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 57

System / cell line: comparison ✕ Assay: haplotype ✕ Clear

Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

PMID 18193213 · PMC2206249 · Immunogenetics · 2008 · 8 claims · 6 setups

Full-text index only

Comparison of eight HLA-homozygous MHC haplotype sequences identified >44,000 variations (substitutions and indels), submitted to dbSNP

hla-homozygous same mhc indel clone-by-clone gene hla
Computation of haplotypes on SNPs subsets: advantage of the "global method".

PMID 17067372 · PMC1636337 · BMC genetics · 2006 · 6 claims · 4 setups

Full-text index only

The global method for subhaplotyping always yields a lower error rate than the direct method across datasets and SNP subset sizes

gh1 apoe coalescent-model-simulated griv computational genetic
Software for tag single nucleotide polymorphism selection.

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

Full-text index only

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
The gentle art of gene arrangement: the meaning of gene clusters.

PMID 11897017 · PMC139018 · Genome biology · 2002 · 8 claims · 7 setups

Full-text index only

Gene order in eukaryotic genomes is likely optimized by natural selection rather than arising purely by chance reshuffling.

populations mhc interphase cartilaginous sequence codon comparative
Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups

Full-text index only

Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.

european-american yoruban japanese case sanger snp linkage
Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

PMID 19907653 · PMC2771352 · PloS one · 2009 · 8 claims · 7 setups

Full-text index only

IL10 haplotype 1 (rs1800871, rs1800872, rs3024490, rs1554286) is associated with a pro-inflammatory ex vivo cytokine response (lower IL-10, higher TNF-alpha) relative to the population mean

population blood genomic hapmap snp survival allele
Whole genome association mapping by incompatibilities and local perfect phylogenies.

PMID 17042942 · PMC1624851 · BMC bioinformatics · 2006 · 8 claims · 8 setups

Full-text index only

Blossoc scores the perfect phylogenetic tree spanning the largest compatible region around each marker as a decision tree for case/control status to detect association

coalescent-simulated artificial empirical same perfect-phylogeny hapminer haplotype
A model-based approach to selection of tag SNPs.

PMID 16776821 · PMC1525207 · BMC bioinformatics · 2006 · 7 claims · 5 setups

Full-text index only

The Li and Stephens hidden Markov model outperforms other tested models (simple Markov, two-state HMM, HMM-4D, greedy GR-1/GR-2) in description code-length, tag set information content, and prediction of tagged SNPs.

hapmap encode enr112 tag cross-validated entropy tagged
htSNPer1.0: software for haplotype block partition and htSNPs selection.

PMID 15740612 · PMC1274247 · BMC bioinformatics · 2005 · 6 claims · 1 setups

Full-text index only

The GBB algorithm finds the globally optimal minimal htSNP set with far less computing time than exhaustive/enumeration search.

chromosome haplotype
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

Full-text index only

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
Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

PMID 17026745 · PMC1630699 · BMC genetics · 2006 · 8 claims · 6 setups

Full-text index only

Identified 32 male-specific Y-chromosome sequences totaling 24159 bp via combined Blast (human Y chromosome match, absence from female dog genome) and PCR male-specificity screening of a male poodle shotgun genome.

poodle dogs y-chromosome blast pcr nested
Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

Full-text index only

SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

genome autosomal hapmap chromosome snp chromosomal minor
Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'.

PMID 17980034 · PMC2180187 · BMC bioinformatics · 2007 · 6 claims · 4 setups

Full-text index only

CubeX, a Python program/web tool, computes the exact algebraic (Cardan/Nickalls) solution(s) of Hill's cubic equation to estimate pairwise haplotype frequencies, D', r2 and chi-square for each solution

simulated real apoe igf2 cubic pairwise haplotype
Increasing the number of SNP loci does not necessarily improve prediction power at least in the comparison of MTHFR SNP and haplotypes.

PMID 19075497 · PMC4771609 · Journal of epidemiology · 2008 · 7 claims · 6 setups

Full-text index only

Increasing the number of typed SNP loci does not necessarily improve prediction power, at least for the MTHFR gene

healthy genomic genotype trial randomized snp haplotype
HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

PMID 17117180 · PMC2360759 · British journal of cancer · 2006 · 6 claims · 5 setups

Full-text index only

Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.

white same hapmap snp haplotype tagging
Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

Full-text index only

The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage
The dystrobrevin binding protein 1 (DTNBP1) gene is associated with schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample.

PMID 19800201 · PMC2783814 · Schizophrenia research · 2009 · 8 claims · 7 setups

Full-text index only

Common alleles at DTNBP1 SNPs, particularly rs760761, are associated with schizophrenia in the ICCSS sample

irish chimpanzee dtnbp1 snp haplotype case
Absence of the TAP2 human recombination hotspot in chimpanzees.

PMID 15208713 · PMC423135 · PLoS biology · 2004 · 6 claims · 7 setups

Full-text index only

The human TAP2 recombination hotspot is absent from the homologous region in western chimpanzees.

western haplotype males simulated resequencing ld-based sperm
SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis.

PMID 15980517 · PMC1160189 · Nucleic acids research · 2005 · 8 claims · 4 setups

Full-text index only

SNPAnalyzer is an integrated web-based workbench that performs four statistical SNP analyses (Hardy-Weinberg equilibrium, haplotype estimation, linkage disequilibrium, and QTL analysis) in one common computational environment.

african simulated hardy-weinberg haplotype linkage
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

Full-text index only

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

Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

Computation of haplotypes on SNPs subsets: advantage of the "global method".

Software for tag single nucleotide polymorphism selection.

The gentle art of gene arrangement: the meaning of gene clusters.

Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

Whole genome association mapping by incompatibilities and local perfect phylogenies.

A model-based approach to selection of tag SNPs.

htSNPer1.0: software for haplotype block partition and htSNPs selection.

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

Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'.

Increasing the number of SNP loci does not necessarily improve prediction power at least in the comparison of MTHFR SNP and haplotypes.

HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

The dystrobrevin binding protein 1 (DTNBP1) gene is associated with schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample.

Absence of the TAP2 human recombination hotspot in chimpanzees.

SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis.

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.