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).

• Ontological visualization of protein-protein interactions.

  PMID 15707487 · PMC550656 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  Aggregating independently made GO 'protein binding' (IPI) annotations reveals larger, previously undescribed mouse protein-protein interaction networks

  gene interacting interaction annotation yeast co-immunoprecipitation

• 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

• 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

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  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

• TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.

  PMID 17199898 · PMC1774580 · BMC bioinformatics · 2007 · 7 claims · 8 setups

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  TPRpred detects divergent/remote-homolog TPR repeat units that existing resources (Pfam, SMART, REP) fail to detect

  scop-derived malt nr-70 scop profile-based dali remote

• Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease.

  PMID 34297416 · PMC8766893 · Neuropathology and applied neurobiology · 2022 · 8 claims · 5 setups

  Has reproduction · 92

  Systematic review of 306 eligible articles identified 196 distinct proteins constituting the ADRA (AD reactive astrocyte) protein set

  post-mortem adra immunohistochemistry protein-protein pathway

• Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

  PMID 19115125 · PMC2947716 · Journal of neurovirology · 2009 · 7 claims · 5 setups

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  HIV-1 isolates from CI patients induce a distinct macrophage proteome signature compared to isolates from NC patients and SF162

  monocyte-derived mdm mdms western p24 seldi-tof sds-page

• Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.

  PMID 18974882 · PMC2570797 · PLoS pathogens · 2008 · 8 claims · 6 setups

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  Midgut (oocyst-derived) and salivary gland sporozoite proteomes are markedly different despite near-identical morphology, consistent with their differing hepatocyte infectivity

  falciparum berghei nano-lc-ms targeted gene

• The Proteomic Code: a molecular recognition code for proteins.

  PMID 17999762 · PMC2206014 · Theoretical biology & medical modelling · 2007 · 8 claims · 8 setups

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  The Proteomic Code is a set of rules by which genetic information is transferred into the physico-chemical properties of amino acids, determining protein-protein interactions and folding; it is part of the redundant Genetic Code.

  anti-peptide sequence exon smooth radioimmunoassay pairwise genome-wide

• Serum S100A6 concentration predicts peritoneal tumor burden in mice with epithelial ovarian cancer and is associated with advanced stage in patients.

  PMID 19888321 · PMC2765613 · PloS one · 2009 · 8 claims · 8 setups

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  Serum S100A6 concentration correlates with peritoneal tumor burden in a mouse OVCA xenograft model, based on inverse regression calibration against bioluminescent imaging data.

  serum skov-3 pooled ovca lc-ms antigen whole-animal

• Human Protein Reference Database--2009 update.

  PMID 18988627 · PMC2686490 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  HPRD is a curated database of experimentally derived human protein-protein interactions, post-translational modifications, and tissue expression data

  mastl proteins phosphorylation yeast mass

• An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation.

  PMID 34772928 · PMC8590018 · Nature communications · 2021 · 8 claims · 5 setups

  Has reproduction · 92

  PISA-Express is a method that simultaneously measures protein expression and thermal stability (solubility) changes using only two samples per replicate per cell type

  hi12 ipsc ht29 foreskin pisa expression cellular

• MACSIMS: multiple alignment of complete sequences information management system.

  PMID 16792820 · PMC1539025 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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  MACSIMS is a multiple alignment-based information management system combining knowledge-based database mining with ab initio sequence predictions

  balibase-derived sequences same query automatic database initio

• Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery.

  PMID 19936259 · PMC2775948 · PloS one · 2009 · 8 claims · 8 setups

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  Integrated proteomic analysis of a cancer mouse model and human cancer cell populations provides an effective approach to identify potential circulating protein biomarkers.

  k-ras ovarian lists tumor quantitative pathway immunoblot

• Novel insights into adipogenesis from omics data.

  PMID 19689276 · PMC2765082 · Current medicinal chemistry · 2009 · 8 claims · 8 setups

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  Pparg and Cebpa are the two master transcriptional regulators governing adipogenesis

  3t3-l1 embryonic multipotent nih-3t3 microarray gel non-gel-based

• Whither genomics?

  PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

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  Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

  mammalian budding yeast general expression genome-wide synthetic

• Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry.

  PMID 17166507 · PMC7094463 · Journal of chromatography. A · 2007 · 8 claims · 8 setups

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  Standardizing sample preparation procedures for serum/plasma profiling is critical for obtaining reliable biomarkers, since slight procedural changes can produce very different protein profiles.

  serum aqueous maldi-tof seldi-tof peak

• CD70 (TNFSF7) is expressed at high prevalence in renal cell carcinomas and is rapidly internalised on antibody binding.

  PMID 16892042 · PMC2360640 · British journal of cancer · 2006 · 6 claims · 6 setups

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  CD70 was identified by proteomic analysis of plasma membrane preparations as highly expressed in A498 and SW839 RCC-derived cell lines

  a498 frozen normal proteomics flow immunohistochemistry

• 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

• Development of animal models to test the fundamental basis of gene-environment interactions.

  PMID 19037209 · PMC2703424 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 8 setups

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  Selective breeding for low and high intrinsic aerobic treadmill running capacity produced divergent rat lines (LCR and HCR) that contrast in propensity for complex disease

  nih-derived lcr carotid treadmill body maximal

• 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

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  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