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).

• Extraction of human kinase mutations from literature, databases and genotyping studies.

  PMID 19758464 · PMC2745582 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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  A literature mining pipeline combining MutationFinder, false-positive filtering, and SVM-based classification can extract and disambiguate single-point mutation mentions from abstracts and full text

  pubmed large labeled swissprot literature supervised comparative

• Lineage specific recombination rates and microevolution in Listeria monocytogenes.

  PMID 18842152 · PMC2576243 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  Recombination is more prevalent in lineage II than in lineage I

  listeria allelic unique monocytogenes multilocus sawyer's genealogical

• Profiling critical cancer gene mutations in clinical tumor samples.

  PMID 19924296 · PMC2774511 · PloS one · 2009 · 7 claims · 4 setups

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  OncoMap, a panel of ~400 mass-spectrometric genotyping assays targeting 33 cancer genes, enables robust mutation profiling of clinical fresh-frozen and FFPE tumor DNA.

  clinical fresh same pediatric mass sanger barcoded

• Web services and workflow management for biological resources.

  PMID 16351751 · PMC1866383 · BMC bioinformatics · 2005 · 8 claims · 4 setups

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  Workflow management systems combined with Web Services are a promising ICT approach for automating access to and integration of biomedical data.

  cabri iarc taverna web workflow database

• Recurrent and multiple bladder tumors show conserved expression profiles.

  PMID 18590527 · PMC2483988 · BMC cancer · 2008 · 8 claims · 7 setups

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  Recurrent and multiple bladder tumors from the same patient display remarkably similar gene expression profiles despite genomic differences.

  urothelial genomic tumor processed gene comparative loh

• G2Cdb: the Genes to Cognition database.

  PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups

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  G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.

  brain nervous genome synaptic proteomic large-scale sequence

• DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

  PMID 38600112 · PMC11006913 · Nature communications · 2024 · 8 claims · 5 setups

  Has reproduction · 93

  Many of the 92 assayed HD missense variants alter DNA binding affinity and/or specificity compared to their corresponding reference alleles

  homeodomain hoxd13 cerevisiae amino universal chip-seq electrophoretic

• Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.

  PMID 35044202 · PMC8768832 · Microbiology spectrum · 2022 · 8 claims · 7 setups

  Has reproduction · 79

  AgrVATE, a novel kmer-based BLASTn and in silico PCR/Snippy pipeline, enables fast, standardized agr group typing and frameshift/null mutation detection from genome assemblies

  aureus complete extracted agr kmer-based sheep mash

• High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

  PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

  genomic ecotilling non-synonymous ecotilling sanger universal-primer

• Evolution of the NANOG pseudogene family in the human and chimpanzee genomes.

  PMID 16469101 · PMC1457002 · BMC evolutionary biology · 2006 · 7 claims · 5 setups

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  The NANOG gene and all pseudogenes except NANOGP8 occupy orthologous chromosomal positions in the chimpanzee genome, indicating they originated before the human-chimpanzee divergence.

  chimpanzee megablast pcr flanking-sequence

• High-throughput crystallography for structural genomics.

  PMID 19765976 · PMC2764548 · Current opinion in structural biology · 2009 · 8 claims · 8 setups

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  SG programs use genomic sequence data to select structurally novel protein targets, avoiding proteins with known structural homologues

  recombinant recalcitrant hundred family hydrogen situ site-directed

• 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