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: algorithm ✕ Assay: snp ✕ Clear

Optimal step length EM algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping.

PMID 12529185 · PMC149347 · BMC bioinformatics · 2003 · 5 claims · 4 setups

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OSLEM (Optimal Step Length EM), which approximates an optimal step length via a fixed-point search (D_N = D_{N-1} + λ(D_preN - D_{N-1})), runs about twice as fast as standard EM while producing the same haplotype frequency estimates.

real tailored blood algorithm snp
SNP haplotype tagging from DNA pools of two individuals.

PMID 12709267 · PMC156884 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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An algorithm can reconstruct haplotypes from pools of two individuals' DNA under very general conditions, without requiring Hardy-Weinberg equilibrium.

add2 pooling computational exhaustive
Evolutionary algorithms for the selection of single nucleotide polymorphisms.

PMID 12875658 · PMC183839 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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Evolutionary algorithms are well suited to multiobjective optimization problems with large, intractable search spaces such as SNP selection, unlike exact methods (exhaustive enumeration) or single-objective search techniques (tabu search, simulated annealing).

simulated mhc evolutionary multiobjective
PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

PMID 16199750 · PMC1240117 · Nucleic acids research · 2005 · 7 claims · 6 setups

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The PPC algorithm, which applies a probe-pair-specific second-degree polynomial correction, increases the accuracy of allele frequency estimates from pooled DNA compared with previously described algorithms

individually reference equimolar independently snp reference pooled
Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants.

PMID 17672919 · PMC1973086 · BMC bioinformatics · 2007 · 6 claims · 8 setups

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The Not-N algorithm, incorporated into the Minimum SNPs program, identifies small marker sets diagnostic for user-defined subgroups of genetic variants with 0% false negatives

hcv campylobacter yersinia clostridium snp comparative cgh
SNP-RFLPing: restriction enzyme mining for SNPs in genomes.

PMID 16503968 · PMC1386656 · BMC genomics · 2006 · 8 claims · 2 setups

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SNP-RFLPing accepts three flexible input types (dbSNP rs#/ss# IDs, HUGO gene name/Entrez gene ID, or free-form SNP-in-sequence including IUPAC or [dNTP1/dNTP2] formats) for human, rat, and mouse genomes

software existing string-matching feature
SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data.

PMID 16262895 · PMC1280925 · BMC genomics · 2005 · 8 claims · 5 setups

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Poorly performing SNPs (NoCall rate ≥25%) fail primarily due to inadequate training/localization of the MPAM statistical model call zone, not detection filter failure

genomic genotype genotyped chromosomal snp clustering mendelian
Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition.

PMID 15850495 · PMC1090572 · BMC genetics · 2005 · 8 claims · 6 setups

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Haplotype block definitions based on LD measures (Definitions 1, 2, 3, 5) produce fewer, shorter blocks with limited sequence coverage compared to the haplotype diversity-based method (Definition 4)

unrelated same snps haplotype snp haplotype pairwise
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
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
Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

genomic genotype 293t pcr-amplified pcr haplotype cell-cell
Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.

PMID 18803882 · PMC2566316 · BMC genomics · 2008 · 8 claims · 5 setups

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About 20% of the 909,622 SNPs on the SNP Array 6.0 are monomorphic in the Japanese population

genomic japanese reference snp concentration agarose
High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups

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WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.

genomic whole-genome same call snp technical genotype
Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.

PMID 19956714 · PMC2776354 · PloS one · 2009 · 8 claims · 5 setups

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3,019 CNVs (2,381 autosomal, 638 X chromosome) were identified across 985 Caucasian and 692 Asian individuals using the Affymetrix 500K array

same caucasian cau autosomal snp copy population
Software for tag single nucleotide polymorphism selection.

PMID 16004730 · PMC3525260 · Human genomics · 2005 · 8 claims · 3 setups

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Pairwise R2 methods tend to pick more tagging SNPs than strictly needed because they miss redundancy where two or more tag SNPs jointly predict an untagged SNP with no single direct surrogate.

tgfbr1 encode candidate tag haplotype
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
High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

genomic ecotilling non-synonymous ecotilling sanger universal-primer
An evaluation of the performance of tag SNPs derived from HapMap in a Caucasian population.

PMID 16532062 · PMC1391920 · PLoS genetics · 2006 · 8 claims · 5 setups

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CEU HapMap-derived tSNPs capture most of the genetic variation observed in the Estonian (EGP) population sample

individuals hapmap egp snp tag median-joining
Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.

PMID 18923431 · PMC2692715 · Genes and immunity · 2009 · 7 claims · 6 setups

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A two-stage strategy (Random Forest filtering followed by decision tree modeling) can integrate categorical genetic and continuous proteomic data to identify biomarkers of AE risk

ebv-transformed serum combined rf-filtered snp serum random
An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.

PMID 18302794 · PMC2292209 · BMC genetics · 2008 · 7 claims · 5 setups

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Among the four HapMap populations, CHB shows the best correlation with the Shanghai population on allele frequencies, LD, and haplotype frequencies

unrelated shanghai tsnps snp allele linkage

Experiments

Optimal step length EM algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping.

SNP haplotype tagging from DNA pools of two individuals.

Evolutionary algorithms for the selection of single nucleotide polymorphisms.

PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants.

SNP-RFLPing: restriction enzyme mining for SNPs in genomes.

SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data.

Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition.

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.

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

Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.

High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.

Software for tag single nucleotide polymorphism selection.

Computational tradeoffs in multiplex PCR assay design for SNP genotyping.

High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

An evaluation of the performance of tag SNPs derived from HapMap in a Caucasian population.

Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.

An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.