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).

• Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS.

  PMID 15731331 · PMC549577 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  Multiplexed base-specific cleavage/MALDI-TOF MS (Multiplexed Comparative Sequence Analysis) enables simultaneous discovery of sequence polymorphisms across multiple target regions

  ensembl genomic simulation pcr maldi-tof

• Assessing Bos taurus introgression in the UOA Bos indicus assembly.

  PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups

  Has reproduction · 86

  Aligning divergent (cross-subspecies) sequence data detects substantially more SNVs than aligning to a same-subspecies reference, indicating reference/assembly bias in variant calling.

  cattle breed-pooled indian merged whole-genome snv template

• Association of polymorphisms in cyclooxygenase (COX)-2 with coronary and carotid calcium in the Diabetes Heart Study.

  PMID 18768181 · PMC2699582 · Atherosclerosis · 2009 · 8 claims · 6 setups

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  COX-2 promoter SNP rs689466 is associated with lower coronary calcified plaque (CorCP)

  whole-blood-derived subjects dhs unrelated snp coronary carotid

• Minisequencing mitochondrial DNA pathogenic mutations.

  PMID 18402672 · PMC2377236 · BMC medical genetics · 2008 · 7 claims · 7 setups

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  A minisequencing multiplex assay can interrogate 25 pathogenic mtDNA mutations across the whole mtDNA genome in a single reaction using 13 amplicons.

  blood-derived same genomic pcr minisequencing automatic multiplex

• Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

  PMID 19808877 · PMC2788925 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 6 setups

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  Reads mapped to the reference genome show a significant bias toward the reference allele at heterozygous SNPs

  lymphoblastoid simulated hapmap genes rna-seq read-mapping eqtl

• Exome sequencing of a multigenerational human pedigree.

  PMID 20011588 · PMC2788131 · PloS one · 2009 · 8 claims · 6 setups

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  Microarray-based exome capture combined with 454 GS FLX NGS is an efficient and reliable method to enrich for chromosomal regions of interest, validated on eight individuals from a three-generation pedigree

  genomic eluted captured pcr microarray-based qpcr next-generation

• Characterizing natural variation using next-generation sequencing technologies.

  PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups

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  Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.

  pichia individuals saccharomyces individual whole-genome partial comparative

• 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

• Outlook on Thailand's genomics and computational biology research and development.

  PMID 18654621 · PMC2446437 · PLoS computational biology · 2008 · 8 claims · 8 setups

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  Thai government policy support, infrastructure investment, education programs, and human resource development have substantially advanced genomics and bioinformatics research capacity in Thailand

  burkholderia rice healthy thai genome snp htsnp

• Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).

  PMID 37137526 · PMC10214862 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  First high-quality chromosome-level genome assembly and annotation of P. lilfordi, generated via a mixed sequencing strategy (10X linked reads, ONT long reads, Hi-C) plus RNAseq/Iso-Seq

  liver-derived muscle heart pooled 10x oxford hi-c

• MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

  PMID 19758471 · PMC2745589 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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  MtSNPscore, a weighted scoring pipeline combining literature evidence, in silico predictions, and case/control frequency, can prioritize likely pathogenic mtDNA variations

  sporadic mitochondrial reported ataxia mitochondrial functional compensatory

• The UCSC Genome Browser database: update 2010.

  PMID 19906737 · PMC2808870 · Nucleic acids research · 2010 · 8 claims · 5 setups

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  The UCSC Genome Browser provides a large database of publicly available sequence and annotation data with an integrated tool set for examining, comparing, aligning, and displaying genomes

  genome vertebrate individuals personal snp sequence genome-wide

• DDBJ dealing with mass data produced by the second generation sequencer.

  PMID 18927114 · PMC2686496 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  DDBJ collected and released 2,368,110 entries (1,415,106,598 bases) of original DNA sequence data from July 2007 to June 2008.

  plasmodium oryzias gut drosophila solexa wgs metagenomic

• Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids.

  PMID 18616806 · PMC2530870 · Genome biology · 2008 · 8 claims · 8 setups

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  Lake Malawi cichlids are phenotypically and behaviorally diverse but appear genetically like a single subdivided population rather than distinct species

  five cichlid pairwise lake low-coverage blastx multi-species