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).

• Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

  PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 82

  An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

  exemplar paired-end cleaned assembled transcriptome read novo

• Type 1 diabetes in the Spanish population: additional factors to class II HLA-DR3 and -DR4.

  PMID 15842729 · PMC1097726 · BMC genomics · 2005 · 7 claims · 4 setups

  Full-text index only

  The ancestral haplotype AH 18.2 (DR3-TNFa1b5) confers significantly increased T1D risk compared to other DR3-positive haplotypes in the Spanish population.

  blood same genotype hla microsatellite haplotype

• SNP identification in unamplified human genomic DNA with gold nanoparticle probes.

  PMID 15659576 · PMC548375 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  A microarray-based method allows multiplex SNP genotyping in total human genomic DNA without target amplification or complexity reduction

  unamplified genomic fragmented factor multiplex sequencing poly

• Does excitatory fronto-extracerebral tDCS lead to improved working memory performance?

  PMID 24555105 · PMC3869492 · F1000Research · 2013 · 8 claims · 4 setups

  Has reproduction · 61

  Active anodal left DLPFC tDCS with a contralateral cheek reference did not significantly enhance 3-back working memory performance over sham across the two-day experiment (no main effect of group, no group x time interaction).

  healthy 3-back linear

• Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

  PMID 16895434 · PMC1534073 · PLoS computational biology · 2006 · 8 claims · 7 setups

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  The density of transmembrane gene duplicates positively correlates with the estimated maximum number of cell types of common ancestors

  transmembrane simulated age duplicate maximum kernel monte

• Transcriptome analysis reveals differential splicing events in IPF lung tissue.

  PMID 24647608 · PMC3960165 · PloS one · 2014 · 8 claims · 6 setups

  Has reproduction · 81

  873 genes are differentially expressed in IPF lung tissue versus healthy controls at FDR<5%, with more up-regulated than down-regulated genes.

  lung discovery gene gse24206 sequencing rna-seq real-time

• Rbfox2 controls autoregulation in RNA-binding protein networks.

  PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups

  Has reproduction · 48

  Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.

  v6.5 fhfox2 top introns iclip sequencing rt-pcr

• Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis.

  PMID 18053270 · PMC2222245 · BMC medical genetics · 2007 · 8 claims · 6 setups

  Full-text index only

  PITX1 polymorphisms and haplotypes are significantly associated with autism

  agre pitx1 parental family-based extended haplotype

• The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins.

  PMID 17932789 · PMC2140095 · Journal of structural and functional genomics · 2007 · 8 claims · 6 setups

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  A family-based target selection approach (rather than genome-wide or fold-novelty based selection) maximizes cross-member methodological transfer and biological insight

  recombinant target coli x-ray differential analytical

• Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema.

  PMID 17895298 · PMC2533592 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 7 setups

  Full-text index only

  Nucleotide and amino acid substitution trends between human-mouse orthologs are highly asymmetric and polarized in opposite directions for high-GC versus low-GC gene groups.

  human-mouse high aarm orthologous content pairwise

• Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

  PMID 17713557 · PMC2435172 · Genes and immunity · 2007 · 7 claims · 8 setups

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  SNPs in LECT2 and TGFBI show independent associations with the DTH+ phenotype, indicating two separate genes in this region control DTH+

  blood family unrelated subjects snp family-based linkage

• Progressive nonfluent aphasia associated with a new mutation V363I in tau gene.

  PMID 17712160 · PMC10846119 · American journal of Alzheimer's disease and other dementias · 2007 · 7 claims · 5 setups

  Full-text index only

  A novel heterozygous MAPT mutation (2274 G→A, exon 12, causing V363I) was identified in the proband, 2 of 3 tested children, and 1 sibling, but not in 194 healthy control individuals from the same population.

  genomic proband proband's pcr tau neuropsychological

• Does distance matter? Variations in alternative 3' splicing regulation.

  PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

  intronic human-mouse same comparative polypyrimidine branch

• Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.

  PMID 24782521 · PMC4066758 · Nucleic acids research · 2014 · 8 claims · 5 setups

  Has reproduction · 79

  EDD is a new algorithm that detects broad (megabase-size) enrichment domains from ChIP-seq data of widely distributed chromatin proteins such as A- and B-type lamins.

  normal dermal analysis set chip-seq chip-qpcr rna-seq

• Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.

  PMID 17554261 · PMC2628541 · Nature genetics · 2007 · 8 claims · 8 setups

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  IRGM SNPs (rs13361189, rs4958847) show strong replicated association with Crohn disease; IRGM induces autophagy and control of intracellular bacteria

  wtccc replication population cases genome-wide taqman snp

• Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR.

  PMID 17439964 · PMC1888819 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Bisulfite treatment causes DNA strand breakage (via abasic site formation and beta-elimination) in addition to cytosine deamination.

  genomic synthetic bisulfite-treated cloned methylation-sensitive quantitative gel

• Genetic distance and heterogenecity between quasispecies is a critical predictor to IFN response in Egyptian patients with HCV genotype-4.

  PMID 17300723 · PMC1805740 · Virology journal · 2007 · 7 claims · 7 setups

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  Genetic distance and heterogeneity between HCV quasispecies is a critical predictor of IFN response in Egyptian genotype-4 patients

  serum pcr cloned 5'utr rt-pcr molecular sequencing

• Neuroacanthocytosis associated with a defect of the 4.1R membrane protein.

  PMID 17298666 · PMC1805452 · BMC neurology · 2007 · 8 claims · 8 setups

  Full-text index only

  Four unrelated NA patients show a novel erythrocyte membrane defect: 4.1R protein deficiency

  erythrocyte genomic peripheral erythrocytes sds-page non-denaturing direct

• Malignant perinatal variant of long-QT syndrome caused by a profoundly dysfunctional cardiac sodium channel.

  PMID 19808432 · PMC2725366 · Circulation. Arrhythmia and electrophysiology · 2008 · 8 claims · 7 setups

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  G1631D causes profound cardiac sodium channel dysfunction: markedly slowed inactivation (~10-fold), increased persistent current, depolarized voltage dependence of activation/inactivation, and slowed recovery from inactivation

  newborn tsa201 perinatal genetic whole-cell single-channel

• Clinical and genetic findings in Hungarian patients with X-linked juvenile retinoschisis.

  PMID 19093009 · PMC2603250 · Molecular vision · 2008 · 8 claims · 6 setups

  Full-text index only

  OCT detects foveal and lamellar macular retinoschisis more frequently than funduscopy alone

  xlrs genomic optical full-field multifocal