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).

• Natural history of S-adenosylmethionine-binding proteins.

  PMID 16225687 · PMC1282579 · BMC structural biology · 2005 · 8 claims · 6 setups

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  The last universal common ancestor (LUCA) of cellular life had between 10 and 20 SAM-binding proteins from at least 5 fold classes

  arabidopsis nicotianamine rossmann-fold cyclopropane psi-blast pdbblast comparative

• From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.

  PMID 33960035 · PMC9292448 · Molecular ecology · 2021 · 7 claims · 8 setups

  Has reproduction · 59

  382 genomic regions contain SNPs whose frequencies are consistently zonated (vary with intertidal position) across all surveyed North Atlantic habitats (Maine, Rhode Island, Norway)

  semibalanus rocky individual ld-thinned pool-seq field morphometric

• A DNA microarray survey of gene expression in normal human tissues.

  PMID 15774023 · PMC1088941 · Genome biology · 2005 · 6 claims · 6 setups

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  Unsupervised hierarchical clustering of gene expression groups normal tissue samples largely according to anatomic location, cellular composition, or physiologic function.

  normal common computational each two-color comparative unsupervised

• Distinct lncRNA transcriptional fingerprints characterize progressive stages of multiple myeloma.

  PMID 26895470 · PMC4924754 · Oncotarget · 2016 · 8 claims · 8 setups

  Has reproduction · 36

  160 lncRNAs are differentially expressed between normal plasma cells and MGUS, SMM, MM, or PCL patients, with 31 lncRNAs shared across at least three comparisons

  bone gene plasma normal microarray custom unsupervised

• Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle.

  PMID 18500686 · PMC2516917 · The Prostate · 2008 · 8 claims · 5 setups

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  Identified 32 genes (38 cDNAs) with an expression pattern of highest levels in seminal vesicle, lower in normal prostate, and lowest in prostate cancer

  normal prostate microarray cdna cross-tissue gene

• 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

• Genomic expression during human myelopoiesis.

  PMID 17683550 · PMC2045681 · BMC genomics · 2007 · 8 claims · 5 setups

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  An integrated myelopoiesis expression dataset of 9,425 genes, each mapped to a unique genomic position, was generated from 24 microarray experiments across 8 myeloid cell types.

  myeloid same cd34+ gene microarray unsupervised sam

• Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases.

  PMID 18842138 · PMC2760875 · Genome biology · 2008 · 8 claims · 6 setups

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  AD-related genes (APOE, A2M, PON2, MAP4) and CVD-associated genes (COMT, CBS, WNK1) congregate in a single co-expression module, linking AD and CVD at the transcriptional level

  entorhinal subjects expression differentially microarray significance principal

• Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer.

  PMID 36140751 · PMC9498802 · Genes · 2022 · 7 claims · 6 setups

  Has reproduction · 51

  Clair3 and Human-SNP-wf (which incorporates Clair3) achieved the highest performance among the six variant callers tested.

  giab hg001 brca1 filtered long-read read bam

• Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

  PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups

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  Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.

  lung gene differentially significantly laser histology principal