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).

• Logical Analysis of Data (LAD) model for the early diagnosis of acute ischemic stroke.

  PMID 18616825 · PMC2492849 · BMC medical informatics and decision making · 2008 · 7 claims · 5 setups

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  An LAD classification model built from a support-set of 3 peptide peaks can distinguish stroke patients from controls with 75% accuracy on an independent validation set

  plasma discretized seldi-tof serum logical

• Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ).

  PMID 19902006 · PMC2774473 · Journal of biomedicine & biotechnology · 2010 · 8 claims · 5 setups

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  iTRAQ labelling combined with 4800 MALDI TOF/TOF can detect quantitative differences in the maternal plasma proteome between DS and euploid pregnancies

  maternal tryptic scx-fractionated identified itraq immunodepletion strong

• Metabolomic profiling in LRRK2-related Parkinson's disease.

  PMID 19847307 · PMC2761616 · PloS one · 2009 · 7 claims · 3 setups

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  Metabolomic profiles of both idiopathic PD and LRRK2 PD are clearly separated from controls

  plasma preprocessed untargeted targeted pls-da

• New perspectives on an old disease: proteomics in cancer research.

  PMID 17472735 · PMC1895992 · Genome biology · 2007 · 8 claims · 8 setups

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  The HUPO Plasma Proteome Project has catalogued over 3,020 non-redundant gene products (>7,000 proteins/isoforms) in human plasma, many originating from tissues/organs rather than being plasma-intrinsic.

  plasma breast tumor genetically shotgun proteomics glycopeptide

• Multilocus analysis of SNP and metabolic data within a given pathway.

  PMID 16412218 · PMC1382210 · BMC genomics · 2006 · 8 claims · 7 setups

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  The combinatorial partitioning method (CPM) with optimal thresholds can identify SNPs associated with quantitative metabolite levels rather than only categorical traits.

  healthy plasma genomic chi-square combinatorial leave-one-out

• A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

  PMID 18547137 · PMC2504036 · PLoS medicine · 2008 · 7 claims · 8 setups

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  GEM models combined with in-depth proteomic analysis provide a useful strategy to identify candidate cancer markers applicable to human disease with potential for early detection

  plasma immunodepleted pancreatic shotgun two-dimensional immunodepletion

• 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

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  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

• Collisionless relaxation of a disequilibrated current sheet and implications for bifurcated structures.

  PMID 34145266 · PMC8213726 · Nature communications · 2021 · 6 claims · 3 setups

  Has reproduction · 95

  Collisionless transitions among four single-particle orbit classes are responsible for the relaxation/equilibration of a disequilibrated current sheet.

  harris disequilibrated earth's single-particle particle-in-cell spacecraft

• 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

• Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

  PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

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  Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

  hiv-1 same sequenced gag single-genome mhc hypermutation

• The molecular characterization and clinical management of multiple myeloma in the post-genome era.

  PMID 19657360 · PMC3686133 · Leukemia · 2009 · 8 claims · 8 setups

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  GEP identifies distinct molecular subgroups of MM associated with differing clinical features and survival outcomes

  myeloma cd138-immunomagnetically plasma bone-marrow filter-based gene-expression targeted

• Detection of venous thromboembolism by proteomic serum biomarkers.

  PMID 17579716 · PMC1891085 · PloS one · 2007 · 5 claims · 8 setups

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  A neural network-based classifier built from direct MALDI-TOF MS serum protein expression profiles can diagnose VTE with sensitivity/specificity that exceeds D-dimer assays

  serum anova-selected citrated depleted direct artificial d-dimer

• LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise.

  PMID 17386085 · PMC1847688 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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  LIMPIC is a computational method for detecting protein peaks from linear-mode MALDI-TOF-MS data using background noise reduction and baseline removal followed by non-uniform threshold peak detection and multi-spectra detection-rate classification.

  in-vitro plasma maldi-tof signal baseline

• Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.

  PMID 36192523 · PMC9529974 · Communications biology · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  Built an integrated horse gut microbiome gene catalog (~25 million unique genes) and 372 metagenome-assembled genomes (MAGs) spanning 4179 genera and 95 phyla

  fecal horse dominant plasma shotgun taxonomic functional

• The process chain for peptidomic biomarker discovery.

  PMID 16410650 · PMC3850862 · Disease markers · 2006 · 8 claims · 3 setups

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  Peptidomics (comprehensive analysis of peptides and small proteins <20 kDa) fills a methodological gap left by standard proteomics, which mainly addresses proteins in the ~10-200 kDa range.

  general body patients 2d-gel peptidomics peptidomic

• Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

  PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups

  Has reproduction · 88

  COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.

  peripheral leukocytes plasma degs bulk single-cell plasma

• Dissecting lncRNA-mRNA competitive regulatory network in human islet tissue exosomes of a type 1 diabetes model reveals exosome miRNA markers.

  PMID 36440209 · PMC9682028 · Frontiers in endocrinology · 2022 · 6 claims · 7 setups

  Has reproduction · 50

  lncRNA-mRNA ceRNA networks differ substantially between control and cytokine-treated islet exosomes, sharing lncRNAs more than mRNAs, implying state-dependent regulatory functions

  pancreatic database-derived plasma saliva sequencing exosome lncrna-mirna

• Specific Marker Gene Analysis for Primary Central Nervous System Lymphoma Based on Methylation Difference and Development of Detection Primers.

  PMID 41097902 · PMC12528802 · Brain and behavior · 2025 · 6 claims · 6 setups

  Has reproduction · 62

  RHEB promoter hypermethylation is a PCNSL-specific biomarker distinguishing PCNSL from other CNS diseases.

  datasets cns tcga gdc 450k rrbs roc

• Proteomics as a method for early detection of cancer: a review of proteomics, exhaled breath condensate, and lung cancer screening.

  PMID 18095050 · PMC2150625 · Journal of general internal medicine · 2008 · 8 claims · 7 setups

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  Protein expression is closely aligned with cellular activity, unlike genomic changes which may have no functional significance

  serum resected plasma lower microarray two-dimensional proteomic

• Toxicoproteomics: a parallel approach to identifying biomarkers.

  PMID 12940285 · PMC1241639 · Environmental health perspectives · 2003 · 8 claims · 8 setups

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  Combining parallel DNA microarray and proteomic analyses on the same tissues merges microarray's gene discovery power with proteomics' ability to exploit post-translational modifications for biomarker identification.

  liver serum peptide digested two-dimensional seldi maldi