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).

• Towards alignment independent quantitative assessment of homology detection.

  PMID 17205117 · PMC1762415 · PloS one · 2006 · 8 claims · 6 setups

  Full-text index only

  The Fhom Estimator uses the prevalence of a conserved protein feature (X) in two protein sets to estimate the fraction of true homologs among paired proteins, independent of alignment quality.

  curated homologene swiss-prot fruit signalp homologene-based fhom

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

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

  Full-text index only

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

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

• Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

  PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

  c57bl orthologous alpha-defensin defensin manual comparative sequence

• The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

  PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

  tetramorium bicarinatum vpg venom whole-genome blast gene

• A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.

  PMID 17521420 · PMC1929158 · Genome biology · 2007 · 7 claims · 6 setups

  Full-text index only

  mtcPTM is a hierarchically organized database of human and mouse phosphosites that preserves experimental context, enabling comparison of phosphorylation patterns across conditions

  nonredundant database high-throughput homology

• A mouse plasma peptide atlas as a resource for disease proteomics.

  PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups

  Full-text index only

  A publicly available, high-quality mouse plasma peptide/protein repository (mouse PeptideAtlas) was built from 568 LC-MS/MS runs on four reference plasma pools.

  plasma peptides fully tissues lc-ms anion database

• A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation.

  PMID 19888438 · PMC2771280 · Journal of biomedicine & biotechnology · 2010 · 6 claims · 6 setups

  Full-text index only

  iTRAQ labelling combined with OFFGEL fractionation improves proteome coverage of human plasma compared to iTRAQ alone or no iTRAQ

  pooled plasma prefractionated immunodepleted itraq 1-dimensional fluorescence-based

• Macrel: antimicrobial peptide screening in genomes and metagenomes.

  PMID 33384902 · PMC7751412 · PeerJ · 2020 · 8 claims · 8 setups

  Has reproduction · 83

  Macrel introduces a novel set of 22 peptide features (6 local, 16 global), including a new Free Energy Transition (FET) feature group, for AMP and hemolytic activity classification

  curated hemopi-1 xiao peptide random benchmark homology-aware

• The Proteomics Identifications database: 2010 update.

  PMID 19906717 · PMC2808904 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  PRIDE has become one of the main repositories for MS-based proteomics data, with substantial growth in data holdings over the last two years.

  species plasma caenorhabditis secretory ms-based quantitative

• De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate.

  PMID 31217263 · PMC6686947 · G3 (Bethesda, Md.) · 2019 · 8 claims · 8 setups

  Has reproduction · 91

  De novo transcriptome assemblies were generated for larval P. cultripes and S. couchii, providing new genomic resources for spadefoot toads

  whole-body cultripes expression-filtered bulk novo transcriptome

• AgBase: a functional genomics resource for agriculture.

  PMID 16961921 · PMC1618847 · BMC genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  AgBase is a curated, web-accessible database providing structural and functional (GO) annotation for agricultural genomes and their pathogens.

  pasteurella chicken maize gene proteogenomic mudpit differential

• Better smelling through genetics: mammalian odor perception.

  PMID 18938244 · PMC2590501 · Current opinion in neurobiology · 2008 · 8 claims · 8 setups

  Full-text index only

  Odorant receptor (OR) gene repertoire size and pseudogene fraction vary dramatically across mammalian species

  mammals subjects v1r trpc2 comparative genetic targeted

• High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

  PMID 18597682 · PMC2483986 · BMC genomics · 2008 · 8 claims · 5 setups

  Full-text index only

  High-accuracy MS proteomics (LTQ-Orbitrap) can be used to verify and improve gene annotation by identifying peptides specific to one of two competing annotation datasets.

  tuberculosis sanger spectra lc-ms sds-page signal

• Large-scale and high-confidence proteomic analysis of human seminal plasma.

  PMID 16709260 · PMC1779515 · Genome biology · 2006 · 8 claims · 6 setups

  Full-text index only

  923 proteins were identified with high confidence in seminal plasma from a single individual, combining results from three ejaculate samples

  seminal same list combined sds-page database decoy

• Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

  PMID 16481312 · PMC1373602 · Nucleic acids research · 2006 · 8 claims · 7 setups

  Full-text index only

  The number of protein families continues to expand steadily as more genomes are sequenced, showing no sign of saturation.

  non-identical gene3d cath whole-gene domain transmembrane

• Pseudofam: the pseudogene families database.

  PMID 18957444 · PMC2686518 · Nucleic acids research · 2009 · 8 claims · 7 setups

  Full-text index only

  Pseudofam is an online database of pseudogene families built by mapping pseudogenes to Pfam protein families, providing query tools, statistics, and sequence alignments

  eukaryotic over pseudogenes pseudogene blast family sequence

• In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.

  PMID 19764811 · PMC2783959 · Journal of proteome research · 2009 · 8 claims · 6 setups

  Full-text index only

  This is the first large-scale in vivo phosphoproteomic study of human skeletal muscle

  vastus skeletal spectra identified phosphopeptide in-solution strong

• LOCATE: a mammalian protein subcellular localization database.

  PMID 17986452 · PMC2238969 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  LOCATE is a curated, web-accessible database housing membrane organization and subcellular localization data for mouse and human proteins.

  hela proteome indirect automated computational

• Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains.

  PMID 18560578 · PMC2409963 · PloS one · 2008 · 8 claims · 6 setups

  Full-text index only

  Ovarian cancer cells exhibit extensive shedding of extra-cellular domains from cell surface proteins into the extracellular milieu.

  ovcar3 analysis lc-ms cell-surface silac

• From single cells to whole organisms.

  PMID 16420683 · PMC1414103 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  The genetic-interaction map in S. cerevisiae is roughly four times as complex as the protein-protein interaction map, and genetic interactions do not overlap with physical interactions but instead predict functional neighborhoods

  saccharomyces caenorhabditis mammalian cylindromatosis automated interference rnai