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).

• Fucosylated glycoproteins as markers of liver disease.

  PMID 19126969 · PMC3827789 · Disease markers · 2008 · 8 claims · 6 setups

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  Core alpha 1,6-linked fucosylation of AFP (AFP-L3) is increased in HCC and is a more specific marker of HCC than total AFP

  afp pooled larger igg lectin fucose-specific immunoblot

• A workflow reproducibility scale for automatic validation of biological interpretation results.

  PMID 37150537 · PMC10164546 · GigaScience · 2022 · 8 claims · 4 setups

  Has reproduction · 100

  Comparing output files by checksum alone is insufficient to verify reproducibility, since checksums can differ even when the underlying biological interpretation is unchanged

  nf-core sam vcf workflow checksum biological workflow

• Sediment Resuspension as a System-Wide Driver of Legacy and Bioavailable Phosphorus Release in Lake Erie.

  PMID 41960750 · PMC13130958 · Environmental science & technology · 2026 · 7 claims · 8 setups

  Has reproduction · 90

  Sediment resuspension is a major episodic internal phosphorus source releasing bioavailable P far exceeding previously reported aerobic diffusive fluxes.

  western sediment lake great sediment sequential beryllium-7

• Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.

  PMID 41491791 · PMC12771794 · BMC microbiology · 2026 · 6 claims · 6 setups

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  Swab material (Core Swab A, Core Swab B, Pap Brush) causes minimal variation in bacterial composition, DNA yield, and host DNA contamination.

  vaginal artificial clinical 16s pacbio extraction host

• Identification of transcription start sites and preferential expression of select CB2 transcripts in mouse and human B lymphocytes.

  PMID 19757078 · PMC2843092 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2009 · 7 claims · 8 setups

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  Human B cells express one CB2 transcript while mouse B cells express three CB2 transcripts

  splenocytes pbmc-derived splenic genbank race pcr quantitative

• Microproteomics: analysis of protein diversity in small samples.

  PMID 18271009 · PMC2743962 · Mass spectrometry reviews · 2008 · 8 claims · 8 setups

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  Changes in gene/mRNA expression often do not correlate well with changes in protein expression, due to precursor cleavage, post-translational modification, localization, and variable protein lifetimes.

  lcm-dissected single few dense gel maldi capillary

• CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation.

  PMID 41400832 · PMC12790814 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 6 setups

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  CholeraSeq is an automated, V. cholerae-specific Nextflow pipeline that processes WGS outbreak data from raw reads/assemblies to high-quality SNPs and phylogenies in near-real-time.

  cholerae recombination-masked pis read reference-based recombination

• Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.

  PMID 29335641 · PMC5864184 · The ISME journal · 2018 · 8 claims · 7 setups

  Has reproduction

  Increasing salinity to ≥43 ppt inhibits Trichodesmium growth while stimulating growth of the associated Alteromonas

  alteromonas trichodesmium differential classical smrt

• Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions.

  PMID 37085932 · PMC10120106 · Environmental microbiome · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  Root and corm endosphere communities are significantly richer and compositionally distinct from leaf endosphere communities across Musa genotypes

  root musa assembled prokka-annotated shotgun culture-free metagenome

• EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

  PMID 41527854 · PMC12796812 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  EpiXFormer achieves high accuracy (mean AUROC ~0.99) predicting binding sites of both TFs and non-sequence-specific DBPs across 199 DBP-cell type pairs

  dbps tfs common ctcf deep comparative feature-ablation