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).

• Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

  PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups

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  A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.

  liver simulated conserved nearly gene simulation kolmogorov-smirnov

• Benchmarking ortholog identification methods using functional genomics data.

  PMID 16613613 · PMC1557999 · Genome biology · 2006 · 8 claims · 7 setups

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  InParanoid is the best overall ortholog identification method for identifying functionally equivalent proteins when sensitivity and selectivity are combined into an overall score.

  known human-mouse expression interpro co-expression

• A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts.

  PMID 32718933 · PMC7467002 · G3 (Bethesda, Md.) · 2020 · 7 claims · 8 setups

  Has reproduction · 89

  Across datasets re-analyzed with a unified workflow, there is a general lack of global Wolbachia gene regulation.

  wolbachia wbm differentially rna-seq comparative co-expression

• Next-generation high-density self-assembling functional protein arrays.

  PMID 18469824 · PMC3070491 · Nature methods · 2008 · 8 claims · 7 setups

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  A next-generation NAPPA method produces high-density protein microarrays displaying over 1500 unique proteins with >90% expression success

  test high-density amine-coated array picogreen anti-gst fluorescently

• The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

  PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

  putative nonredundant homo genes computational pssm semantic

• T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

  PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

  kidney scrna-seq microarray meblack microarray single-cell scissor

• 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