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).

• A statistical model to identify differentially expressed proteins in 2D PAGE gels.

  PMID 19763172 · PMC2734266 · PLoS computational biology · 2009 · 7 claims · 5 setups

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  A mixture likelihood model incorporating both detected and non-detected proteins has higher statistical power to detect differential expression than standard approaches like the Student's t-test.

  plasma simulated page simulated

• Decoding of superimposed traces produced by direct sequencing of heterozygous indels.

  PMID 18654614 · PMC2429969 · PLoS computational biology · 2008 · 7 claims · 3 setups

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  A dynamic programming method (implemented as web app Indelligent) can decode superimposed allelic sequences from a single mixed trace, using only the observed string of ambiguous peak calls, without a reference sequence or reverse trace.

  genomic artificial simulated direct computational comparative

• Genomics in space life sciences.

  PMID 18558380 · PMC5054090 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 6 setups

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  Sudden changes in gravity alter mRNA levels of various genes, indicating molecular-level effects of microgravity

  keratinocyte wi-38 candida rice microarray suppression pathogenicity

• CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data.

  PMID 17962311 · PMC2238989 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  CEBS is a public repository that integrates study design, timeline, clinical chemistry and histopathology data with microarray and proteomics data

  subcellular laboratory cebs microarray gel clinical

• Genomic variability within an organism exposes its cell lineage tree.

  PMID 16261192 · PMC1274291 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  Somatic mutations accumulated during normal development implicitly encode an organism's entire cell lineage tree with very high precision.

  robinia arabidopsis randomly genotyping multiplex computer

• High resolution array-CGH analysis of single cells.

  PMID 17178751 · PMC1807964 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  Single copy number changes as small as 8.3 Mb can be detected reliably in single cells using GenomePlex WGA combined with high-resolution tiling-path array-CGH.

  769p hct116 peripheral single array-cgh gel fish

• Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

  PMID 18505588 · PMC2430713 · BMC genomics · 2008 · 8 claims · 8 setups

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  Comparative genomics of B. longum DJO10A (minimally cultured) and NCC2705 (culture collection strain) reveals 17 unique DNA regions in DJO10A and 6 in NCC2705 despite otherwise high genome collinearity and identity

  bifidobacterium longum xbai-digested whole-genome base codon