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).

• LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise.

  PMID 17386085 · PMC1847688 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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  LIMPIC is a computational method for detecting protein peaks from linear-mode MALDI-TOF-MS data using background noise reduction and baseline removal followed by non-uniform threshold peak detection and multi-spectra detection-rate classification.

  in-vitro plasma maldi-tof signal baseline

• PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

  PMID 16199750 · PMC1240117 · Nucleic acids research · 2005 · 7 claims · 6 setups

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  The PPC algorithm, which applies a probe-pair-specific second-degree polynomial correction, increases the accuracy of allele frequency estimates from pooled DNA compared with previously described algorithms

  individually reference equimolar independently snp reference pooled

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc

• How many human genes can be defined as housekeeping with current expression data?

  PMID 18416810 · PMC2396180 · BMC genomics · 2008 · 8 claims · 4 setups

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  Current EST and microarray transcriptome sampling is far from saturated, limiting gene detectability and understanding of tissue-specific expression

  tissues genes est microarray comparative

• MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.

  PMID 36451166 · PMC9710047 · Genome biology · 2022 · 7 claims · 6 setups

  Has reproduction · 50

  MoDLE is a high-performance stochastic model that simulates DNA-DNA contacts from loop extrusion genome-wide in minutes using less than 1 GB of RAM

  genome synthetic h1-hesc stochastic molecular ctcf