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).

• Improving the specificity of exon prediction using comparative genomics.

  PMID 18831778 · PMC2559877 · BMC genomics · 2008 · 8 claims · 6 setups

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  A log-odds ratio scoring method based on codon conservation across human-mouse/human-dog alignments and adjacent-codon dependency can classify putative exons as coding vs non-coding.

  human-mouse human-dog genome simulated comparative single-genome simulated

• 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

• CLEAN: CLustering Enrichment ANalysis.

  PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

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  The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

  four breast combined hierarchical cluster csimm-based

• PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

  PMID 16620382 · PMC1459209 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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  PedGenie is a valid, flexible statistical tool for genetic association analysis in pedigrees of arbitrary size and structure using Monte Carlo significance testing

  simulated gaw12 breast monte pedigree-based genetic

• Having a BLAST with bioinformatics (and avoiding BLASTphemy).

  PMID 11597340 · PMC138974 · Genome biology · 2001 · 8 claims · 4 setups

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  BLAST is the most widely used tool for searching biological sequences for regions of local similarity

  superfamilies blocks query pairwise phylogenetic sequence heuristic

• HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

  PMID 17117180 · PMC2360759 · British journal of cancer · 2006 · 6 claims · 5 setups

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  Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.

  white same hapmap snp haplotype tagging

• Single nucleotide polymorphisms of the APC gene and colorectal cancer risk: a case-control study in Taiwan.

  PMID 16569251 · PMC1488868 · BMC cancer · 2006 · 7 claims · 4 setups

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  Three novel APC germline mutations were identified in Taiwanese subjects: a frameshift deletion at codon 460 (g.1378delG), and two missense substitutions p.V1125A and p.S1126R

  genomic taiwanese dhplc pcr sanger

• Nutrigenetic association of the 5-lipoxygenase gene with myocardial infarction.

  PMID 18842779 · PMC3014055 · The American journal of clinical nutrition · 2008 · 8 claims · 4 setups

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  A significant gene x diet interaction exists between 5-LO promoter short alleles (3,4 repeats) and dietary AA intake in determining MI risk

  costa buffy genetic real-time allele-specific

• Sequence variation in the human transcription factor gene POU5F1.

  PMID 18254969 · PMC2275747 · BMC genetics · 2008 · 7 claims · 5 setups

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  POU5F1 is highly polymorphic, with a higher polymorphism density than most genes

  genomic multi-species inferred international resequencing comparative haplotype

• Discovering cancer genes by integrating network and functional properties.

  PMID 19765316 · PMC2758898 · BMC medical genomics · 2009 · 8 claims · 6 setups

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  Cancer genes have distinct PPI network topology (higher connectivity, higher clustering coefficient, shorter path length to known cancer genes) compared to non-cancer genes

  genes gene colon ppi pfam term

• Investigating the genetic association between ERAP1 and ankylosing spondylitis.

  PMID 19692350 · PMC2758148 · Human molecular genetics · 2009 · 8 claims · 8 setups

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  The genetic association between ERAP1 and AS is confirmed in an independent replication cohort

  patients cases genotype comparison snp meta-analysis resequencing

• Species-specific protein sequence and fold optimizations.

  PMID 12487631 · PMC139977 · BMC bioinformatics · 2002 · 7 claims · 7 setups

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  Environmental niche is a significant factor explaining variability in amino acid composition across 100 complete genomes

  predicted mean over orf principal hierarchical domain-based

• Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

  PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups

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  An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.

  pcr candidate embl clinical snp manual homology

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies.

  PMID 17953491 · PMC2039766 · PLoS genetics · 2007 · 8 claims · 5 setups

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  CNVs are not easily tagged by SNPs and often fall in genomic regions poorly covered by whole-genome SNP arrays or not genotyped by HapMap, so current GWASs have largely missed their contribution to complex disorders.

  genome-wide genome cohorts array-based snp bac

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence

• Frequency of single nucleotide polymorphisms in NOD1 gene of ulcerative colitis patients: a case-control study in the Indian population.

  PMID 19723304 · PMC2748065 · BMC medical genetics · 2009 · 7 claims · 4 setups

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  Three NOD1 Exon 6 SNPs (W219R, L349P, L370R) show statistically significant association with ulcerative colitis compared to controls

  genomic pcr patients dhplc cloning pcr-rflp