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).

• SNPdetector: a software tool for sensitive and accurate SNP detection.

  PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

  inbred unrelated zebra same pcr manual comparative

• A colorimetric method for point mutation detection using high-fidelity DNA ligase.

  PMID 16257979 · PMC1275593 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  High-fidelity Tth DNA ligase combined with allele-specific ligation-based gold nanoparticle assembly enables colorimetric single-base discrimination without precise temperature control

  p3-modified nanoparticle synthetic ligated uv-vis colorimetric melting

• Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.

  PMID 16246909 · PMC1266070 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  The BioCyc collection has been expanded to 160 pathway/genome databases (PGDBs) organized into three curation tiers.

  sequenced cmr-derived uniprot cogent computational genome sequence

• A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.

  PMID 23496952 · PMC3655071 · BMC genomics · 2013 · 8 claims · 8 setups

  Has reproduction · 69

  Representative de novo transcriptome assemblies are generated with as few as ~20 million reads for single-tissue samples and ~30 million reads for whole animals at the mRNA-coverage level.

  mus chuniphyes hormiphora pleuromamma rna-seq homology

• Genome amplification of single sperm using multiple displacement amplification.

  PMID 15942023 · PMC1143700 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  MDA was applied for the first time to whole-genome amplification of single sperm cell DNA

  single sperm pcr sanger real-time

• Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition.

  PMID 15850495 · PMC1090572 · BMC genetics · 2005 · 8 claims · 6 setups

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  Haplotype block definitions based on LD measures (Definitions 1, 2, 3, 5) produce fewer, shorter blocks with limited sequence coverage compared to the haplotype diversity-based method (Definition 4)

  unrelated same snps haplotype snp haplotype pairwise

• Insights into vertebrate evolution from the chicken genome sequence.

  PMID 15693954 · PMC551526 · Genome biology · 2005 · 8 claims · 6 setups

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  Chicken has expanded gene families involved in egg production (e.g., avidin) and feather/scale/claw formation (avian-specific keratins) not present or lost in mammals

  red chicken whole-genome comparative synteny

• Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

  PMID 17175533 · PMC1802619 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  202 novel box H/ACA RNA-related sequences were identified in the human genome

  genome chimpanzee aca flanking megablast comparative sequence

• PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.

  PMID 17135190 · PMC1747181 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  PeroxisomeDB integrates the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae into interrelated 'Genes', 'Functions', 'Metabolic pathways' and 'Diseases' sections with links to NCBI, ENSEMBL and UCSC

  homo peroxisomal bona eukaryotic annotation comparative sequence

• Systematic identification of pseudogenes through whole genome expression evidence profiling.

  PMID 16945953 · PMC1636364 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Developed a novel bioinformatics method that identifies pseudogenes by profiling whole-genome transcript and protein expression evidence

  genome ensembl vega celera spliced protein-to-genome pseudogene

• Widespread ectopic expression of olfactory receptor genes.

  PMID 16716209 · PMC1508154 · BMC genomics · 2006 · 8 claims · 6 setups

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  OR genes show widespread, locus-dependent, heterogeneous ectopic expression across dozens of non-olfactory human and mouse tissues

  tissues olfactory intact probesets microarray est custom

• The RCSB PDB information portal for structural genomics.

  PMID 16381872 · PMC1347482 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  The RCSB PDB Structural Genomics Information Portal integrates three resources: Structural Genomics Initiatives, Targets (TargetDB/PepcDB), and Structures (functional coverage analysis).

  structural nih genome sequence target production

• EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

  PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

  sequences homologous proteins coding pairwise single sequence

• Efficacy assessment of SNP sets for genome-wide disease association studies.

  PMID 17726055 · PMC2034459 · Nucleic acids research · 2007 · 6 claims · 4 setups

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  τ, derived from Shannon entropy and swept radius ɛ, approximates the relative sample size efficiency of a marker set for mapping a causal variant at a given map position compared to a maximally polymorphic SNP

  hapmap affymetrix illumina genome-wide swept comparative

• Power analysis for genome-wide association studies.

  PMID 17725844 · PMC2042984 · BMC genetics · 2007 · 8 claims · 6 setups

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  Developed a method to compute genome-wide association study power using tag SNPs and representative population genotype data (HapMap), equivalent to the cumulative r2-adjusted power of Jorgenson and Witte.

  hapmap power pairwise tag

• Comparative genomic analysis of three Leishmania species that cause diverse human disease.

  PMID 17572675 · PMC2592530 · Nature genetics · 2007 · 8 claims · 6 setups

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  L. infantum and L. braziliensis genomes were sequenced and show marked conservation of synteny with L. major, with only ~200 genes differentially distributed among the three species

  infantum major braziliensis leishmania whole-genome comparative pcr

• SNAP: predict effect of non-synonymous polymorphisms on function.

  PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

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  SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

  combined escherichia bacteriophage hiv-1 neural benchmark comparative

• Human neuronal cell protein responses to Nipah virus infection.

  PMID 17553172 · PMC1896155 · Virology journal · 2007 · 8 claims · 4 setups

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  NiV infection induces differential protein expression in SK-N-MC human neuronal cells detectable by 2D-PAGE

  sk-n-mc spots 2d-page maldi-tof tandem

• The HuRef Browser: a web resource for individual human genomics.

  PMID 19036787 · PMC2686481 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  The HuRef Browser is a unified web application integrating assembly, annotation, and assembly-to-assembly comparison (ATAC) views for the diploid HuRef individual human genome.

  individual huref whole-genome assembly-to-assembly variant

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

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

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  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