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).

• Polymorphism at the C-reactive protein locus influences gene expression and predisposes to systemic lupus erythematosus.

  PMID 14645206 · PMC3707088 · Human molecular genetics · 2004 · 8 claims · 5 setups

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  The minor (rare) allele of CRP SNP 'CRP 4' is associated/linked with development of SLE in family-based transmission studies.

  crp simplex same serum direct family-based linkage

• Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system.

  PMID 18664269 · PMC2515158 · BMC microbiology · 2008 · 8 claims · 7 setups

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  18 STR loci (1-5 base repeat units, copy number 4-26) were identified in the M. genitalium G37 genome via bioinformatics analysis.

  genitalium clinical selected 246-bp bioinformatics pcr plasmid

• Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

  PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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  The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

  bac genome metaphase overlapping manual repeat fluorescence

• Multilocus analysis of SNP and metabolic data within a given pathway.

  PMID 16412218 · PMC1382210 · BMC genomics · 2006 · 8 claims · 7 setups

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  The combinatorial partitioning method (CPM) with optimal thresholds can identify SNPs associated with quantitative metabolite levels rather than only categorical traits.

  healthy plasma genomic chi-square combinatorial leave-one-out

• Machine-learning approaches for classifying haplogroup from Y chromosome STR data.

  PMID 18551166 · PMC2396484 · PLoS computational biology · 2008 · 8 claims · 5 setups

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  Y-STR allelic variability is partitioned more by differences among haplogroups than by differences among populations, suggesting Y-STRs carry haplogroup information

  globally same computational publicly y-str snp supervised

• Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa.

  PMID 19890396 · PMC2767505 · PloS one · 2009 · 8 claims · 4 setups

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  Rifampicin resistance (rpoB) and pyrazinamide resistance (pncA) mutations occur at different nucleotide positions in the MDR and XDR strains, showing they were acquired independently and that the XDR strain did not evolve directly from this MDR strain.

  tuberculosis additional whole-genome spoligotyping comparative

• MitoVariome: a variome database of human mitochondrial DNA.

  PMID 19958475 · PMC2788364 · BMC genomics · 2009 · 8 claims · 5 setups

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  MitoVariome is a web-based, integrated variome database for human mitochondrial DNA that unifies sequence variation, haplogroup, and disease annotation information not jointly available in prior databases (MITOMAP, mtDB, Mitome, MitoRes).

  mitochondrial korean sequence short restriction

• Variation resources at UC Santa Cruz.

  PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

  chimpanzee affymetrix hapmap perlegen snp fixed linkage

• PigGIS: Pig Genomic Informatics System.

  PMID 17090590 · PMC1669765 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  PigGIS identified 15,700 pig consensus sequences covering 18.5 Mb of homologous human exons

  million pig matched wgs blastx repeat sequence

• A single-step sequencing method for the identification of Mycobacterium tuberculosis complex species.

  PMID 18618024 · PMC2453075 · PLoS neglected tropical diseases · 2008 · 7 claims · 8 setups

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  ETR-D sequencing allows accurate, single-step identification of MTC species, circumventing the expensive polyphasic approach.

  mtc tuberculosis phenotypic pcr mptr

• Haplotype analysis of common variants in the BRCA1 gene and risk of sporadic breast cancer.

  PMID 15743496 · PMC1064127 · Breast cancer research : BCR · 2005 · 7 claims · 5 setups

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  A common BRCA1 haplotype (haplotype 2, C A G G) is associated with a modest increase in sporadic breast cancer risk

  individuals nested same nurses whole-gene snp statistical

• Phenotypic features and genetic characterization of male breast cancer families: identification of two recurrent BRCA2 mutations in north-east of Italy.

  PMID 16764716 · PMC1586026 · BMC cancer · 2006 · 8 claims · 6 setups

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  The 9106C>T (Q2960X) and IVS16-2A>G BRCA2 mutations are recurrent in MBC families from North-East Italy and may reflect a founder effect.

  blood germline tumor family mutation mlpa microsatellite

• Association of Escherichia coli O157:H7 tir polymorphisms with human infection.

  PMID 17718910 · PMC2063500 · BMC infectious diseases · 2007 · 8 claims · 6 setups

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  tir polymorphisms 255 T>A and RR1-RU3 (presence/absence) associate strongly with human vs bovine isolate source

  stec pcr multiplex elisa

• 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

• Insights into the differentiation and adaptation within Circaeasteraceae from Circaeaster agrestis genome sequencing and resequencing.

  PMID 36895650 · PMC9988679 · iScience · 2023 · 8 claims · 8 setups

  Has reproduction · 49

  C. agrestis and K. uniflora are sister species with contrasting reproductive modes, providing a natural system to test effects of sexual vs asexual reproduction on genome evolution

  circaeaster agrestis genome gene kmer-based

• Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

  PMID 17784912 · PMC2169797 · Molecular microbiology · 2007 · 8 claims · 6 setups

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  MG192 is highly variable among and within M. genitalium strains both in vitro and in vivo

  genitalium clinical urine pairwise pcr serial

• Country-wide assessment of the genetic polymorphism in Plasmodium falciparum and Plasmodium vivax antigens detected with rapid diagnostic tests for malaria.

  PMID 18957099 · PMC2582241 · Malaria journal · 2008 · 7 claims · 8 setups

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  pfhrp2 and pfhrp3 genes show markedly higher polymorphism than the P. falciparum and P. vivax aldolase and pldh genes

  falciparum vivax extracted febrile pcr nested species-specific

• Spinocerebellar ataxia type 23: a genetic update.

  PMID 19089525 · PMC2694919 · Cerebellum (London, England) · 2009 · 8 claims · 6 setups

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  The SCA23 disease locus maps to chromosome 20p13-12.3, spanning ~6 Mb and containing 97 known/predicted genes.

  members post-mortem candidate coding genome-wide neuropathological southern

• Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.

  PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.

  calanus sinicus genomic rna-seq novo sequence

• Genetic variants of chemokine receptor CCR7 in patients with systemic lupus erythematosus, Sjogren's syndrome and systemic sclerosis.

  PMID 17587445 · PMC1913537 · BMC genetics · 2007 · 6 claims · 4 setups

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  CCR7 gene variants occur at extremely low frequency (allelic frequencies ≤5%) in the German population

  genomic hut78 t-cells direct pcr dual