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).

• pTARGET: a web server for predicting protein subcellular localization.

  PMID 16844995 · PMC1538910 · Nucleic acids research · 2006 · 7 claims · 3 setups

  Full-text index only

  pTARGET web server predicts nine distinct subcellular localizations in eukaryotic non-plant proteins using an algorithm based on location-specific Pfam domain occurrence patterns and amino acid composition (AAC)

  eukaryotic complete pfam amino subcellular

• DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.

  PMID 17980028 · PMC2186358 · BMC bioinformatics · 2007 · 7 claims · 3 setups

  Full-text index only

  The DAVID Gene Concept, a single-linkage algorithm, merges gene clusters from Entrez Gene, UniRef100, and PIR-NREF100 that share protein IDs and species into unified DAVID gene clusters, improving cross-referencing between NCBI and UniProt systems

  members entire usp8 sequence annotation

• TRED: a transcriptional regulatory element database, new entries and other development.

  PMID 17202159 · PMC1899102 · Nucleic acids research · 2007 · 8 claims · 3 setups

  Full-text index only

  TRED collects mammalian cis- and trans-regulatory elements together with experimental evidence, mapped onto assembled genomes

  cancer-related computational literature database

• iRefIndex: a consolidated protein interaction database with provenance.

  PMID 18823568 · PMC2573892 · BMC bioinformatics · 2008 · 6 claims · 3 setups

  Full-text index only

  A reproducible key (ROG) for each protein interactor and a corresponding key (RIG) for each interaction record can be generated by anyone using only primary sequence, taxonomy identifier, and the SHA-1 algorithm (SEGUID).

  sequence nine interactor seguid parsing mapping

• BLASTO: a tool for searching orthologous groups.

  PMID 17483516 · PMC1933156 · Nucleic acids research · 2007 · 7 claims · 2 setups

  Full-text index only

  BLASTO treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences

  randomly sequences blast blasto

• nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.

  PMID 15980516 · PMC1160133 · Nucleic acids research · 2005 · 6 claims · 4 setups

  Full-text index only

  nsSNPAnalyzer is a web server that predicts whether a query nsSNP is disease-associated or functionally neutral using a Random Forest classifier combining structural and evolutionary information

  curated homologous structure random structural secondary

• 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

• GenBank.

  PMID 16381837 · PMC1347519 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  GenBank is a comprehensive public database of nucleotide sequences with supporting bibliographic and biological annotation, built and distributed by NCBI.

  sapiens organisms genbank large-scale genome expressed blast

• Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser.

  PMID 15826305 · PMC1087836 · BMC bioinformatics · 2005 · 8 claims · 3 setups

  Full-text index only

  Statistical Viewer is a plug-in package for Ensembl that displays disease study-specific linkage and/or association data as 2D plots within Ensembl's Contig View and Cyto View pages.

  genome decode ensembl marker-to-genome genetic-to-physical linkage

• PI3K inhibitors protect against glucocorticoid-induced skin atrophy.

  PMID 30737086 · PMC6441871 · EBioMedicine · 2019 · 8 claims · 8 setups

  Has reproduction · 76

  Drug repurposing screen of the LINCS transcriptional signature database identified PI3K/mTOR/Akt inhibitors as the most prominent pharmacological class capable of repressing REDD1/FKBP51 expression.

  keratinocytes hacat skin ear computational rt-pcr western

• Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

  PMID 35328546 · PMC8949970 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Generated the first draft genome assembly of A. coronaria by Illumina sequencing a haploid androgenetic plant

  haploid mistral assembled masked whole-genome k-mer genome-wide

• Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

  PMID 15642101 · PMC549070 · Genome biology · 2005 · 8 claims · 4 setups

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  PeptideAtlas, a public database integrating MS/MS-derived peptide identifications with the human genome, was built as an expandable resource for proteomic data.

  subset drosophila ensembl lc-ms icat peptide-to-genome

• The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions.

  PMID 15610565 · PMC544599 · BMC genomics · 2004 · 6 claims · 4 setups

  Full-text index only

  Alu repeats are a source of AREs at 3' UTRs of human mRNA, via poly-A regions of Alu generating complementary poly-T/poly-U regions that acquire regular adenine insertions to form ARE motifs.

  utr computationally are repeat positional

• Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote.

  PMID 15479470 · PMC526369 · BMC genomics · 2004 · 8 claims · 4 setups

  Full-text index only

  65 ePK sequences were identified in the P. falciparum genome and classified via phylogenetic analysis relative to the seven established ePK groups

  falciparum individual recombinant cmgc-group genome-wide blastp kinase

• WebGestalt: an integrated system for exploring gene sets in various biological contexts.

  PMID 15980575 · PMC1160236 · Nucleic acids research · 2005 · 8 claims · 6 setups

  Full-text index only

  WebGestalt is an integrated web-based system composed of four modules: gene set management, information retrieval, organization/visualization, and statistics.

  genes gene est-based enrichment kegg

• The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.

  PMID 15774027 · PMC1088945 · Genome biology · 2005 · 7 claims · 4 setups

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  P. falciparum encodes substantially more membrane transport proteins than originally annotated

  falciparum genome-wide bioinformatic quantification

• The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment.

  PMID 25506420 · PMC4257144 · F1000Research · 2013 · 8 claims · 8 setups

  Has reproduction · 42

  The EPD between Cβ atoms of consecutive residues provides unique signatures of amino acid pair types and can discriminate native from decoy protein structures.

  non-homologous same pisces structures finite-difference electrostatic sequence-distance

• 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

• Finding disease candidate genes by liquid association.

  PMID 17915034 · PMC2246280 · Genome biology · 2007 · 7 claims · 6 setups

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  LA can detect functionally associated genes that are not directly co-expressed by identifying a mediating gene Z whose expression level changes the correlation between X and Y.

  nci_cdna gnf_2002 finnish gnf_2004 liquid transmission correlation

• Gene-disease relationship discovery based on model-driven data integration and database view definition.

  PMID 19042916 · PMC2639000 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 4 setups

  Full-text index only

  Explicit gene–disease relationships can be formulated as candidate gene definitions (e.g., co-localization, dysregulation, functional similarity) that may include intermediary orthologous or interacting genes

  acgr disease term-based database case