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).

• 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

• Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

  PMID 15722479 · PMC549431 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  Two base deletion probes display the highest average hybridization specificity, followed by single base substitution, single base deletion, and single base insertion probes.

  atm hybridized probe oligonucleotide transcription microarray

• 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

• A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

  PMID 19751529 · PMC2755474 · Journal of biomedical science · 2009 · 8 claims · 5 setups

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  Pre-S1 and pre-S2 deletion mutants of the HBV LHBS gene are highly associated with HBV-related HCC

  serum plasmids coli pcr oligonucleotide chip

• Quantitative analysis of SMN1 gene and estimation of SMN1 deletion carrier frequency in Korean population based on real-time PCR.

  PMID 15608400 · PMC2816285 · Journal of Korean medical science · 2004 · 7 claims · 6 setups

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  Developed a reliable quantitative real-time PCR assay using SMN1-specific primers, SYBR Green I dye, and the comparative Ct (ΔΔCt) method, normalized to albumin, to determine SMN1 copy number

  genomic peripheral quantitative multiplex pcr-restriction

• Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

  PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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  Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

  normalized individuals subset same affymetrix fluorescent snp

• An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

  PMID 19012953 · PMC2990916 · Cell · 2008 · 7 claims · 8 setups

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  shRNA pools targeting genes recurrently deleted in human HCC accelerate hepatocarcinogenesis in vivo, whereas randomly selected shRNA pools do not.

  hepatocellular p53 genomic hepatoma array-based pooled shrna

• QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

  PMID 17341461 · PMC1874617 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  QuantiSNP (OB-HMM) provides probabilistic quantification of copy number states and significantly improves accuracy of segmental aneuploidy identification and breakpoint mapping relative to existing tools (BeadStudio/Illumina)

  genomic same pseudo-normal artificially snp fish molecular

• Additional EFNB1 mutations in craniofrontonasal syndrome.

  PMID 18627045 · PMC2774847 · American journal of medical genetics. Part A · 2008 · 8 claims · 4 setups

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  Loss-of-function mutations in EFNB1 (Xq13.1) are the cause of CFNS in the majority of patients

  lymphoblastoid cfns patients additional pcr multiplex molecular

• Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

  PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups

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  A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys

  personal genomic pcr-validated unrelated short-read pcr sanger

• One-pot shotgun quantitative mass spectrometry characterization of histones.

  PMID 19764812 · PMC2798817 · Journal of proteome research · 2009 · 8 claims · 8 setups

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  One-pot propionylation and trypsin digestion of unfractionated bulk histones enables quantitative Bottom Up MS characterization of histone PTMs without prior off-line HPLC or SDS-PAGE purification

  hela wild-type set2δ yeast bottom rp-hplc one-pot

• BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

  PMID 19668202 · PMC3661775 · Nature methods · 2009 · 8 claims · 8 setups

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  BreakDancer (BreakDancerMax + BreakDancerMini) is a software package that predicts a wide variety of structural variants including deletions, insertions, inversions, and intra/inter-chromosomal translocations from paired-end short-insert sequencing reads.

  reads yoruban cytogenetically predicted simulated paired-end whole-genome

• Familial Wolfram syndrome due to compound heterozygosity for two novel WFS1 mutations.

  PMID 18660851 · PMC2483297 · Molecular vision · 2008 · 8 claims · 6 setups

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  The four affected siblings are compound heterozygotes for two novel WFS1 mutations, one from each parent, causing Wolfram syndrome.

  genomic affected microsatellite pcr allele-specific

• 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

• Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling.

  PMID 19825513 · PMC2787914 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  Multidimensional phenotypic profiling leverages information content from multiple parallel or multiplexed measurements of compound action on cells, unlike hierarchical screening which filters to few 'interesting' compounds.

  one nci60 cerevisiae cancer multidimensional cellular two-color

• Integrative functional genomics.

  PMID 15239826 · PMC463286 · Genome biology · 2004 · 8 claims · 8 setups

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  Ultra-conserved noncoding elements exist across human, mouse and rat genomes at very high sequence identity, often far from genes

  yeast tissue-cultured mammalian genomic comparative targeted chip-chip

• The VIZIER project: preparedness against pathogenic RNA viruses.

  PMID 18083241 · PMC7114271 · Antiviral research · 2008 · 8 claims · 6 setups

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  Almost all newly emerging human pathogenic viruses are RNA viruses, largely because their error-prone RNA-dependent RNA polymerases and zoonotic reservoirs allow rapid adaptation to new hosts.

  viruses virus coli soluble large-scale bioinformatic recombinant