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).

• Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

  PMID 19761607 · PMC2759961 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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  2LOmb performs an omnibus permutation test on ensembles of two-locus analyses via a four-step algorithm (two-locus analysis, permutation test, global p-value determination, progressive ensemble search)

  simulated same snp type two-locus 2lomb benchmark

• A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

  PMID 16271148 · PMC1310624 · BMC genomics · 2005 · 8 claims · 5 setups

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  Integrating EST-based expression data with phylogenetic analysis is a valid new method for functionally annotating multigenic protein families

  pad phylogenetic est est-based

• The PeptideAtlas project.

  PMID 16381952 · PMC1347403 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  PeptideAtlas provides an automated repository that identifies peptides by MS/MS, statistically validates identifications, and maps them to eukaryotic genomes to enable data exchange and integration with genomic data.

  plasma drosophila yeast tandem sequence

• PhylomeDB: a database for genome-wide collections of gene phylogenies.

  PMID 17962297 · PMC2238872 · Nucleic acids research · 2008 · 7 claims · 6 setups

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  PhylomeDB is a publicly accessible database storing complete, genome-wide collections of gene phylogenies (phylomes).

  seed homologous trimmed homology sequence neighbor

• Proteomics data repositories.

  PMID 19795424 · PMC2908408 · Proteomics · 2009 · 5 claims · 5 setups

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  The YRC Public Data Repository (YRC PDR) provides a single unified interface disseminating multi-technology proteomics data (mass spectrometry, yeast two-hybrid, fluorescence microscopy, structure prediction) linked to protein annotations from many source databases.

  multi-organism yeast proteomes cerevisiae tandem yeast fluorescence

• Determination of glycosylation sites and site-specific heterogeneity in glycoproteins.

  PMID 19700364 · PMC2749913 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  Mass spectrometry has emerged as the premier tool for structural determination of oligosaccharides/glycans and glycopeptides

  glycoproteins n-linked serum complex maldi tryptic nonspecific

• Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.

  PMID 35784648 · PMC9243631 · Cell reports methods · 2022 · 8 claims · 7 setups

  Has reproduction · 66

  A purification-free hyperTRIBE method (FMR1-ADARcd-V5) can identify stress granule RNAs in bulk and single Drosophila S2 cells and in Drosophila neurons

  fmr1-adarcd-v5 single bioinformatic drosophila immunofluorescence western bulk

• Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.

  PMID 38548265 · PMC11954816 · Journal of advanced research · 2025 · 8 claims · 8 setups

  Has reproduction · 79

  Meta-analysis confirmed a positive association between DED and DEP occurrence

  patients taiwan biobank twb meta-analysis genome-wide score

• Genomics Define Malignant Transformation in Myeloma Precursor Conditions.

  PMID 41061199 · PMC12614327 · Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2026 · 7 claims · 5 setups

  Has reproduction · 78

  Genomic profiling can identify malignant transformation in MGUS/SMM patients, distinguishing 'genomic MM' from 'genomic MGUS' despite identical clinical/morphologic presentation

  cd138+ mgus whole-exome whole-genome copy-number

• Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.

  PMID 33743211 · PMC7951565 · Cell · 2021 · 8 claims · 8 setups

  Has reproduction · 84

  ChIRP-MS of SARS-CoV-2 RNA in infected Huh7.5 and Vero E6 cells identifies a comprehensive set of 309 host proteins that bind the viral RNA during active infection

  huh7.5 vero schmidt lung chirp-ms chirp-rna-seq sds-page

• Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

  PMID 36305682 · PMC9836360 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  18 new mitochondrial genomes were assembled for Aspergillus section Flavi species, complementing 3 existing reference mitogenomes, for a total of 20 species analyzed.

  aspergillus circularized core orthologous mitogenome read organellar

• Analysis of Tumor-Infiltrating T-Cell Transcriptomes Reveal a Unique Genetic Signature across Different Types of Cancer.

  PMID 36232369 · PMC9569723 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 87

  Common genes shared across five cancer types differ from those found in nonmalignant tissue-resident T-cells for each subset (CD4-T, CD8-T, Treg)

  breast lung colorectal melanoma single-cell gene reactome

• Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans.

  PMID 36752777 · PMC9997745 · Microbial genomics · 2023 · 8 claims · 8 setups

  Has reproduction · 89

  Dogs are the dominant host of E. coli ST372, and clusters within the ST372 population structure exhibit distinctive O:H types.

  coli st372 core draft whole-genome core population

• BRCA1 and BRCA2 mutations in central and southern Italian patients.

  PMID 11056688 · PMC13918 · Breast cancer research : BCR · 2000 · 8 claims · 4 setups

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  Deleterious germline BRCA1/BRCA2 mutations were detected in 11 of 136 (8%) unrelated Italian breast/ovarian cancer probands.

  genomic peripheral truncation single-strand direct

• Finding the needle in the haystack: why high-throughput screening is good for your health.

  PMID 12100740 · PMC138735 · Breast cancer research : BCR · 2002 · 8 claims · 8 setups

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  HTS is essential for finding lead compounds, especially for novel targets whose active-site structure is unknown

  raf-1 mitotic mutant tumor biochemical cell-based conformational

• Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

  PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups

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  Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.

  serum frozen ig-depleted clinical seldi-tof maldi lc-ms

• Comparing protein abundance and mRNA expression levels on a genomic scale.

  PMID 12952525 · PMC193646 · Genome biology · 2003 · 8 claims · 8 setups

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  Correlations between mRNA expression and protein abundance are generally poor or limited across most studies reviewed, including in yeast and human cancers

  yeast laser-dissected serum myeloid two-dimensional seldi-tof isotope-coded

• The use of laser capture microscopy in proteomics research--a review.

  PMID 15502248 · PMC3839334 · Disease markers · 2004 · 8 claims · 8 setups

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  LCM allows purification of specific, histologically defined cell populations from heterogeneous tissue for downstream proteomic analysis

  breast prostate esophageal head maldi-tof automated two-dimensional

• Proteomics approaches to identify tumor antigen directed autoantibodies as cancer biomarkers.

  PMID 15502247 · PMC3839398 · Disease markers · 2004 · 8 claims · 8 setups

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  Proteomics approaches (2D Western blot, protein microarray, multiplex ELISA) can identify tumor antigen-directed autoantibodies as candidate cancer biomarkers

  lung pancreatic hepatocellular renal gel microarray multiplex

• Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

  PMID 16105176 · PMC1201154 · BMC structural biology · 2005 · 8 claims · 5 setups

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  Interaction patterns across obligatory and non-obligatory interfaces are different, with obligatory contacts predominantly non-polar

  pdb obligatory same psi-blast solvent residue