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).

• 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

• PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

  PMID 17202160 · PMC1899096 · Nucleic acids research · 2007 · 7 claims · 5 setups

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  PolyA_DB 2 catalogs poly(A) sites for genes in human, mouse, rat, chicken and zebrafish, identified by aligning cDNA/ESTs with genome sequences

  sequences poly cdna trace pssm-based

• Genomics: applications in mechanism elucidation.

  PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups

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  Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.

  extract panel saccharomyces inbred affinity cytotoxicity genome-wide

• The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

  PMID 19094205 · PMC2637867 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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  AR was duplicated into two paralogs, AR-A and AR-B, during a teleost-specific whole genome duplication (WGD), after the split of Acipenseriformes but before the divergence of Osteoglossiformes.

  fish full-length tetraodon rt-pcr database molecular

• A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.

  PMID 19087293 · PMC2636810 · BMC bioinformatics · 2008 · 6 claims · 6 setups

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  A theoretical exon-exon junction protein database accounting for all in-phase (frame-preserving) exon combinations can be built from the Ensembl Core Database using Perl/Bioperl/MySQL/Ensembl API.

  ensembl liver candidate same database tandem decoy

• Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

  PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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  A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

  myeloid reference selected genome-localized microarray promoter k-medoids

• The HuRef Browser: a web resource for individual human genomics.

  PMID 19036787 · PMC2686481 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  The HuRef Browser is a unified web application integrating assembly, annotation, and assembly-to-assembly comparison (ATAC) views for the diploid HuRef individual human genome.

  individual huref whole-genome assembly-to-assembly variant

• Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

  PMID 19004867 · PMC2602793 · Nucleic acids research · 2008 · 7 claims · 4 setups

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  Methylation patterns of the five GR promoters activated in PBMCs are highly variable between individuals.

  chromosome genomic pbmc multi-species phylogenetic bisulphite

• Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.

  PMID 18990211 · PMC2585095 · BMC microbiology · 2008 · 8 claims · 7 setups

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  The 55 clinical B. cereus isolates were phylogenetically diverse, comprising 38 sequence types (STs) distributed across two of three previously described clades.

  clinical concatenated cereus isolates multilocus phylogenetic pcr

• Evolutionary history of the UCP gene family: gene duplication and selection.

  PMID 18980678 · PMC2584656 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  The UCP gene family arose through two ancestral gene duplications early in vertebrate evolution, producing the UCP1, UCP2 and UCP3 lineages.

  vertebrate ucp human-mouse ucp1 sequence phylogenetic gene

• Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease.

  PMID 18974839 · PMC2572839 · PloS one · 2008 · 7 claims · 6 setups

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  Pseudomonas 16S rDNA is significantly more prevalent in ileal biopsies of CD patients than non-IBD patients

  ileal p16s otu pseudomonas nested cloning

• Evolutionary genomics reveals lineage-specific gene loss and rapid evolution of a sperm-specific ion channel complex: CatSpers and CatSperbeta.

  PMID 18974790 · PMC2572835 · PloS one · 2008 · 8 claims · 6 setups

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  The CatSper channel complex (four CatSpers plus CatSperβ) originated as early as primitive metazoans such as the Cnidarian Nematostella vectensis

  metazoan catsper pore chicken tblastn maximum sequence

• A new mutation in BFSP2 (G1091A) causes autosomal dominant congenital lamellar cataracts.

  PMID 18958306 · PMC2573734 · Molecular vision · 2008 · 8 claims · 7 setups

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  The disease locus maps to chromosome 3q21-25, linked to markers D3S2322 and D3S1541

  four-generation bfsp2 wild-type microsatellite direct denaturing

• Novel transglutaminase-1 mutations and genotype-phenotype investigations of 104 patients with autosomal recessive congenital ichthyosis in the USA.

  PMID 18948357 · PMC3044481 · Journal of medical genetics · 2009 · 8 claims · 6 setups

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  TGM1 germline mutations were identified in 55% (57/104) of patients with ARCI

  arci unrelated dog direct sequence blast

• Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes.

  PMID 18948297 · PMC2602764 · Nucleic acids research · 2008 · 6 claims · 8 setups

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  Incorporating a biotin tag into the HTA probe enables purification of labeled heteroduplexes and direct sequencing of the separated query strand, allowing recovery of minor variant sequences

  hiv-1 biotin-hta-purified original recovered heteroduplex rt-pcr sanger

• Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs.

  PMID 18838389 · PMC2582632 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  Although 86% of individual human exons are conserved in the mouse genome, only a small fraction (431/20392, ~2%) of human AS variants are perfectly conserved AS variants in mice.

  genome full-length ~3x10^7 isoform whole-genome full-length polysome

• G-quadruplexes: the beginning and end of UTRs.

  PMID 18832370 · PMC2577360 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  UTRs show significant strand asymmetry with C-PQS more common than G-PQS, consistent with general depletion of G-quadruplex-forming RNA

  genome 5'-utr simulated protein-coding computational high-resolution utr

• Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

  PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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  Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

  hgmd refseq aligned svm svm reciprocal inter-species

• Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

  PMID 18786246 · PMC2556353 · BMC genomics · 2008 · 6 claims · 6 setups

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  PLP, Sox10, SOD3, and Ptn are direct regulatory targets of Sox10, confirmed by chromatin immunoprecipitation binding to conserved cis-elements

  rt4d6 gst-sox10 microarray comparative real

• Variants in the ATM gene associated with a reduced risk of contralateral breast cancer.

  PMID 18701470 · PMC2562548 · Cancer research · 2008 · 7 claims · 4 setups

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  Carriers of common ATM variants (>=1% frequency) have a statistically significant reduction in risk of contralateral breast cancer (CBC)

  peripheral wecare atm mutation case-control variant