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).

• The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information.

  PMID 15642099 · PMC549068 · Genome biology · 2005 · 7 claims · 1 setups

  Full-text index only

  The MP Ontology enables robust, standardized annotation of mammalian phenotypes for mutations, QTLs, and strains used as models of human biology and disease.

  genome free-text

• A biomedically enriched collection of 7000 human ORF clones.

  PMID 18231609 · PMC2211400 · PloS one · 2008 · 8 claims · 4 setups

  Full-text index only

  Produced and made available over 7000 fully sequence-verified plasmid ORF clones representing over 3400 unique human genes, in both closed (stop codon) and fusion (no stop codon) formats.

  genes mgc plasmid literature pcr sequence

• Feature context-dependency and complexity-reduction in probability landscapes for integrative genomics.

  PMID 18783599 · PMC2559821 · Theoretical biology & medical modelling · 2008 · 8 claims · 2 setups

  Full-text index only

  Probability landscapes permit systematic detection, analysis, and utilization of feature context-dependency in genomic data.

  specified probability microarray

• Analytical code sharing practices in biomedical research.

  PMID 38983240 · PMC11232620 · PeerJ. Computer science · 2024 · 8 claims · 4 setups

  Has reproduction · 92

  Nearly half (49.9%) of 453 examined biomedical manuscripts failed to share the analytical code used to generate their results

  biomedical manuscripts journals subset bibliometric chi-square odds

• QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL.

  PMID 16381937 · PMC1347390 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  QTL MatchMaker integrates QTL information with physical, genetic and cytogenetic maps across human, mouse and rat genomes

  pubmed ucsc laser-captured literature genome comparative

• 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

  Full-text index only

  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

• Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

  PMID 19728866 · PMC2768980 · Genome biology · 2009 · 6 claims · 6 setups

  Full-text index only

  Integrating 16 genomic features (32 sub-features) via a naïve Bayes classifier produces a genome-scale FLN of 21,657 human genes and 22,388,609 weighted links that outperforms any individual data source for inferring functional linkages.

  genome gene omim known naïve linkage disease-centric

• Hit selection with false discovery rate control in genome-scale RNAi screens.

  PMID 18628291 · PMC2504311 · Nucleic acids research · 2008 · 8 claims · 3 setups

  Full-text index only

  A Bayesian FDR-controlling methodology for hit selection in genome-scale RNAi HTS is proposed, using a direct posterior probability approach analogous to Newton et al.

  hela hepatitis simulated genome-scale simulation

• Ensembl 2005.

  PMID 15608235 · PMC540092 · Nucleic acids research · 2005 · 8 claims · 4 setups

  Full-text index only

  Ensembl's automatic gene build system can flexibly and reliably annotate a wide variety of genomes with limited species-specific evidence.

  chicken genomes vertebrate annotated experimental gene pairwise

• Biocomputing enters its adolescence.

  PMID 15960815 · PMC1175967 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  A 'match augmentation' algorithm efficiently matches structural motifs by prioritizing functionally significant residues, enabling function prediction between evolutionarily unrelated proteins

  bank antibody-antigen yeast genome protein-protein empirical integrative

• BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.

  PMID 17202167 · PMC1899097 · Nucleic acids research · 2007 · 7 claims · 6 setups

  Full-text index only

  BRENDA is the largest publicly available enzyme information system worldwide, manually curated from primary literature and covering all identified enzymes regardless of source.

  pubmed randomly enzyme full text-mining manual transmembrane

• PubMatrix: a tool for multiplex literature mining.

  PMID 14667255 · PMC317283 · BMC bioinformatics · 2003 · 8 claims · 3 setups

  Full-text index only

  PubMatrix is a web-based CGI tool that queries PubMed with two lists of terms (search terms vs modifier terms) and returns a matrix of pairwise co-occurrence frequency counts

  pubmed ovarian genome literature cdna

• FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

  PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

  user-supplied gene predicted interactome gene kegg transcription

• 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

  Full-text index only

  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

• Systems biology in human health and disease.

  PMID 17893698 · PMC2013921 · Molecular systems biology · 2007 · 8 claims · 5 setups

  Full-text index only

  High-throughput quantitative proteomics of signaling networks (e.g., HER2 overexpression) can be correlated with biological responses like proliferation and migration to better understand pathways deregulated in cancer.

  her2 biological prostate model quantitative combinatorial genome-wide

• Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter.

  PMID 38587191 · PMC11077057 · Nucleic acids research · 2024 · 6 claims · 8 setups

  Has reproduction · 68

  A dual fluorescence (GFP-mCherry) readthrough reporter with a PAS inserted between the two reporters enables measurement of 3' end processing efficiency in living cells.

  hek293 coli dual genome-wide western

• PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome.

  PMID 16845094 · PMC1538814 · Nucleic acids research · 2006 · 7 claims · 2 setups

  Full-text index only

  Selecting primers using the stringent hybridization ratio (requiring an 'executable temperature' where target hybridization ratio >0.99 and off-target ratio <0.05) yields more specific genomic primers than the conventional melting-temperature-based approach, which only guarantees >0.5 vs <0.5

  chrx entire multiplex computational

• G2Cdb: the Genes to Cognition database.

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

  Full-text index only

  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

• Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

  PMID 19779614 · PMC2745575 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  A protein-centric data integration approach (Master Protein Directory) enables integration and mining of heterogeneous pathogen-host omics data across multiple research centers

  macrophage hela vaccinia bacillus gene protein-protein comparative