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 26

System / cell line: in-silico ✕ Assay: primer ✕ Clear

BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes.

PMID 15653630 · PMC546182 · Nucleic acids research · 2005 · 7 claims · 4 setups

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BiSearch is a new web-available primer-design software for bisulfite-treated genomes that also analyzes primer pairs for mispriming sites via a novel search algorithm.

tyrosine homo hek primer post-design pcr
EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

PMID 16381980 · PMC1347508 · Nucleic acids research · 2006 · 7 claims · 4 setups

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EPD is an annotated, non-redundant collection of experimentally defined eukaryotic POL II promoters accessed via genome position pointers.

rice preliminary primer sequence quality
CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification.

PMID 36304334 · PMC9580850 · Frontiers in bioinformatics · 2022 · 8 claims · 5 setups

Has reproduction · 88

CIRCprimerXL is a high-throughput, user-friendly circRNA RT-qPCR primer design pipeline available as both a web tool and a standalone Nextflow/Docker pipeline

synthetic sw480 circrnas rt-qpcr circrna primer
Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

PMID 16042802 · PMC1190169 · BMC genomics · 2005 · 7 claims · 6 setups

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Achieving high-multiplexing/high-coverage multiplex PCR designs is subject to a computational phase transition as the SNP-pair compatibility probability crosses a critical threshold

simulated real chromosome randomly simulation multiplex coverage-vs-n
RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.

PMID 19958502 · PMC2788391 · BMC genomics · 2009 · 7 claims · 4 setups

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RExPrimer integrates local SNP, indel, pseudogene, and CNV/structural variation databases with the Primer3 core algorithm to avoid mis-priming and SNP-in-Primer effects.

genomic cyp2d6 genome pcr penta-plex sequence
Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories.

PMID 18712842 · PMC2906129 · Journal of medical virology · 2008 · 8 claims · 5 setups

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Coverage of naturally occurring BKV strains varies substantially among current PCR diagnostic assays due to primer/probe mismatches

bkv virus sequence primer cross-reactivity
SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.

PMID 15980532 · PMC1160243 · Nucleic acids research · 2005 · 7 claims · 3 setups

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SOP 3 v2 is a web-based application that outputs recommended forward/reverse PCR primers plus a sequencing primer optimized for sequence-based genotyping of human and mouse polymorphisms

genomic ncbi laboratory primer genomic
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

PMID 19796657 · PMC3568755 · Journal of microbiological methods · 2009 · 8 claims · 6 setups

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The 16S rRNA V5 hypervariable region, amplified as a short ~82-base segment, provides reliable taxonomic identification of oral bacteria against public databases like HOMD.

pooled 16s sequenced topo 16s primer taxonomic
A method for accurate detection of genomic microdeletions using real-time quantitative PCR.

PMID 16351727 · PMC1327677 · BMC genomics · 2005 · 8 claims · 5 setups

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A qPCR method using unique-sequence primers can reproducibly detect chromosomal microdeletions and microduplications

genomic genome pcr real-time fluorescence sequence
PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.

PMID 24747190 · PMC4411361 · Genomics, proteomics & bioinformatics · 2014 · 8 claims · 3 setups

Has reproduction · 90

PrimerSeq is a user-friendly stand-alone software with a GUI for systematic design and visualization of RT-PCR primers for alternative splicing analysis using user-provided RNA-seq data.

heart genome rna-seq rt-pcr
MuPlex: multi-objective multiplex PCR assay design.

PMID 15980531 · PMC1160138 · Nucleic acids research · 2005 · 8 claims · 3 setups

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MuPlex is a web-enabled system that designs multiplex PCR assays by selecting primer pairs for SNPs and partitioning them into multiplex-compatible tube sets.

user-submitted candidate genomic multiplex primer homogeneous
V-MitoSNP: visualization of human mitochondrial SNPs.

PMID 16907992 · PMC1564046 · BMC bioinformatics · 2006 · 6 claims · 4 setups

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V-MitoSNP integrates RFLP genotyping information with mitochondria-related cancer/disease data in a user-friendly, interactive, color-coded visual web interface

blood blood-derived mtdna standard agarose rflp
Leveraging human genomic information to identify nonhuman primate sequences for expression array development.

PMID 16288651 · PMC1314899 · BMC genomics · 2005 · 8 claims · 6 setups

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Human genomic DNA sequence can be leveraged to obtain 3' end sequence of NHP orthologs, which can then be used to generate NHP oligonucleotide microarrays

refseq macaca genomic rhesus exon pcr molecular
PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

PMID 17105657 · PMC1657037 · BMC bioinformatics · 2006 · 6 claims · 5 setups

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PathogenMIPer designs unique, target-specific MIP probes, assembling all probe components (target-specific sequences, barcodes, universal primers, restriction sites) into ready-to-order probes for any genome.

hpv clinical biotinylated pcr mip molecular microarray
Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.

PMID 27092297 · PMC4820441 · Frontiers in cellular and infection microbiology · 2016 · 6 claims · 8 setups

Has reproduction · 89

STEC prevalence in surface water varies by watershed and by season in the Lower Mainland of British Columbia.

surface sediment isolate presumptive hydrophobic stx monoplex
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
Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

PMID 18622261 · PMC2680356 · Pharmacogenetics and genomics · 2008 · 7 claims · 7 setups

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UGT2B7 haplotype 4 is associated with increased enzyme activity (M3G and M6G formation)

liver caucasian ugt2b7 gene snp enzymatic
CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping.

PMID 16686952 · PMC1471797 · BMC genetics · 2006 · 7 claims · 1 setups

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CapsID identifies snip-SNPs (SNPs that alter restriction endonuclease recognition sites) within reference sequence alignments and designs PCR primers around them

sequence restriction
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
A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

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A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

cetacea amel-y amel-x cetartiodactyla pcr sanger molecular

Experiments

BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes.

EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification.

Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.

Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories.

SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

A method for accurate detection of genomic microdeletions using real-time quantitative PCR.

PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data.

MuPlex: multi-objective multiplex PCR assay design.

V-MitoSNP: visualization of human mitochondrial SNPs.

Leveraging human genomic information to identify nonhuman primate sequences for expression array development.

PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.

Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS.

Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping.

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

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.