGA3+6; GGA4 orthologous to MGA4+9), both involving centromeres.

  chicken turkey broiler chromosome single fish

• Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.

  PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups

  Has reproduction · 58

  Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.

  dissected concatenated yakuba reference whole-transcriptome novo read