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 14

System / cell line: random ✕ Assay: screening ✕ Clear

An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.

PMID 36352408 · PMC9648005 · BMC biology · 2022 · 7 claims · 5 setups

Has reproduction · 84

A signal transduction/gene regulatory network model of the articular chondrocyte was built combining knowledge-based curation and data-driven (machine learning) network inference

osteoarthritic articular chondrocyte microarray computational high-throughput
ATM variants 7271T>G and IVS10-6T>G among women with unilateral and bilateral breast cancer.

PMID 14562025 · PMC2394328 · British journal of cancer · 2003 · 8 claims · 4 setups

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Women with bilateral breast cancer show greater genetic predisposition (higher family history prevalence) than women with unilateral breast cancer

blood-derived blood random dhplc microsatellite duplicate
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

PMID 18682527 · PMC2532719 · Nucleic acids research · 2008 · 8 claims · 7 setups

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Biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA analysis

faecal rsr 16s sargasso shotgun blastn-based 16s
Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.

PMID 35038924 · PMC8764539 · mBio · 2022 · 7 claims · 8 setups

Has reproduction · 63

Of 42 isolates flagged as MRSA by screening agar, only 9 were PBP2a- and mecA-positive true MRSA, while the remaining 33 were mecA-negative and largely met criteria for BORSA

clinical nicu genomic maldi-tof pbp2a cefoxitin
Genome-wide analysis of the human Alu Yb-lineage.

PMID 15588477 · PMC3525081 · Human genomics · 2004 · 8 claims · 6 setups

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1,733 Alu Yb-lineage elements are present on human autosomal chromosomes

genome genomic non-human yb7 computational pcr-based pcr
A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.

PMID 16237125 · PMC1258171 · Nucleic acids research · 2005 · 8 claims · 6 setups

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A genome-wide computational survey identifies 245 genes in mammals (264 across six species) that produce RREO events in expressed sequences

expressed representative random genes computational orf statistical
Mutations in APC, CTNNB1 and K-ras genes and expression of hMLH1 in sporadic colorectal carcinomas from the Netherlands Cohort Study.

PMID 16356174 · PMC1334229 · BMC cancer · 2005 · 8 claims · 5 setups

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CTNNB1 mutations at phosphorylation sites are rare and of minor importance in sporadic colorectal cancer

archival colorectal formalin-fixed tumour mutation immunohistochemistry microsatellite
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
Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

PMID 17406619 · PMC2688820 · Nature protocols · 2007 · 8 claims · 7 setups

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Combining three human-optimized DOP-PCR primers before a secondary amino-labeled PCR increases array hybridization sensitivity and reproducibility sixfold compared to the standard 6MW DOP-PCR primer

large-insert patients test genomic array-cgh manual automated
Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 6 setups

Has reproduction

Expression stability in CHO cell lines is controlled at three levels: choice of integration site, integrity/concatemerization pattern of the transgene, and stress-related cellular processes.

horizon six cho-k1 cho genome rna-seq targeted
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
Automated recognition of retroviral sequences in genomic data--RetroTector.

PMID 17636050 · PMC1976444 · Nucleic acids research · 2007 · 8 claims · 8 setups

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RetroTector uses 'fragment threading' (detection of chains of conserved retroviral motifs satisfying distance constraints) combined with LTR detection and protein reconstruction to identify ERVs in genomic sequences

reference genome chimpanzee red motif whole-genome simulated
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.

PMID 17984082 · PMC2239001 · Nucleic acids research · 2008 · 8 claims · 7 setups

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The Biodefense Proteomics Resource Center (RC) is a public cyberinfrastructure that stores, integrates, and disseminates experimental data from seven Proteomics Research Centers (PRCs) on biodefense pathogens and host interactions

brucella toxoplasma bacillus homo label-free mass genomic
Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

coriell myeloma duplicate snp targeted genotyping machine

Experiments

An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.

ATM variants 7271T>G and IVS10-6T>G among women with unilateral and bilateral breast cancer.

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.

Genome-wide analysis of the human Alu Yb-lineage.

A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.

Mutations in APC, CTNNB1 and K-ras genes and expression of hMLH1 in sporadic colorectal carcinomas from the Netherlands Cohort Study.

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

Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

Automated recognition of retroviral sequences in genomic data--RetroTector.

An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.

Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.