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 biology and the host response to viral infection.

  PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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  Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

  lung cd4 rhesus kshv microarray quantitative genomic

• Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design.

  PMID 34553212 · PMC8458035 · GigaScience · 2021 · 8 claims · 7 setups

  Has reproduction · 87

  Genetic variation–based demultiplexing tools can be effectively deployed on cancer scRNA-seq tissue using a pooled experimental design, achieving high recall at acceptable precision-recall tradeoffs in both high-CNV (HGSOC) and high-SNV (lung adenocarcinoma) cancers, even with extremely high doublet proportions.

  high-grade lung hgsoc healthy single-cell matched doublet

• Lysine 63-polyubiquitination guards against translesion synthesis-induced mutations.

  PMID 16789823 · PMC1513265 · PLoS genetics · 2006 · 8 claims · 8 setups

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  K63-polyubiquitin chain formation protects human cells against translesion synthesis-induced mutations by promoting error-free recovery of blocked replication forks.

  a549 western proliferation clonogenic

• TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity.

  PMID 25391375 · PMC4315292 · Genome research · 2015 · 8 claims · 8 setups

  Has reproduction · 80

  TP53 binding events fall into three distinct categories defined by the local chromatin environment: TSS (H3K4me3+), enhancer (H3K4me1+/H3K4me3-), and distal (H3K4me1-/H3K4me3-) peaks.

  imr90 hct116 chip-seq rna-seq atac-seq

• 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

• Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

  PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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  Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

  embryonic high-quality unique m15e est sequence comparative

• DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

  PMID 19910371 · PMC2808897 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  DBTSS update adds ~330 million new TSS Seq tags from 31 different human/mouse cell types or culture conditions.

  normal dld1 beas2b ramos tss comparative