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).

• High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

  PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

  genomic ecotilling non-synonymous ecotilling sanger universal-primer

• A novel peak detection approach with chemical noise removal using short-time FFT for prOTOF MS data.

  PMID 19681055 · PMC2782493 · Proteomics · 2009 · 8 claims · 2 setups

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  PDA_stFFT is a novel automatic peak detection method for prOTOF MS data that does not require a priori knowledge of protein masses

  peptide serum maldi-tof

• Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information.

  PMID 19651875 · PMC2761287 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  The LCV approach predicts HTH motifs with 93.29% accuracy, 93.93% sensitivity and 92.66% specificity using only primary sequence information

  quintessentialset-88 hth same newly lcs svm traditional

• Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.

  PMID 33138772 · PMC7607865 · BMC genomics · 2020 · 8 claims · 6 setups

  Has reproduction · 83

  scPPIN integrates scRNA-seq-derived p-values with PPINs to detect maximum-weight connected subgraphs (active/functional modules) via an exact Steiner-tree approach

  liver hepatocyte detected adipose single-cell differential protein-protein

• Are gene expression microarray analyses reliable? A review of studies of retinoic acid responsive genes.

  PMID 15626329 · PMC5171945 · Genomics, proteomics & bioinformatics · 2003 · 6 claims · 8 setups

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  Published microarray studies aiming to identify RA-responsive genes show substantial, often contradictory, differences in results across research groups.

  nb4 tf1 tracheobronchial moser affymetrix cdna microarray

• The effects of quercetin on SW480 human colon carcinoma cells: a proteomic study.

  PMID 15748282 · PMC555539 · Nutrition journal · 2005 · 8 claims · 4 setups

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  20 μM quercetin treatment of SW480 cells for 48 h consistently decreased expression of three proteins and increased expression of one protein across four independent experiments.

  sw480 excised two-dimensional quantitative mass

• Equivalent change enrichment analysis: assessing equivalent and inverse change in biological pathways between diverse experiments.

  PMID 32093613 · PMC7041296 · BMC genomics · 2020 · 7 claims · 3 setups

  Has reproduction · 62

  The Equivalent Change Index (ECI), a gene-level statistic ranging from -1 to 1, quantifies whether a gene was changed to the same (1) or completely opposite (-1) degree across two experiments relative to their controls.

  simulated white model simulation gene