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).

• Coexistence of two different pseudohypoparathyroidism subtypes (Ia and Ib) in the same kindred with independent Gs{alpha} coding mutations and GNAS imprinting defects.

  PMID 19858129 · PMC3030964 · Journal of medical genetics · 2010 · 7 claims · 5 setups

  Full-text index only

  Two unrelated PHP-I families each include at least one patient with a Gsα coding mutation (PHP-Ia) and another with GNAS imprinting defects (PHP-Ib)

  genomic erythrocyte gnas sanger methylation-specific microsatellite

• 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

• Determination of complete chromosomal haplotypes by bulk DNA sequencing.

  PMID 33957932 · PMC8101039 · Genome biology · 2021 · 8 claims · 8 setups

  Has reproduction · 97

  A hierarchical computational strategy that first builds high-confidence local haplotype blocks from long-range/linked-read linkage and then concatenates them into whole-chromosome haplotypes using Hi-C contacts

  rpe-1 na12878 aneuploid linked-read hi-c bulk

• 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

  Full-text index only

  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 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

• Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex.

  PMID 38883333 · PMC11179850 · Horticulture research · 2024 · 7 claims · 7 setups

  Full-text index only

  A haplotype-resolved telomere-to-telomere (T2T) genome of plum (P. salicina cv. 'Fengtangli') was assembled into two gap-free haplotypes of 251.25 and 251.29 Mb.

  plum four appm genes pacbio hi-c k-mer

• Complex genetic diseases: controversy over the Croesus code.

  PMID 11532206 · PMC138948 · Genome biology · 2001 · 8 claims · 3 setups

  Full-text index only

  The common disease/common variant hypothesis is predicted by population genetic theory (founder population dynamics, mutation-drift-selection balance) and supported by empirical examples such as APOE*E4.

  chromosome northern disease large-scale genome-wide database

• Assaying chromosomal inversions by single-molecule haplotyping.

  PMID 16721377 · PMC2690135 · Nature methods · 2006 · 8 claims · 4 setups

  Full-text index only

  Haplotype Fusion PCR (HF-PCR) juxtaposes sequences flanking an inversion breakpoint on single DNA molecules via emulsion PCR, generating orientation-specific fusion products diagnostic of inversion genotype

  genomic yac haplotype pulsed template

• Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

  PMID 17877794 · PMC2238324 · BMC bioinformatics · 2007 · 7 claims · 7 setups

  Full-text index only

  lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses without requiring a database or complex software infrastructure

  chromosome user-submitted hannon-elledge gene linkage rnai shrna

• More breast cancer genes?

  PMID 11305950 · PMC138680 · Breast cancer research : BCR · 2001 · 8 claims · 7 setups

  Full-text index only

  A new high-risk breast cancer gene termed BRCAX may exist on chromosome 13q, identified via CGH and linkage analysis in Nordic families

  tumours five independent ataxia-telangiectasia comparative haplotype linkage

• Searching for genes for cleft lip and/or palate based on breakpoint analysis of a balanced translocation t(9;17)(q32;q12).

  PMID 19929093 · PMC2945731 · The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association · 2009 · 8 claims · 4 setups

  Full-text index only

  The translocation breakpoints disrupt SLC31A1 (intron 1) on chromosome 9 and a predicted gene containing CCL2 (5'UTR/exons) on chromosome 17

  family genomic case-control case fluorescence long-range mutation

• Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions.

  PMID 19772609 · PMC2759955 · BMC genetics · 2009 · 8 claims · 5 setups

  Full-text index only

  Saudi Arabia differs from other Arabian Peninsula countries by a significantly higher presence of J2-M172 lineages.

  saudi same j1-m267 y-chromosome y-str amova

• polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.

  PMID 36792366 · PMC9985148 · Genome biology and evolution · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  polishCLR is a reproducible, containerized Nextflow workflow that implements best practices for polishing PacBio CLR genome assemblies.

  helicoverpa alternate contigs assemblies long-read short-read duplicate

• Haplotype analysis of Lrrk2 R1441H carriers with parkinsonism.

  PMID 18952485 · PMC2749264 · Parkinsonism & related disorders · 2009 · 5 claims · 3 setups

  Full-text index only

  The LRRK2 R1441H substitution has arisen on multiple independent occasions rather than from a single common founder

  genomic haplotype direct full

• A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis.

  PMID 34545398 · PMC8527503 · G3 (Bethesda, Md.) · 2021 · 8 claims · 8 setups

  Has reproduction · 79

  A chromosome-scale genome assembly of H. californensis spans 110 Mb in 44 scaffolds, with 99.47% of bases in 13 scaffolds

  californensis chromosome pacbio illumina

• Genetic polyploid phasing from low-depth progeny samples.

  PMID 35692633 · PMC9184567 · iScience · 2022 · 8 claims · 7 setups

  Has reproduction · 73

  WH-PPG phases polyploid parental samples by scoring informative variant pairs with a Bayesian log-likelihood model of progeny allele depths, clustering alleles by co-occurrence likelihood, and assigning clusters to haplotypes via interval scheduling

  solanum illumina pacbio wh-ppg

• 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

• Selecting additional tag SNPs for tolerating missing data in genotyping.

  PMID 16259642 · PMC1316880 · BMC bioinformatics · 2005 · 7 claims · 6 setups

  Full-text index only

  There exists a subset of SNPs (robust tag SNPs) that can distinguish all distinct haplotypes even when up to m SNPs are missing

  simulated hudson's chromosome robust

• Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.

  PMID 19844255 · PMC2824775 · European journal of human genetics : EJHG · 2010 · 7 claims · 7 setups

  Full-text index only

  A locus on chromosome 16q23-24 affects HDL-C levels in two independent French-Canadian family studies (QUE and SLSJ)

  que slsj candidate skin genome-wide sanger tagging

• Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree.

  PMID 19716302 · PMC2748900 · Current biology : CB · 2009 · 7 claims · 4 setups

  Full-text index only

  Direct sequencing of a 13-generation pedigree yields a Y-chromosome mutation rate of 3.0 × 10^-8 mutations/nucleotide/generation

  flow-sorted cell-line family lymphoblastoid y-chromosome capillary y-str