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 36

System / cell line: snp ✕ Assay: sensitivity ✕ Clear

Searching for SNPs with cloud computing.

PMID 19930550 · PMC3091327 · Genome biology · 2009 · 8 claims · 4 setups

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Crossbow combines the Bowtie short-read aligner and SOAPsnp SNP caller into a seamless, automatic Hadoop/MapReduce pipeline for whole-genome resequencing analysis

han local short simulated whole-genome cloud
Needles in the haystack: identifying individuals present in pooled genomic data.

PMID 19798441 · PMC2747273 · PLoS genetics · 2009 · 8 claims · 7 setups

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The distribution of T for null samples (individuals not in F or G) deviates strongly from the assumed standard normal, in both location and width.

cgems hapmap genetic-distance within-population snp-count
The promise and reality of personal genomics.

PMID 19723346 · PMC2768970 · Genome biology · 2009 · 7 claims · 6 setups

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Despite being the most complete and accurate individually sequenced human genome to date, AK1 sequencing still misses a substantial fraction of variants, showing sequencing technology remains far from complete/reliable.

ak1 six whole-genome copy-number genotyping-based
Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

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A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

gbs clinical bioinformatic eburst kinetic
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
A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.

PMID 18194558 · PMC2248205 · BMC genetics · 2008 · 8 claims · 5 setups

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A hierarchical/modular approach integrating quality control, LD, physical distance, and gene ontology identifies authentic associations among those found by statistical tests in pooled DNA GWAS

pooled sickle centenarian snp pooled gene
Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.

PMID 16026601 · PMC1637030 · BMC bioinformatics · 2005 · 8 claims · 2 setups

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DF-SNPs, a novel adaptation of the Decision Forest method, can classify esophageal cancer cases vs. controls based on SNP genotype data with high concordance, sensitivity, and specificity.

genomic snp high-throughput decision
CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

PMID 16504045 · PMC1402331 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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CARAT is a novel algorithm that uses SNP probe intensity and genotype-based allelic dosage response in a regression framework to estimate allele-specific copy number genome-wide.

normal genomic sk-br-3 cancer snp quantitative allele-specific
Extension of type 2 diabetes genome-wide association scan results in the diabetes prevention program.

PMID 18544707 · PMC2518503 · Diabetes · 2008 · 8 claims · 4 setups

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None of the selected GWAS-identified SNPs individually were associated with increased diabetes incidence in the DPP cohort

dpp snp cox oral
Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

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Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

european african individuals nondiabetic snp variant direct
A pharmacogene database enhanced by the 1000 Genomes Project.

PMID 19745786 · PMC2935084 · Pharmacogenetics and genomics · 2009 · 7 claims · 4 setups

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The database provides a convenient portal for immediate utilization of newly released 1000 Genomes Project (KGP) data in pharmacogenetic studies

ceu hapmap lymphoblastoid genotype-phenotype whole-genome low-coverage
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning.

PMID 34461978 · PMC8407037 · Genome medicine · 2021 · 8 claims · 6 setups

Has reproduction · 78

GenTB is a free, open, web-based application offering two ML predictors (Random Forest and WDNN) that predict resistance to 13 and 10 anti-TB drugs, respectively.

clinical tuberculosis registered whole-genome targeted retraining
Use of genomic data in risk assessment.

PMID 11983054 · PMC139345 · Genome biology · 2002 · 8 claims · 4 setups

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New genomic technologies (CGH, SNP analysis, restriction landmark genome scanning, spectral karyotyping, transcript profiling) can be applied to improve risk assessment accuracy

glioma lung animal genome sensitivity expression snp
Polymorphism at the C-reactive protein locus influences gene expression and predisposes to systemic lupus erythematosus.

PMID 14645206 · PMC3707088 · Human molecular genetics · 2004 · 8 claims · 5 setups

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The minor (rare) allele of CRP SNP 'CRP 4' is associated/linked with development of SLE in family-based transmission studies.

crp simplex same serum direct family-based linkage
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
Genetic polymorphisms in monoamine neurotransmitter systems show only weak association with acute post-surgical pain in humans.

PMID 16848906 · PMC1543620 · Molecular pain · 2006 · 8 claims · 5 setups

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COMT SNP5 (rs740603, intron 1) shows significant association with maximum post-operative pain rating

surgical candidate haplotype allele
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
BOAT: Basic Oligonucleotide Alignment Tool.

PMID 19958483 · PMC2788372 · BMC genomics · 2009 · 7 claims · 3 setups

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BOAT can accurately and efficiently map sequencing reads to a reference genome while handling several substitutions and indels simultaneously

same short-read snp
Genetic variants of adiponectin receptor 2 are associated with increased adiponectin levels and decreased triglyceride/VLDL levels in patients with metabolic syndrome.

PMID 16700915 · PMC1482678 · Cardiovascular diabetology · 2006 · 8 claims · 6 setups

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A haplotype of three AdipoR2 variants (+795G/A, +870C/A, +963C/T) in perfect linkage disequilibrium is associated with higher plasma adiponectin levels and lower fasting triglyceride, VLDL-triglyceride, and VLDL-cholesterol levels

peripheral plasma subjects adipor1 sequencing plasma preparative
Application of machine learning in SNP discovery.

PMID 16398931 · PMC1955739 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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PolyBayes produces high false-positive SNP predictions even with stringent parameters

diverse soybean candidate same sts polybayes polyphred

Experiments

Searching for SNPs with cloud computing.

Needles in the haystack: identifying individuals present in pooled genomic data.

The promise and reality of personal genomics.

Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

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.

A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.

Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.

CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

Extension of type 2 diabetes genome-wide association scan results in the diabetes prevention program.

Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

A pharmacogene database enhanced by the 1000 Genomes Project.

GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning.

Use of genomic data in risk assessment.

Polymorphism at the C-reactive protein locus influences gene expression and predisposes to systemic lupus erythematosus.

Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

Genetic polymorphisms in monoamine neurotransmitter systems show only weak association with acute post-surgical pain in humans.

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

BOAT: Basic Oligonucleotide Alignment Tool.

Genetic variants of adiponectin receptor 2 are associated with increased adiponectin levels and decreased triglyceride/VLDL levels in patients with metabolic syndrome.

Application of machine learning in SNP discovery.