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).

• A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population.

  PMID 16904005 · PMC1779589 · Genome biology · 2006 · 8 claims · 7 setups

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  Eight SNPs with extreme European-branch locus-specific branch length (LSBL) were selected from a genome-wide FST dataset as candidates for selection in Europe.

  snp irish french fst-based microsatellite genome-wide

• Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists.

  PMID 16351744 · PMC1866390 · BMC bioinformatics · 2005 · 5 claims · 3 setups

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  OMIM Clinical Synopsis free-text phenotype and location names can be normalized and hierarchically structured into a controlled vocabulary suitable for computational analysis

  omim gene text statistical gene

• Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

  PMID 16417627 · PMC1382246 · BMC genetics · 2006 · 8 claims · 7 setups

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  Heterozygous truncating BRCA2 mutations occur in 47% (7/15) of gastrointestinal MSI cancer cell lines/xenografts, a higher rate than previously reported

  gastrointestinal ls174t pl3 msi gene rt-pcr rad51

• In silico analysis of missense substitutions using sequence-alignment based methods.

  PMID 18951440 · PMC3431198 · Human mutation · 2008 · 8 claims · 7 setups

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  Carefully validated PMSA-based computational algorithms can achieve predictive values of ~75-95% for classifying missense substitutions as pathogenic or neutral.

  clinically sequence curated deep blosum62 sift align-gvgd

• Different Intestinal Microbiota with Growth Stages of Three-Breed Hybrid Pig.

  PMID 35978648 · PMC9377885 · BioMed research international · 2022 · 7 claims · 5 setups

  Has reproduction · 75

  The composition and relative abundance of intestinal microbiota in three-breed hybrid pigs differ significantly across growth stages (60, 120, 180 days)

  fecal same 16s otu alpha

• Identification of gene interactions associated with disease from gene expression data using synergy networks.

  PMID 18234101 · PMC2258206 · BMC systems biology · 2008 · 8 claims · 4 setups

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  Synergy of a gene pair with respect to disease, defined as I(G1,G2;C) - [I(G1;C)+I(G2;C)], identifies gene pairs that interact cooperatively with respect to a phenotype rather than independently.

  prostate simulated microarray simulated permutation

• GeneTrail--advanced gene set enrichment analysis.

  PMID 17526521 · PMC1933132 · Nucleic acids research · 2007 · 8 claims · 2 setups

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  GeneTrail is a comprehensive, easy-to-use web-based tool for gene set enrichment analysis supporting both Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA)

  example sorted over-representation gene

• The origins of lactase persistence in Europe.

  PMID 19714206 · PMC2722739 · PLoS computational biology · 2009 · 8 claims · 5 setups

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  The −13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly linked to the Linearbandkeramik culture.

  simulated simulation 910*t farming demic approximate comparison

• CanPredict: a computational tool for predicting cancer-associated missense mutations.

  PMID 17537827 · PMC1933186 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  CanPredict is a web application providing public access to a random forest classifier that combines SIFT, LogR.E-value, and GOSS scores to predict whether a missense mutation is cancer-associated

  missense observed sjoblom refseq cross-validation recurrence comparative

• Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

  PMID 18989397 · PMC2565504 · PLoS computational biology · 2008 · 7 claims · 5 setups

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  The locations of sequence variants are correlated between paralogous human proteins more than expected by chance.

  dbsnp best-hit omicia hgmd genome-wide correlation disease

• Testing whether genetic variation explains correlation of quantitative measures of gene expression, and application to genetic network analysis.

  PMID 18444230 · PMC2729096 · Statistics in medicine · 2008 · 8 claims · 3 setups

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  A statistical test (delta method and Steiger-Browne optimal linear composites) is developed to test equality of the marginal correlation and the partial correlation of two gene expression traits conditional on a set of covariates.

  simulated real analytical simulation application

• Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements.

  PMID 20008508 · PMC2836564 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Most TEs insert within specific 'hotspots' along the targeted TE rather than uniformly.

  genome sequences unique nested chi-square position-specific

• Recurring genomic breaks in independent lineages support genomic fragility.

  PMID 17090315 · PMC1636669 · BMC evolutionary biology · 2006 · 6 claims · 6 setups

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  The propensity of a chromosomal region to break is significantly correlated among independent lineages, even after accounting for covariates like region length and functional class.

  hg17 genome computationally comparative marker segmental

• Bias of selection on human copy-number variants.

  PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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  Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

  genome human-mouse cnv-encompassed inbred comparative randomization molecular

• ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

  PMID 17984078 · PMC2238997 · Nucleic acids research · 2008 · 6 claims · 4 setups

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  ARED Organism and ARED-Integrated are new/updated public databases cataloguing ARE-containing mRNAs/genes in human, mouse and rat

  6x6 ortholog 3'utr comparative chi-squared

• 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

• High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.

  PMID 25122613 · PMC4216921 · Genome research · 2014 · 8 claims · 7 setups

  Has reproduction · 87

  mRNA codon and amino acid pools are highly stable across mouse development and across tissues, simply reflecting the genomic background distribution of any possible transcriptome.

  c57bl strand-specific pol computational

• Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.

  PMID 19779549 · PMC2739292 · PLoS computational biology · 2009 · 8 claims · 8 setups

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  Human disease genes are much closer to aging genes in the PPI network than expected by chance

  protein-protein randomized dan aging network degree-conserved closeness

• Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

  PMID 35328546 · PMC8949970 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Generated the first draft genome assembly of A. coronaria by Illumina sequencing a haploid androgenetic plant

  haploid mistral assembled masked whole-genome k-mer genome-wide

• Detecting transcriptionally active regions using genomic tiling arrays.

  PMID 16859498 · PMC1779562 · Genome biology · 2006 · 8 claims · 4 setups

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  A non-parametric method (TranscriptionDetector) integrates single-channel p-values from multiple replicate arrays into a multi-channel p-value (MCPV) to identify transcribed probed loci without assumptions about intensity distributions.

  anopheles chromosomes simulated genomic high-density sequence-based