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).

• miRge 2.0 for comprehensive analysis of microRNA sequencing data.

  PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups

  Has reproduction · 89

  miRge 2.0 introduces a novel SVM-based miRNA detection method using both hairpin structure and isomiR composition, yielding higher specificity for miRNA identification

  pooled colon datasets small a-to-i novel

• Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps.

  PMID 36828829 · PMC9958023 · Nature communications · 2023 · 8 claims · 7 setups

  Has reproduction · 52

  A shared genetic toolkit of caste-associated genes exists across vespid wasp species spanning different levels of social complexity

  vespid single-copy brain caste-biased bulk orthology principal

• Proteomics analysis reveals novel components in the detergent-insoluble subproteome in Alzheimer's disease.

  PMID 19746990 · PMC2784247 · Journal of proteome research · 2009 · 8 claims · 5 setups

  Full-text index only

  A label-free XIC-based LC-MS/MS quantitation strategy, combined with an FTLD-U comparator cohort, can be used to identify AD-specific changes in the detergent-insoluble brain subproteome.

  pooled postmortem individual detergent-insoluble lc-ms sequential sds-page

• Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.

  PMID 18984577 · PMC2649809 · Molecular & cellular proteomics : MCP · 2009 · 8 claims · 6 setups

  Full-text index only

  Brain-specific proteins are 1.8 times more likely to be observed in CSF than in plasma

  csf brain normal 2d-dige label-free isotopic

• Synaptic proteins linked to HIV-1 infection and immunoproteasome induction: proteomic analysis of human synaptosomes.

  PMID 19693676 · PMC2824116 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2010 · 8 claims · 7 setups

  Full-text index only

  Proteomic screening of human synaptosomes identifies a set of proteins differentially expressed in HIV/AIDS brain

  frontal excised synaptosome paraffin-embedded 2d-page maldi-tof western

• Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry.

  PMID 19654045 · PMC2818068 · Methods (San Diego, Calif.) · 2010 · 8 claims · 5 setups

  Full-text index only

  Voxelation combined with LC-MS enables high-throughput spatial mapping of protein abundance across mouse brain voxels

  brain digested voxel amt-tag lc-ms bca

• Celline: a flexible tool for one-step retrieval and integrative analysis of public single-cell RNA sequencing data.

  PMID 41458999 · PMC12738925 · Frontiers in bioinformatics · 2025 · 8 claims · 7 setups

  Has reproduction · 64

  Celline is a Python package executing an entire scRNA-seq workflow (retrieval, preprocessing, integration, analysis) using single-line commands per step

  mus brain integrated homo droplet-based scrna-seq cell-type

• Proteomic analysis of Alzheimer's disease cerebrospinal fluid from neuropathologically diagnosed subjects.

  PMID 19689240 · PMC2832860 · Current Alzheimer research · 2009 · 8 claims · 6 setups

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  2D DIGE analysis of postmortem V-CSF pools identified 21-22 protein spots that significantly differ among neuropathologically-diagnosed AD, non-demented controls (NDC), and non-AD dementia (non-ADD) groups

  postmortem trypsin-digested individual subjects difference mass micro