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).

• Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

  PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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  A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

  refseq tp53 tumor 154-gene est paired array

• Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

  PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

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  Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

  biomedical refseq training independent text-mining data-mining candidate

• 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

• Function2Gene: a gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge.

  PMID 18631403 · PMC2500032 · BMC bioinformatics · 2008 · 6 claims · 5 setups

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  Function2Gene is a set of Perl programs that queries public databases (NCBI, GeneCards, Harvester, with Uniprot/Ensembl also supported) using expert-selected keywords to rank genes by prior probability of disease association.

  gene nuclear sle tdt keyword-based snp transmission

• Wide-Open: Accelerating public data release by automating detection of overdue datasets.

  PMID 28594819 · PMC5464523 · PLoS biology · 2017 · 7 claims · 5 setups

  Has reproduction · 74

  Wide-Open is a general text-mining approach that automatically detects overdue datasets by scanning PubMed articles for dataset accession identifiers and querying repositories to determine if the datasets remain private.

  open-access geo sra text database web

• Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

  PMID 16757574 · PMC1475747 · Nucleic acids research · 2006 · 6 claims · 8 setups

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  Applying seven independent computational disease-gene prioritization methods in concert to 9556 positional candidate genes identifies a prioritized set of likely T2D and obesity candidate genes

  pubmed genes same randomly geneseeker evoc disease

• Update of the G2D tool for prioritization of gene candidates to inherited diseases.

  PMID 17478516 · PMC1933178 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  G2D is a web server that prioritizes candidate genes for inherited diseases using three distinct algorithms based on different input information.

  genome genomic etrb computational literature go-similarity

• Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

  PMID 18828907 · PMC2760872 · Genome biology · 2008 · 8 claims · 8 setups

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  A combinatorial bioinformatics pipeline (evolutionary double filtering comparative genomics, GXD/ZFIN database queries, MEDLINE text mining) can rapidly and specifically identify PAX2/5/8 direct downstream targets in the otic vesicle

  genome candidate gxd medline evolutionary gene expression

• Genomics research and malaria control: great expectations.

  PMID 14624242 · PMC261879 · PLoS biology · 2003 · 8 claims · 8 setups

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  Genomics research on humans, P. falciparum, and An. gambiae holds great promise for developing new drugs, vaccines, diagnostics, and vector control tools for malaria.

  plasmodium anopheles malaria whole-genome computational microarray

• Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

  PMID 35857869 · PMC9335242 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 6 claims · 8 setups

  Has reproduction · 80

  AvrPm17 is encoded by a paralogous, tandemly duplicated effector gene pair located in a pericentromeric, mildew sublineage-specific effector cluster (family E003) showing signs of recurring gene conversion.

  b.g parental nicotiana benthamiana qtl comparative rna-sequencing

• Towards precise classification of cancers based on robust gene functional expression profiles.

  PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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  Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

  nci60 lymphoma fep go-annotated cdna recursive hypergeometric

• Linking disease-associated genes to regulatory networks via promoter organization.

  PMID 15701758 · PMC549397 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  Pairs of TFBSs conserved both vertically (orthologous genes) and horizontally (co-regulated genes) can serve as seeds to build promoter models representing potential co-regulation networks

  orthologous eukaryotic genomatix pubmed promoter model additional

• Comparative analysis of cancer genes in the human and chimpanzee genomes.

  PMID 16438707 · PMC1382208 · BMC genomics · 2006 · 7 claims · 6 setups

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  All 333 examined human cancer genes have intact, highly conserved orthologs in the chimpanzee genome (99.38% protein identity).

  chimpanzee non-human cancer comparative pcr targeted

• Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

  PMID 18618001 · PMC2442223 · PLoS genetics · 2008 · 8 claims · 6 setups

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  Zebrafish whole-adult-organism chemogenomics generates robust prediction models that discriminate P(H)AHs from ECs across independent experiments

  zebrafish computational seven consolidated whole-adult-organism supervised quantitative

• ChimerDB 2.0--a knowledgebase for fusion genes updated.

  PMID 19906715 · PMC2808913 · Nucleic acids research · 2010 · 8 claims · 4 setups

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  ChimerDB 2.0 is an updated knowledgebase integrating fusion transcripts from GenBank transcriptome analysis with Sanger CGP, OMIM, PubMed, and Mitelman's database data.

  genbank sra pubmed transcript-to-genome ngs literature