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).

• HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

  PMID 17117180 · PMC2360759 · British journal of cancer · 2006 · 6 claims · 5 setups

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  Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.

  white same hapmap snp haplotype tagging

• ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

  PMID 16845048 · PMC1538778 · Nucleic acids research · 2006 · 6 claims · 4 setups

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  ProMiR II improves on the original ProMiR by integrating free energy, G/C ratio, conservation score and entropy for more controllable miRNA prediction

  genome cytomegalovirus six probabilistic 5-fold directional

• The Genographic Project public participation mitochondrial DNA database.

  PMID 17604454 · PMC1904368 · PLoS genetics · 2007 · 7 claims · 4 setups

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  The Genographic Project created the largest standardized human mtDNA database to date, comprising 78,590 genotypes from the first 18 months of public participation.

  buccal reference entire direct coding-region leave-one-out

• A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish.

  PMID 16271140 · PMC1309616 · BMC genomics · 2005 · 8 claims · 4 setups

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  149 putative MHC gene loci and their paralogues were identified in the zebrafish genome using sequence similarity searches against the Zv4 draft assembly.

  zebrafish sequence comparative cross-validation

• Using ESTs to improve the accuracy of de novo gene prediction.

  PMID 16817966 · PMC1534067 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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  TWINSCAN_EST combines EST alignments with TWINSCAN via a trainable 'ESTseq' representation and improves exact gene structure prediction accuracy on the whole C. elegans genome

  elegans genome chromosome novo gene partial

• Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

  PMID 19728866 · PMC2768980 · Genome biology · 2009 · 6 claims · 6 setups

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  Integrating 16 genomic features (32 sub-features) via a naïve Bayes classifier produces a genome-scale FLN of 21,657 human genes and 22,388,609 weighted links that outperforms any individual data source for inferring functional linkages.

  genome gene omim known naïve linkage disease-centric

• Transcriptome annotation using tandem SAGE tags.

  PMID 17709346 · PMC2034470 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  A novel algorithm pairs tandem SAGE tags anchored on two different restriction sites (CATG and GATC) to define tag-delimited genomic sequences (TDGS)

  monocyte-derived unigene genome macrophage sage modified virtual

• Prodepth: predict residue depth by support vector regression approach from protein sequences only.

  PMID 19759917 · PMC2742725 · PloS one · 2009 · 8 claims · 8 setups

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  Residue depth can be reliably predicted solely from protein primary sequence using support vector regression on sequence-derived features.

  structure sequences sequence residue dssp psi-blast

• Does distance matter? Variations in alternative 3' splicing regulation.

  PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

  intronic human-mouse same comparative polypyrimidine branch

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome