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).

Publications 1.3k Datasets 392.5k Experiments 35

System / cell line: per ✕ Assay: direct ✕ Clear

Decoding of superimposed traces produced by direct sequencing of heterozygous indels.

PMID 18654614 · PMC2429969 · PLoS computational biology · 2008 · 7 claims · 3 setups

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A dynamic programming method (implemented as web app Indelligent) can decode superimposed allelic sequences from a single mixed trace, using only the observed string of ambiguous peak calls, without a reference sequence or reverse trace.

genomic artificial simulated direct computational comparative
Mutation survey of known LCA genes and loci in the Saudi Arabian population.

PMID 18936139 · PMC2695987 · Investigative ophthalmology & visual science · 2009 · 7 claims · 4 setups

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Mutations in the 13 known LCA genes were identified in only 24% (9/37) of Saudi Arabian LCA families, far lower than the ~65% mutation detection rate reported in European populations

leukocyte affected kkesh-060 direct str homozygosity
Collagen VI glycine mutations: perturbed assembly and a spectrum of clinical severity.

PMID 18825676 · PMC2743946 · Annals of neurology · 2008 · 8 claims · 6 setups

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All eight new patients had heterozygous glycine substitution mutations toward the N-terminal end of the collagen VI triple helix

dermal skeletal fibroblast confluent rt-pcr immunohistochemistry biosynthetic
Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection.

PMID 16102740 · PMC7124242 · Clinica chimica acta; international journal of clinical chemistry · 2006 · 6 claims · 7 setups

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The Luminex xMAP system uses spectrally distinct dyed microspheres (up to 100 sets) read by dual lasers to enable simultaneous multiplexed analysis of up to 100 reactions in one vessel.

genomic apoe hla whole-genome direct oligonucleotide single
Direct maximum parsimony phylogeny reconstruction from genotype data.

PMID 18053244 · PMC2222657 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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The paper presents the first practical method for computing maximum parsimony phylogenies directly from genotype data, using integer linear programming.

simulated mitochondrial lipoprotein coalescent maximum sliding-window
Novel transglutaminase-1 mutations and genotype-phenotype investigations of 104 patients with autosomal recessive congenital ichthyosis in the USA.

PMID 18948357 · PMC3044481 · Journal of medical genetics · 2009 · 8 claims · 6 setups

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TGM1 germline mutations were identified in 55% (57/104) of patients with ARCI

arci unrelated dog direct sequence blast
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.

PMID 18413340 · PMC2425484 · Nucleic acids research · 2008 · 8 claims · 8 setups

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CpG-rich regions (CpG islands) show low and similar methylation levels across individuals, but the sequential order of the few methylated CpGs among the many unmethylated ones varies randomly between individuals.

cd4+ computational hep direct simulation epigraph
MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets.

PMID 32256520 · PMC7089958 · Frontiers in genetics · 2020 · 7 claims · 8 setups

Has reproduction · 50

MasterOfPores is a NextFlow-based, containerized workflow that processes raw FAST5 direct RNA sequencing data through base-calling, demultiplexing, filtering, QC, mapping, and quantification, plus downstream RNA modification and polyA tail length analyses.

saccharomyces cerevisiae barcoded direct base-calling read
Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.

PMID 35464437 · PMC9019466 · Frontiers in immunology · 2022 · 8 claims · 8 setups

Has reproduction · 90

Differential polyadenylation occurs in infected Calu-3 and Vero cells at a late time point (48 hpi)

vero calu-3 genes direct pcr poly
The detection of K-ras mutations in colorectal cancer using the amplification-refractory mutation system.

PMID 9579832 · PMC2150152 · British journal of cancer · 1998 · 5 claims · 6 setups

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ARMS reliably detects K-ras codon 12/13 mutations in archival CRC DNA samples even when mutant sequence is under-represented relative to wild-type

archival tumour tumour-derived haematoxylin arms direct pcr
A phase II trial of gefitinib as first-line therapy for advanced non-small cell lung cancer with epidermal growth factor receptor mutations.

PMID 17047648 · PMC2360715 · British journal of cancer · 2006 · 7 claims · 5 setups

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Gefitinib is highly active and well tolerated as first-line therapy for advanced NSCLC with EGFR mutations

paraffin-embedded patients same direct phase kaplan-meier
Frequency and spectrum of c-Ki-ras mutations in human sporadic colon carcinoma, carcinomas arising in ulcerative colitis, and pancreatic adenocarcinoma.

PMID 1773797 · PMC1568060 · Environmental health perspectives · 1991 · 8 claims · 7 setups

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60% (37/61) of sporadic colon carcinomas contain c-Ki-ras codon 12 mutations

sporadic carcinoma pancreatic tumor pcr flow mixing
A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

simulated same mcmc-based direct original
Indirect genomic effects on survival from gene expression data.

PMID 18358079 · PMC2397510 · Genome biology · 2008 · 7 claims · 6 setups

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A novel methodology (dynamic path analysis combined with additive hazard survival regression) can detect and quantify indirect effects of gene expression on survival mediated through transcription factor target genes.

dutch uppsala dlbcl gene gene literature permutation
Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

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Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

hiv-1 same sequenced gag single-genome mhc hypermutation
Expression of p73, a novel protein related to the p53 tumour suppressor p53, and apoptosis in cholangiocellular carcinoma of the liver.

PMID 10362118 · PMC2363034 · British journal of cancer · 1999 · 7 claims · 6 setups

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p73 protein is expressed (nuclear immunostaining) in a substantial subset of cholangiocellular carcinomas

cholangiocellular ccc lysates immunohistochemistry direct western
Molecular variants of the ATM gene in Hodgkin's disease in children.

PMID 14735203 · PMC2409549 · British journal of cancer · 2004 · 8 claims · 4 setups

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Missense variants of the ATM gene occur in childhood Hodgkin lymphoma but at low frequency (9%), and thus do not play a major role in oncogenesis of the disease

frozen matched paired rt-pcr germ-line sscp
Genotypic analysis of two hypervariable human cytomegalovirus genes.

PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

hcmv clinical pcr ul146 pcr nested molecular
A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

PMID 16626494 · PMC1459863 · Malaria journal · 2006 · 8 claims · 5 setups

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Pyrosequencing, after adjustment to a standard curve, provides accurate and precise estimates of allele frequencies in mixed MSP-1_19 infections

falciparum cloned pyrosequencing pcr
Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

PMID 17855397 · PMC2094090 · Nucleic acids research · 2007 · 8 claims · 5 setups

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A new weighted formula that accounts for the number of methylated CpG sites per fragment removes the bias of the original MassCLEAVE™ formula toward higher apparent methylation in fragments with more CpG sites.

inhbb cloned same fresh-frozen rnase masscleave clonal

Experiments

Decoding of superimposed traces produced by direct sequencing of heterozygous indels.

Mutation survey of known LCA genes and loci in the Saudi Arabian population.

Collagen VI glycine mutations: perturbed assembly and a spectrum of clinical severity.

Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection.

Direct maximum parsimony phylogeny reconstruction from genotype data.

Novel transglutaminase-1 mutations and genotype-phenotype investigations of 104 patients with autosomal recessive congenital ichthyosis in the USA.

Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.

MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets.

Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.

The detection of K-ras mutations in colorectal cancer using the amplification-refractory mutation system.

A phase II trial of gefitinib as first-line therapy for advanced non-small cell lung cancer with epidermal growth factor receptor mutations.

Frequency and spectrum of c-Ki-ras mutations in human sporadic colon carcinoma, carcinomas arising in ulcerative colitis, and pancreatic adenocarcinoma.

A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

Indirect genomic effects on survival from gene expression data.

Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

Expression of p73, a novel protein related to the p53 tumour suppressor p53, and apoptosis in cholangiocellular carcinoma of the liver.

Molecular variants of the ATM gene in Hodgkin's disease in children.

Genotypic analysis of two hypervariable human cytomegalovirus genes.

A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.