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).

• Enthoprotin: a novel clathrin-associated protein identified through subcellular proteomics.

  PMID 12213833 · PMC2173151 · The Journal of cell biology · 2002 · 8 claims · 8 setups

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  Subcellular proteomics of purified CCVs identifies enthoprotin (encoded by KIAA0171), a novel ENTH domain-containing protein not previously detected at the protein level.

  brain cos-7 hek-293 clathrin subcellular western ccv

• In Silico screening for functional candidates amongst hypothetical proteins.

  PMID 19754976 · PMC2758874 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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  An in silico selection strategy combining subcellular targeting-signal prediction with protein domain identification can enrich for true functional proteins among hypothetical proteins

  hypothetical targetp-selected mitochondria-predicted subcellular domain database

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

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

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  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

• Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq.

  PMID 34875090 · PMC8887463 · Nucleic acids research · 2022 · 6 claims · 8 setups

  Has reproduction · 56

  Halo-seq pairs a light-activatable Halo-DBF ligand with Click chemistry to label and purify spatially defined RNA populations in living cells with high spatial specificity (~100 nm radius)

  hela apex-seq proximity dot comparative

• MitoP2: the mitochondrial proteome database--now including mouse data.

  PMID 16381964 · PMC1347489 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  MitoP2 is a database integrating manually annotated mitochondrial reference proteins, functions, and disease associations for yeast, human, and mouse, with cross-species orthologue mapping

  saccharomyces yeast heart liver genome-wide single transcriptome

• LOCATE: a mammalian protein subcellular localization database.

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

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

  hela proteome indirect automated computational

• A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage.

  PMID 20026476 · PMC2849709 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

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  A SILAC-based 'spatial proteomics' method can quantitatively measure the relative subcellular distribution of thousands of proteins across cytoplasm, nucleus, and nucleolus.

  hct116 silac silac-based immunofluorescence

• Point mutations in GLI3 lead to misregulation of its subcellular localization.

  PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

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  The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

  hela immunofluorescence real-time luciferase

• RNA structure maps across mammalian cellular compartments.

  PMID 30886404 · PMC6640855 · Nature structural & molecular biology · 2019 · 8 claims · 6 setups

  Has reproduction · 45

  icSHAPE-based cytotopic RNA structuromes across chromatin, nucleoplasm and cytoplasm in human and mouse cells substantially expand the scope of RNA structural information beyond whole-cell data.

  v6.5 mes icshape rt-qpcr western

• Improved tagging strategy for protein identification in mammalian cells.

  PMID 16138932 · PMC1250225 · BMC genomics · 2005 · 7 claims · 7 setups

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  EGFP tagging via the artificial exon did not affect the subcellular localization of the tagged endogenous proteins

  osteosarcoma hos 293t lentiviral flow confocal

• PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

  PMID 15608166 · PMC540074 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  PA-GOSUB significantly extends the coverage of GO molecular function and subcellular localization annotations for 10 model organism proteomes compared with existing databases (GOA, Swiss-Prot).

  sequences query swiss-prot naive-bayes blast feature

• Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.

  PMID 40849297 · PMC12375038 · Nature communications · 2025 · 8 claims · 6 setups

  Has reproduction · 90

  A single-nucleus transcriptomic atlas of 37 human sural nerves (365,708 nuclei) defines 24 cell clusters and reveals unexpected heterogeneity of perineurial cells (periC1-3).

  sural rodent single-nucleus subcellular immunofluorescence

• Phosphoproteomics: new insights into cellular signaling.

  PMID 16168091 · PMC1242200 · Genome biology · 2005 · 8 claims · 8 setups

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  Protein kinases are one of the largest gene families in humans and mice, accounting for 1.7% of the human genome

  yeast hela beta2-adrenergic erk phosphopeptide targeted silac

• Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.

  PMID 19930686 · PMC3091328 · Genome biology · 2009 · 8 claims · 6 setups

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  The human mitochondrial proteome expanded via two prevailing gene duplication modes: intra-mitochondrial and inter-compartmental duplication

  cerevisiae mitocarta mitochondrial tissues comparative subcellular gene

• Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

  PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  Genome-wide transcriptional bursting kinetics (intrinsic noise, burst size, frequency) can be estimated from allele-specific scRNA-seq of hybrid mESCs

  cast inbred gfp mescs single-cell smfish flow

• Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

  PMID 16162288 · PMC1261261 · BMC genomics · 2005 · 8 claims · 5 setups

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  A novel rTS protein isoform, rTSγ, exists with a 27-residue longer N-terminus generated from an alternative upstream start codon relative to rTSβ.

  rts rtsβ ccrf-cem comparative mitochondrial subcellular

• Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity.

  PMID 33837217 · PMC8035321 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 68

  MOCCI (encoded by C15ORF48) is a mito-SEP upregulated during inflammation and infection that promotes host-protective resolution

  aortic failing colon hek293t ribo-seq wgcna-gsea gene

• A global database for modeling tumor-immune cell communication.

  PMID 37438390 · PMC10338499 · Scientific data · 2023 · 7 claims · 6 setups

  Has reproduction · 66

  TICCom integrates 739 experimentally-validated or manually-curated TIC interactions collected from more than 3,000 literatures

  pubmed scrna-seq tcga basal manual scrna-seq bulk

• Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.

  PMID 34745063 · PMC8564382 · Frontiers in microbiology · 2021 · 7 claims · 7 setups

  Has reproduction · 67

  Tn-seq using the TnSC189 mariner transposon identified 329 essential genes in V. anguillarum NB10Sm from a library of 52,662 insertion mutants.

  vibrio coli anguillarum transposon-insertion conjugative functional

• Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.

  PMID 35869080 · PMC9307511 · Nature communications · 2022 · 7 claims · 4 setups

  Has reproduction · 80

  DiffScan is a computational framework combining a Normalization module and a Scan module to identify SVRs at nucleotide resolution from SP data.

  transcripts platforms bacillus multi-subcellular simulated negative benchmark