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).

• Genome Network and FANTOM3: assessing the complexity of the transcriptome.

  PMID 16683037 · PMC1449904 · PLoS genetics · 2006 · 8 claims · 7 setups

  Full-text index only

  63% of the genome is transcribed from at least one strand, versus the earlier belief that only 2% is transcribed into protein-coding mRNA

  fantom3 genome large-scale mammalian cage full-length genome

• Extraction of human kinase mutations from literature, databases and genotyping studies.

  PMID 19758464 · PMC2745582 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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  A literature mining pipeline combining MutationFinder, false-positive filtering, and SVM-based classification can extract and disambiguate single-point mutation mentions from abstracts and full text

  pubmed large labeled swissprot literature supervised comparative

• Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

  PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups

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  Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex

  chinese tissues skeletal pk15 full-length real-time gfp

• With the finished human genome in hand, what next?

  PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups

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  Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.

  domestic saccharomyces systemic schistosoma comparative functional genetic

• Completing the map of human genetic variation.

  PMID 17495918 · PMC2685471 · Nature · 2007 · 8 claims · 5 setups

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  A community resource initiative will sequence fosmid and BAC clone libraries from 62 HapMap individuals to systematically discover and resolve structural genetic variants at nucleotide resolution

  genomic fosmid full hapmap paired targeted genotyping

• BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

  PMID 16417652 · PMC1413985 · Breast cancer research : BCR · 2006 · 8 claims · 7 setups

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  BOADICEA predicts accurately the number of BRCA1 and BRCA2 mutations across family groups and discriminates well between carriers and noncarriers

  french-canadian families brca1-positive same targeted full-length multiplex

• Sequencing of human genomes with nanopore technology.

  PMID 31015479 · PMC6478738 · Nature communications · 2019 · 8 claims · 7 setups

  Has reproduction · 75

  A novel single-sample, reference panel-free, read-based phasing algorithm built on the STITCH model improves nanopore SNV calling from modest baseline levels.

  gm12878 na12878 clinical whole-genome snv read-based

• COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

  PMID 19906727 · PMC2808858 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  COSMIC is the largest public resource for information on somatically acquired mutations in human cancer, freely available without restriction

  cancer tumour manual semi-automated candidate

• The liver as an immunological barrier redefined by single-cell analysis.

  PMID 32176810 · PMC7218664 · Immunology · 2020 · 8 claims · 8 setups

  Has reproduction · 100

  Single-cell RNA-seq enables unbiased characterization of liver cell states, developmental trajectories and rare immune populations that bulk averaging obscures, redefining liver cell-type mapping.

  c57bl liver whole-liver hepatocytes scrna-seq facs-based plate-based

• A near complete genome for goat genetic and genomic research.

  PMID 34507524 · PMC8434745 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 89

  Saanen_v1 is a high-quality de novo goat genome assembly from a male Saanen buck, including the first goat Y chromosome scaffold.

  saanen goat testicular saanen_v1 pacbio illumina hi-c

• ScLRTC: imputation for single-cell RNA-seq data via low-rank tensor completion.

  PMID 34844559 · PMC8628418 · BMC genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  scLRTC imputes dropout entries closest to the original expression values on simulated datasets, outperforming other state-of-the-art methods by SSE and PCC.

  usoskin pollen zeisel yan scrna-seq umap masking

• The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers.

  PMID 15743497 · PMC1064126 · Breast cancer research : BCR · 2005 · 7 claims · 5 setups

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  The AR CAG repeat polymorphism does not modify breast cancer risk in BRCA1 mutation carriers

  peripheral brca1 same simulated fluorescent cox weighted