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).

• Identity rather than 3D position informs splicing of rare introns in the human genome.

  PMID 41561379 · PMC12814444 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 98

  Rare intron classes (minor, minor-like, hybrid, non-canonical) are largely dispersed across the linear human genome, with only two notable clusters (GBP on chr1, TSPY on chrY)

  reference genome k562 computational genome-wide chromomap hi-c

• Genome comparison without alignment using shortest unique substrings.

  PMID 15910684 · PMC1166540 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A number of sequence comparison tasks, including detection of unique genomic regions, can be accomplished efficiently without an alignment step using shortest unique substrings.

  caenorhabditis genome mycoplasma shuffled genome-wide upstream-region local

• Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

  PMID 16805923 · PMC1779541 · Genome biology · 2006 · 8 claims · 6 setups

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  The chimpanzee genome contains at least 42 separate families of endogenous retroviruses, 9 newly identified

  chimpanzee domains genomic hg16 genome-wide sequence ltr-ltr

• Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

  PMID 18003658 · PMC2248751 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  p110 CUX1 is recruited to promoters of cell cycle-related target genes preferentially during S phase

  hela hs578t nih3t3 genomic chap-chip conventional scanning

• Short tandem repeats in human exons: a target for disease mutations.

  PMID 18789129 · PMC2543027 · BMC genomics · 2008 · 8 claims · 6 setups

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  STRs are present in exons of 92% of known human genes, unlike longer tandem repeats which are rare in exons

  reference genome genes genome-wide indel disease

• Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.

  PMID 18722178 · PMC3003864 · Molecular cell · 2008 · 7 claims · 8 setups

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  RBP2 target promoters separate into two functionally distinct classes: differentiation-independent genes (mitochondrial function, RNA/DNA metabolism) and differentiation-dependent genes (cell cycle)

  u937 saos-2 chip-chip chip-on-chip gene

• Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

  PMID 18692127 · PMC3341170 · Genomics · 2008 · 8 claims · 7 setups

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  Autozygosity mapping identified a highly significant homozygous region on chromosome 13q14.11-q14.3 (Z/LOD=10.41)

  family p2ry5 affected snp microsatellite sanger

• Characterization of genome-wide p53-binding sites upon stress response.

  PMID 18474530 · PMC2441782 · Nucleic acids research · 2008 · 7 claims · 7 setups

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  Genome-wide ChIP-on-chip identified 1546 high-confidence p53-binding sites upon Actinomycin D treatment in U2OS cells

  u2os saos-2 chip-on-chip chip-qpcr western

• Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.

  PMID 20018283 · PMC2845297 · Atherosclerosis · 2010 · 8 claims · 7 setups

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  The ADIPOQ locus is the only major gene locus for plasma adiponectin, reaching genome-wide significance in combined and sex-stratified analyses

  population-based cohorts gwa plasma genome-wide replication candidate

• Current status and the future for the genetics of type I diabetes.

  PMID 19956094 · PMC2805458 · Genes and immunity · 2009 · 8 claims · 7 setups

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  A T1DGC genome-wide association meta-analysis of >7500 cases and >9000 controls identified 42 distinct genomic locations associated with T1D at P<10^-6.

  asp subjects t1dgc cases genome-wide mhc candidate

• Given the complexity of the human genome, can 'personalised medicine' or 'individualised drug therapy' ever be achieved?

  PMID 19706359 · PMC3525196 · Human genomics · 2009 · 7 claims · 3 setups

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  The human genome is far too complex, given current understanding, for personalised medicine or individualised drug therapy to be realised in the near term

  populations genome genome-wide genome

• The UCSC Genome Browser Database: update 2009.

  PMID 18996895 · PMC2686463 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  The UCSC Genome Browser Database (GBD) is a publicly available, integrated collection of genome assembly sequences and annotations across many organisms, including extensive comparative-genomic resources.

  chimp vertebrate mrnas genome genome-wide multiz blat

• Genome Network and FANTOM3: assessing the complexity of the transcriptome.

  PMID 16683037 · PMC1449904 · PLoS genetics · 2006 · 8 claims · 7 setups

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  63% of the genome is transcribed from at least one strand, versus the earlier belief that only 2% is transcribed into protein-coding mRNA

  fantom3 genome large-scale mammalian cage full-length genome

• On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

  PMID 17971225 · PMC2246304 · Genome biology · 2007 · 8 claims · 4 setups

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  Genes located in rearranged chromosomes show lower non-coding (KI), synonymous (KS), and non-synonymous (KA) divergence than genes in colinear chromosomes.

  human-chimpanzee orthologous genome-wide pairwise lineage-specific permutation

• High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians.

  PMID 19900272 · PMC3091319 · Genome biology · 2009 · 7 claims · 4 setups

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  Custom whole-genome scan arrays (~200 bp resolution) discover CNV regions not previously reported in the literature

  yoruba selected subset whole-genome targeted pcr

• A genome-wide association analysis identifies 16 novel susceptibility loci for carpal tunnel syndrome.

  PMID 30833571 · PMC6399342 · Nature communications · 2019 · 6 claims · 8 setups

  Has reproduction · 90

  A GWAS of 12,312 CTS cases and 389,344 controls in UK Biobank identifies 16 novel genome-wide significant susceptibility loci for CTS

  biobank surgically gwas transformed genome-wide sequencing gene-based

• Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

  PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  73 IQD gene family members were identified in the wheat genome and classified into six phylogenetic groups

  triticum taiqd wheat rice genome-wide phylogenetic gene

• Data-driven projections of candidate enhancer-activating SNPs in immune regulation.

  PMID 40011812 · PMC11863423 · BMC genomics · 2025 · 7 claims · 7 setups

  Has reproduction · 57

  A data-driven computational protocol combining motif scanning, open-chromatin filtering, gene proximity, dbSNP validation, spacing, and cross-species conservation can prioritize SNPs likely to create functional GAS motifs.

  genome pbmc lung il4-stimulated motif chip-seq bulk

• Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

  PMID 35328546 · PMC8949970 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Generated the first draft genome assembly of A. coronaria by Illumina sequencing a haploid androgenetic plant

  haploid mistral assembled masked whole-genome k-mer genome-wide

• Genome-wide insights into population structure and host specificity of Campylobacter jejuni.

  PMID 33990625 · PMC8121833 · Scientific reports · 2021 · 8 claims · 6 setups

  Has reproduction · 94

  Both core and accessory genome characteristics show strong association with distinct host animal species, indicating multiple independent adaptive trajectories rather than a single common evolutionary path

  jejuni core whole-genome core k-mer