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).

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

  PMID 34553212 · PMC8458035 · GigaScience · 2021 · 8 claims · 6 setups

  Has reproduction · 87

  Genetic variation-based demultiplexing tools can be effectively deployed on pooled scRNA-seq experimental designs in cancer tissue (HGSOC and lung adenocarcinoma) despite somatic variation.

  hgsoc lung healthy scrna-seq bulk downstream

• DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

  PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

  Full-text index only

  Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

  aml tumor novo additional genome snp comparative

• CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.

  PMID 26961683 · PMC4784276 · Genome medicine · 2016 · 8 claims · 4 setups

  Has reproduction · 87

  CoINcIDE is a novel framework for discovering patient subtypes across multiple datasets that requires no between-dataset transformations (e.g., batch correction)

  breast ovarian simulated gene consensus simulated

• CanPredict: a computational tool for predicting cancer-associated missense mutations.

  PMID 17537827 · PMC1933186 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  CanPredict is a web application providing public access to a random forest classifier that combines SIFT, LogR.E-value, and GOSS scores to predict whether a missense mutation is cancer-associated

  missense observed sjoblom refseq cross-validation recurrence comparative

• BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

  PMID 19668202 · PMC3661775 · Nature methods · 2009 · 8 claims · 8 setups

  Full-text index only

  BreakDancer (BreakDancerMax + BreakDancerMini) is a software package that predicts a wide variety of structural variants including deletions, insertions, inversions, and intra/inter-chromosomal translocations from paired-end short-insert sequencing reads.

  reads yoruban cytogenetically predicted simulated paired-end whole-genome

• Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

  PMID 15018647 · PMC365025 · BMC genomics · 2004 · 8 claims · 8 setups

  Full-text index only

  Combined SSH subtractive cloning and array CGH is an efficient strategy to identify overexpressed genes located within DNA amplicons.

  imr-32 subtracted mycn-amplified suppression differential array

• Exploiting noise in array CGH data to improve detection of DNA copy number change.

  PMID 17272296 · PMC1994778 · Nucleic acids research · 2007 · 7 claims · 4 setups

  Full-text index only

  When aberrations are present, noise in BAC, 19k oligo, and 385k oligo array-CGH data is highly non-Gaussian and shows long-range spatial correlations.

  atm-deficient normal simulated array simulated

• 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