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).

• Systems analysis of bone.

  PMID 20046860 · PMC2790199 · Wiley interdisciplinary reviews. Systems biology and medicine · 2009 · 8 claims · 7 setups

  Full-text index only

  Fracture risk and skeletal traits are highly heritable, with over 350 QTLs mapped across the mouse genome and genes such as LRP5, Alox15, and Darc identified as regulators of bone mass.

  intercross long tibiae mandible qtl dual-energy whole-bone

• An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.

  PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups

  Has reproduction · 74

  An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead

  ipsc-derived same top differentially bulk principal hierarchical

• Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.

  PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 6 setups

  Has reproduction · 67

  PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons

  a549 sequence same bulk pathway gene

• Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations.

  PMID 15984912 · PMC1166350 · PLoS biology · 2005 · 8 claims · 6 setups

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  Most mtDNA lineages in Taiwanese aboriginal populations are distinct from those in China and the Taiwan Han population, consistent with descent from the island's initial late Pleistocene settlers

  indigenous b4a-lineage southeast populations mtdna complete rflp

• High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

  PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

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  The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

  universal same lim erythrocyte genome-wide cross-platform rt-pcr

• Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

  PMID 19816605 · PMC2756586 · PloS one · 2009 · 8 claims · 8 setups

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  CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling

  sputum phage metagenomes inferred metagenomic functional diversity

• Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations.

  PMID 19915670 · PMC2771920 · PloS one · 2009 · 8 claims · 6 setups

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  Proteomic analysis of glioma samples reveals three signaling subclasses of GBM associated with predominant EGFR activation, PDGFR activation, or loss of NF1

  surgical standardized glioma gbm western principal k-means