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).

• Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

  PMID 18681973 · PMC2553082 · Virology journal · 2008 · 8 claims · 6 setups

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  14 MEME blocks were identified in the HA protein of H3N2 strains (1968-1999), with blocks 1, 2, 3, and 7 correlating with several biological functions

  h3n2 meme sequence entropy

• SNAP predicts effect of mutations on protein function.

  PMID 18757876 · PMC2562009 · Bioinformatics (Oxford, England) · 2008 · 8 claims · 3 setups

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  SNAP is a publicly available web-server implementation predicting functional effects (neutral/non-neutral) of single amino acid substitutions.

  mutant insulin neural alanine mutation

• The vertebrate genome annotation (Vega) database.

  PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.

  genome zebrafish pig nod manual comparative transcript

• L2L: a simple tool for discovering the hidden significance in microarray expression data.

  PMID 16168088 · PMC1242216 · Genome biology · 2005 · 8 claims · 4 setups

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  L2L systematically compares a user's differentially expressed gene list against a database of published differentially expressed gene lists to find statistically significant overlaps and generate hypotheses about shared mechanisms

  mammalian user-supplied diabetic uniprot compiled l2l re-analysis

• Human SNPs resulting in premature stop codons and protein truncation.

  PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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  Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

  genome transcripts validated x-snp-encoded database blast exon-intron

• Representing and querying disease networks using graph databases.

  PMID 27462371 · PMC4960687 · BioData mining · 2016 · 7 claims · 8 setups

  Has reproduction · 77

  Graph databases are well suited for representing biological information that is highly connected, semi-structured, and unpredictable.

  uniprot proteome asthma tissues all-versus-all graph protein-protein

• How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli.

  PMID 15804363 · PMC1079826 · BMC genomics · 2005 · 7 claims · 7 setups

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  Predicted solubility in E. coli (via CV-CV') depends on hydrolase size, phylogenetic origin, homologous family, and superfamily

  lipase bacterial small genera cv-cv correlation grouped

• Analysis of protein sequence and interaction data for candidate disease gene prediction.

  PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

  ophid biocarta kegg pfam-annotated common benchmarking multiple-interval

• miRBase: tools for microRNA genomics.

  PMID 17991681 · PMC2238936 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  miRBase release 10.0 contains 5071 miRNA hairpin loci from 58 species, expressing 5922 distinct mature miRNA sequences, a growth of over 2000 sequences in 2 years

  species utrs genomic chromosome genome-wide target transcription

• RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

  PMID 18954448 · PMC2605478 · BMC genomics · 2008 · 7 claims · 4 setups

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  Constructed enhanced protein databases integrating annotated SAPs, PTMs, and disease associations for 17 organisms.

  consensus sap query all-against-all blast cross-database

• Human synthetic lethal inference as potential anti-cancer target gene detection.

  PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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  Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

  saccharomyces sapiens ihsln genes database phylogenetic gene

• Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

  PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups

  Has reproduction · 83

  Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.

  species microrna atlas microarray rna-seq microrna

• EGenBio: a data management system for evolutionary genomics and biodiversity.

  PMID 17118150 · PMC1683573 · BMC bioinformatics · 2006 · 7 claims · 7 setups

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  EGenBio is a web-based system for integrated management, filtering, curation, and visualization of large-scale genomic sequences, alignments, and phylogenetic trees for evolutionary genomics and biodiversity research.

  vertebrate sequence mutant phylogenetic sequence coevolution saturation

• A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.

  PMID 19680427 · PMC2714467 · PLoS computational biology · 2009 · 8 claims · 6 setups

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  The naïve mapping approach (present if ≥1 associated function is found) leads to an inflated estimate of biological pathways and overestimates functional diversity of a sample.

  complete genome escherichia environmental comparative pathway local

• Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

  PMID 16646984 · PMC1557991 · Genome biology · 2006 · 8 claims · 4 setups

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  A six-frame genomic ORF translation used as an MS search database can detect novel peptides absent from standard protein databases, revealing incomplete genome annotation.

  pooled genome est novel tandem whole-genome est

• Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

  PMID 18439302 · PMC2432081 · BMC genomics · 2008 · 8 claims · 7 setups

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  Adjacent cassette exon pairs can be categorized by EST-derived correlation coefficient into three groups: mutually exclusive (ME, r<=-0.7), independent (IND, -0.2<=r<=0.2), and linked (LNK, r>=0.7)

  human-mouse adjacent est genome splice

• Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

  PMID 18193213 · PMC2206249 · Immunogenetics · 2008 · 8 claims · 6 setups

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  Comparison of eight HLA-homozygous MHC haplotype sequences identified >44,000 variations (substitutions and indels), submitted to dbSNP

  hla-homozygous same mhc indel clone-by-clone gene hla

• The RCSB PDB information portal for structural genomics.

  PMID 16381872 · PMC1347482 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  The RCSB PDB Structural Genomics Information Portal integrates three resources: Structural Genomics Initiatives, Targets (TargetDB/PepcDB), and Structures (functional coverage analysis).

  structural nih genome sequence target production

• An optimized procedure for the design and evaluation of Ecotilling assays.

  PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

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  An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

  genomic gene pcr cdna ecotilling sequence sanger

• Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.

  PMID 27756200 · PMC5069797 · BMC bioinformatics · 2016 · 8 claims · 5 setups

  Has reproduction · 75

  Roar, a method using PRE/POST read counts around annotated APA sites to compute an m/M ratio and a ratio-of-ratios (roar) statistic, detects differential 3'UTR shortening/lengthening from standard RNA-seq libraries.

  testes normal gene rna-seq sapas cdna