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).

• Ligase detection reaction for the analysis of point mutations using free-solution conjugate electrophoresis in a polymer microfluidic device.

  PMID 19053073 · PMC3010182 · Electrophoresis · 2008 · 8 claims · 7 setups

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  LDR-FSCE (combining LDR with free-solution conjugate electrophoresis) enables single-base resolution separation of LDR products without a polymer sieving matrix

  genomic synthetic k-ras ldr-dt pcr solid-phase ligase

• A common polymorphism in the oxygen-dependent degradation (ODD) domain of hypoxia inducible factor-1alpha (HIF-1alpha) does not impair Pro-564 hydroxylation.

  PMID 14521712 · PMC212228 · Molecular cancer · 2003 · 6 claims · 5 setups

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  Pro582Ser is a common HIF-1α ODD-domain polymorphism occurring at similar frequency in idiopathic erythrocytosis patients (0.109) and normal controls (0.073)

  genomic recombinant 35s-labeled sanger pcr-rflp gst

• 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

• Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA.

  PMID 16582098 · PMC1421508 · Nucleic acids research · 2006 · 6 claims · 5 setups

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  TnT enables parallel amplification of 75 SNPs from sub-nanogram amounts of genomic DNA

  genomic dbsnp tnt duplex bioinformatic

• From genomics to chemical genomics: new developments in KEGG.

  PMID 16381885 · PMC1347464 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  KEGG BRITE has been formally added as a fourth main KEGG database to establish a logical foundation for functional interpretation and pathway reconstruction.

  enzymatic substrate kegg complete chemical number ortholog

• Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector.

  PMID 17317684 · PMC1874629 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  Gene-Collector is a method for multiplex nucleic acid amplification that specifically circularizes only correctly paired (cognate) PCR primer products on a Collector probe, degrading non-cognate artifacts by exonuclease treatment.

  genomic multiplex circularized circular multiplex probe-guided exonuclease

• Ankyrin-linked hereditary spherocytosis in an African-American kindred.

  PMID 18704959 · PMC11304496 · American journal of hematology · 2008 · 6 claims · 7 setups

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  A novel heterozygous initiator methionine mutation (ATG→ATA, Met1Ile), termed ankyrin New Haven, was identified in exon 1 of the ankyrin-1 gene as the cause of HS in this kindred.

  genomic erythrocyte rabbit dhplc sscp nucleotide

• Primase-based whole genome amplification.

  PMID 18559358 · PMC2490742 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  A primase-based Whole Genome Amplification (pWGA) method was developed using T7 gp4 primase to synthesize primers on-template, removing the requirement for synthetic primers

  genomic plasmids circular agarose picogreen dye-terminator

• Rapid detection of SMARCB1 sequence variation using high resolution melting.

  PMID 20003390 · PMC2801682 · BMC cancer · 2009 · 8 claims · 6 setups

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  HRM screening of SMARCB1 amplicons has a zero false negative rate compared to direct sequencing

  genomic same tumor rhabdoid high direct hrm

• Detection of 100% of mutations in 124 individuals using a standard UV/Vis microplate reader: a novel concept for mutation scanning.

  PMID 16554551 · PMC1409816 · Nucleic acids research · 2006 · 7 claims · 8 setups

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  A cleavage-free mismatch oxidation assay using potassium permanganate and a standard UV/Vis microplate reader can detect DNA mismatches spectrophotometrically at 420 nm.

  individual hybridized 38mer pbr322 colorimetric uv-vis mismatch

• Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

  PMID 16141191 · PMC1197137 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  A novel 'bioluminometric assay coupled with terminator (ddNTP) incorporation' (BATI) platform was developed for multiplex SNP typing in a single reaction chamber.

  pcr-amplified same sequence luciferase bioluminometric bati comparison

• A novel approach for determining cancer genomic breakpoints in the presence of normal DNA.

  PMID 17440616 · PMC1847701 · PloS one · 2007 · 8 claims · 6 setups

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  PAMP enriches deletion-breakpoint-spanning DNA because shorter mutant amplicons are preferentially amplified over much longer wild-type sequences when using approximated flanking primer pairs.

  detroit serial hs578t pamp individual nested

• A comprehensive modular map of molecular interactions in RB/E2F pathway.

  PMID 18319725 · PMC2290939 · Molecular systems biology · 2008 · 8 claims · 4 setups

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  A comprehensive, curated map of RB/E2F pathway molecular interactions was built using SBGN notation in CellDesigner and converted to BioPAX 2.0 format

  bladder computational curated literature transcriptome gene network

• Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

  PMID 17003057 · PMC1635253 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Stepwise directed evolution using chimeric FLRT (FRT/genomic hybrid) intermediate sites can generate Flp variants capable of recombining native genomic FRT-like sequences from the human IL10 gene (FL-IL10A, FL-IL10B).

  coli flp il10 flp-holliday recombination site-specific computational

• spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.

  PMID 37602419 · PMC10516669 · Nucleic acids research · 2023 · 8 claims · 4 setups

  Has reproduction · 77

  spotter is the first simulation model to integrate transcription, DNA supercoiling, and translation simultaneously in a single stochastic framework for prokaryotes.

  coli simulated net-seq ribosome stochastic

• 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

• 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

• Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays.

  PMID 15673719 · PMC548352 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Presence of CENP-B box elements is required for efficient de novo centromere formation in HAC vectors

  ht1080 coli ht1080-derived synthetic novo gel transposition

• 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

• Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

  PMID 17713557 · PMC2435172 · Genes and immunity · 2007 · 7 claims · 8 setups

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  SNPs in LECT2 and TGFBI show independent associations with the DTH+ phenotype, indicating two separate genes in this region control DTH+

  blood family unrelated subjects snp family-based linkage