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).

• Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan.

  PMID 16055919 · PMC1182175 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  MDA genotyping call rates and accuracy are only marginally lower than for genomic DNA

  genomic same monozygotic subset genome-wide genome

• Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

  PMID 19329065 · PMC5054122 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 8 setups

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  Nucleotide preference at CpG flanking sites transitions from 5' T (invertebrates) to 5' A (vertebrates) at the invertebrate-vertebrate boundary

  genomes same pufferfish elegans nucleotide genome-wide kruskal-wallis

• Environmental Burkholderia cepacia complex isolates in human infections.

  PMID 17552100 · PMC2725883 · Emerging infectious diseases · 2007 · 6 claims · 4 setups

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  More than 20% of clinical Bcc isolates examined are indistinguishable by MLST from environmental isolates, linking the natural environment to emergence of clinical infections

  clinical environmental subset stabilis multilocus cloning pulsed-field

• A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

  PMID 18940863 · PMC2602776 · Nucleic acids research · 2008 · 7 claims · 4 setups

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  A novel Invader assay-based procedure can accurately determine SNP genotypes in trisomic genomic DNA samples in a simple, cost-effective manner

  genomic same synthetic invader pyrosequencing hplc

• 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

• Multiplex SNaPshot for detection of BRCA1/2 common mutations in Spanish and Spanish related breast/ovarian cancer families.

  PMID 17603881 · PMC1924843 · BMC medical genetics · 2007 · 7 claims · 4 setups

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  Ten recurrent/founder mutations (5 in BRCA1, 5 in BRCA2, including the newly observed BRCA2 c.5374-5377delTATG) account for approximately 50% of BRCA1/2 mutations identified in Spanish families

  genomic same pcr multiplex pcr snapshot

• Detection of mutations in the dystrophin gene via automated DHPLC screening and direct sequencing.

  PMID 11710958 · PMC59832 · BMC genetics · 2001 · 7 claims · 6 setups

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  DHPLC screening combined with direct sequencing detects likely disease-causative point mutations in the dystrophin gene missed by multiplexed PCR deletion/duplication testing

  genomic muscle blood direct dhplc multiplexed

• Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

  PMID 18204449 · PMC2684619 · Nature genetics · 2008 · 8 claims · 8 setups

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  Mutations in GLE1, an mRNA export mediator, cause LCCS1

  lccs1 laahd finnish healthy genomic microsatellite carrier

• Effective quantitative real-time polymerase chain reaction analysis of the parkin gene (PARK2) exon 1-12 dosage.

  PMID 17324265 · PMC1810516 · BMC medical genetics · 2007 · 8 claims · 3 setups

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  Developed a real-time TaqMan PCR method that quantifies PARK2 exon 1-12 copy number by comparing amplification signal to the β-globin internal control gene

  genomic same real-time prior

• Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.

  PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups

  Has reproduction · 58

  Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)

  strain jel427-p9 genes whole-genome snp indel

• Germline mutations of the STK11 gene in Korean Peutz-Jeghers syndrome patients.

  PMID 10780518 · PMC2363369 · British journal of cancer · 2000 · 8 claims · 4 setups

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  Germline mutations of STK11 were found in 5 of 10 Korean PJS patients screened

  genomic pcr pcr-single-strand cloning pcr-sscp

• TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation.

  PMID 15345028 · PMC517934 · BMC medical genetics · 2004 · 8 claims · 4 setups

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  No disease-associated mutations were found in TM4SF10 in 16 XLMR patients from 14 families with linkage to the TM4SF10 locus.

  genomic dog sage pcr northern sage

• Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

  PMID 16824219 · PMC1534050 · BMC neurology · 2006 · 7 claims · 5 setups

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  The C282Y variant allele of HFE is significantly overrepresented in PD patients compared to controls, suggesting it confers higher risk for PD

  genomic same pooled pcr-rflp pcr-based cross-tabulation

• Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

  PMID 19039135 · PMC2746051 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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  Diagnosis and relapse ALL samples show different patterns of CNAs, with relapse-acquired abnormalities preferentially affecting cell cycle regulation and B-cell development genes

  matched bone leukemia diagnosis snp flow quantitative

• The RYR2-encoded ryanodine receptor/calcium release channel in patients diagnosed previously with either catecholaminergic polymorphic ventricular tachycardia or genotype negative, exercise-induced long QT syndrome: a comprehensive open reading frame mutational analysis.

  PMID 19926015 · PMC2880864 · Journal of the American College of Cardiology · 2009 · 8 claims · 6 setups

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  Comprehensive open-reading-frame RYR2 mutational analysis reveals possible CPVT1 mutations located outside the three canonical hot-spot domains

  genomic hair-root reference patients pcr screening multi-tissue

• Angiotensin-converting enzyme gene insertion/deletion polymorphism in migraine patients.

  PMID 18366776 · PMC2311324 · BMC neurology · 2008 · 6 claims · 3 setups

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  ACE I/D genotype and allele distributions do not differ significantly between migraine patients and controls

  genomic migraine pcr clinical

• ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

  PMID 16845044 · PMC1538898 · Nucleic acids research · 2006 · 8 claims · 2 setups

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  The ASPIC algorithm, using an optimization procedure that minimizes splice site predictions and transcript isoforms from multiple EST-genome alignments, outperforms other similar AS-prediction tools in sensitivity and selectivity

  hnrpr specified comparative algorithm

• A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

  PMID 15588494 · PMC3525102 · Human genomics · 2004 · 8 claims · 5 setups

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  PSD-mediated genomic architecture analogous to the 8p23/4p16 inversion regions is not unique to those loci but recurs genome-wide.

  genomic genome extracted pairwise online genome-wide

• Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

  PMID 15790396 · PMC1087472 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  Paircomp, FamilyRelationsII, and Cartwheel together form an integrated system for comparing, viewing, and managing analyses of BAC-sized (~100 kb) genomic sequence pairs.

  otx sea elegans endo16 windowed reporter comparative

• Heterogeneous genomic molecular clocks in primates.

  PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

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  Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

  baboon chimpanzee same human-chimpanzee relative phylogenetic four-species