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 Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.

  PMID 17996079 · PMC2206057 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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  An HMM using paired germline genotype calls and tumour allelic SNP intensities can estimate allele-specific copy-numbers, distinguishing events like uniparental disomy from allelic imbalance.

  hapmap bladder prostate simulated affymetrix simulation

• A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

  PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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  Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

  simulated same mcmc-based direct original

• A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts.

  PMID 15626332 · PMC5172250 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 6 setups

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  Repeats of different copy number have distinct probabilities of appearance in shotgun data, which can be modeled statistically to define recognition thresholds (MDRs) at different shotgun coverages.

  simulated same repeat whole-genome genome

• A statistical change point model approach for the detection of DNA copy number variations in array CGH data.

  PMID 19875853 · PMC4154476 · IEEE/ACM transactions on computational biology and bioinformatics · 2009 · 7 claims · 4 setups

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  A novel mean and variance change point model (MVCM) is proposed to detect CNVs/breakpoints in aCGH data.

  simulated fibroblast breast simulation array

• SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

  PMID 17971856 · PMC2034603 · PloS one · 2007 · 8 claims · 3 setups

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  SiDCoN is a spreadsheet-based application that simulates Ballele and logR plots for all known types of DNA copy number change, with or without stromal contamination, for up to 5000 SNP data points and up to 3 combined aberrations

  sidcon real mixtures snp re-analysis

• 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

• Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

  PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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  Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

  normalized individuals subset same affymetrix fluorescent snp

• QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

  PMID 17341461 · PMC1874617 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  QuantiSNP (OB-HMM) provides probabilistic quantification of copy number states and significantly improves accuracy of segmental aneuploidy identification and breakpoint mapping relative to existing tools (BeadStudio/Illumina)

  genomic same pseudo-normal artificially snp fish molecular

• Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

  PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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  High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

  genomic normalized simulated tiling-resolution snp oligonucleotide

• A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles.

  PMID 32111252 · PMC7049190 · Genome medicine · 2020 · 8 claims · 8 setups

  Has reproduction · 91

  DeClust is a reference profile-free deconvolution method that simultaneously deconvolves bulk tumor expression into cancer, immune, and stromal compartments and clusters samples into cancer cell-intrinsic molecular subtypes, outputting subtype-specific reference profiles for the cohort rather than for individuals.

  solid muscle-invasive ccrcc for bulk single-cell scrna-seq

• Assessing the gene space in draft genomes.

  PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

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  The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

  caenorhabditis toxoplasma homo briggsae cegma blast tblastn

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• CGHPRO -- a comprehensive data analysis tool for array CGH.

  PMID 15807904 · PMC1274268 · BMC bioinformatics · 2005 · 8 claims · 3 setups

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  CGHPRO is a user-friendly, versatile, stand-alone Java tool for normalization, visualization, breakpoint detection and comparative analysis of array-CGH data

  tiling artificially array