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).

• Proteomic analysis of integrin-associated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6.

  PMID 19738201 · PMC2857963 · Science signaling · 2009 · 8 claims · 8 setups

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  A novel ligand-affinity/cross-linking proteomic methodology enables isolation of labile integrin-associated signaling complexes

  α5+ computational k562 embryonic ligand tandem hierarchical

• Technical Brief: a novel strategy for enrichment of trabecular meshwork protease proteome.

  PMID 18490959 · PMC2386506 · Molecular vision · 2008 · 7 claims · 6 setups

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  A novel affinity-enrichment strategy using UV cross-linked protease inhibitor peptides on Protein A/G columns improves capture of the TM protease proteome compared to SDS-PAGE fractionation alone

  cytosolic affinity-eluted porcine affinity-enriched affinity western sds-page

• RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.

  PMID 41755635 · PMC12956339 · Nucleic acids research · 2026 · 7 claims · 8 setups

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  RAPseq is a novel in vitro, antibody-free and cross-linking-free method that profiles RBP binding to native cellular RNA transcriptome-wide using recombinant Halo-tagged RBPs and affinity purification followed by sequencing.

  hepg2 hur igf2bp1 ythdf1 rapseq cross-species co-rapseq

• InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

  PMID 17868464 · PMC2375030 · Genome biology · 2007 · 8 claims · 8 setups

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  InSite predicts protein-pair-specific binding motifs ('Motif M on protein A binds to protein B') by integrating heterogeneous PPI and motif-motif interaction evidence within a Bayesian network trained by EM

  saccharomyces homo bank computational yeast tandem

• Proteomic approaches to cancer biomarkers.

  PMID 19931265 · PMC2873613 · Gastroenterology · 2010 · 8 claims · 8 setups

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  Combining abundant-protein depletion, offline fractionation, and subproteome (e.g., glycoproteome) enrichment with 2D LC-MS/MS increases the dynamic range and depth of blood proteome analysis for biomarker discovery.

  plasma serum capan-2 apcδ580 lectin silac elisa

• Interactome networks: the state of the science.

  PMID 16515723 · PMC1431712 · Genome biology · 2006 · 8 claims · 8 setups

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  Spastin interacts with CHMP1B, an ESCRT-III-associated protein, supporting a role for spastin in intracellular membrane trafficking relevant to hereditary spastic paraplegia

  genes tnfα orf proteins yeast tandem interference

• Disease-specific proteins from rheumatoid arthritis patients.

  PMID 16778393 · PMC2729955 · Journal of Korean medical science · 2006 · 8 claims · 6 setups

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  Fibronectin, semaphorin 7A precursor, growth factor receptor-bound protein 7 (GRB7), and immunoglobulin µ chain specifically associate with antibodies purified from RA synovial fluid

  synovium synovial synoviocytes western affinity antibody-affinity

• A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

  PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters

  orthologous randomized high-score promoters pssm-based comparative motif

• The nuclear pore complex.

  PMID 11574060 · PMC138961 · Genome biology · 2001 · 8 claims · 8 setups

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  NPC structure is broadly conserved across eukaryotes but differs substantially in size and architecture between yeast and vertebrates

  xenopus saccharomyces yeast caenorhabditis cryo-electron proteomic protein-a

• Mutant, wild type, or overall p53 expression: freedom from clinical progression in tumours of astrocytic lineage.

  PMID 15494720 · PMC2409947 · British journal of cancer · 2004 · 8 claims · 7 setups

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  Significant overexpression of p53 protein was found in 48% of 74 astrocytic tumours

  archival subset recombinant same immunohistochemistry antibody cytokeratin

• Identification of novel citrullinated autoantigens of synovium in rheumatoid arthritis using a proteomic approach.

  PMID 17125526 · PMC1794520 · Arthritis research & therapy · 2006 · 8 claims · 6 setups

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  51 citrullinated protein spots were detected in RA synovial tissue, of which 30 (58.8%) were autoantigenic (reactive with RA sera)

  synovial excised coli recombinant two-dimensional maldi-tof recombinant

• The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins.

  PMID 16948836 · PMC1794545 · Genome biology · 2006 · 8 claims · 6 setups

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  Identified 1543 proteins in urine from ten healthy donors while essentially eliminating false-positive identifications

  urine pooled urinary identified sds-page albumin decoy

• Polymorphism and epitope sharing between the alleles of merozoite surface protein-1 of Plasmodium falciparum among Indian isolates.

  PMID 17659072 · PMC1950510 · Malaria journal · 2007 · 7 claims · 6 setups

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  PfMAD20 is the predominant PfMSP-1 allelic type among Indian field isolates

  falciparum escherichia coli-expressed recombinant pcr recombinant sds-page

• A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

  PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

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  Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

  genes hela proteins worm co-expression quantitative functional

• Deep-learning prediction of gene expression from personal genomes.

  PMID 41495833 · PMC12869966 · Genome biology · 2026 · 8 claims · 8 setups

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  Fine-tuning Enformer on paired personal WGS and RNA-seq data (Variformer) corrects Enformer's failure to predict inter-individual gene expression differences across held-out people.

  gtex rosmap same monocyte paired mutagenesis chromhmm