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 23

System / cell line: cross-species ✕ Assay: genome-wide ✕ Clear

QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.

PMID 17962308 · PMC2238983 · Nucleic acids research · 2008 · 8 claims · 3 setups

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QuadBase is a compendium of G4 DNA (quadruplex) motifs focused on their occurrence and conservation in promoters, composed of EuQuad and ProQuad

chimpanzee prokaryotic promoters genome-wide cross-species
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
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
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
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

Has reproduction · 86

CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

tissues predicted tss-enhancer cattle cage extraction coexpression
A third approach to gene prediction suggests thousands of additional human transcribed regions.

PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

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A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

genome 4.4-mb known nucleotide repeat polyadenylation
Translating genome sequences into biological understanding.

PMID 12801409 · PMC193614 · Genome biology · 2003 · 8 claims · 7 setups

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Gene-trap insertional mutagenesis in mouse ES cells (BayGenomics) generates a large resource of cell lines and knockout mice for studying gene expression patterns and function.

embryonic transfectable drosophila computational gene-trap pooled cross-species
Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding.

PMID 33402206 · PMC7784341 · Genome biology · 2021 · 8 claims · 6 setups

Has reproduction · 74

Disome-seq detects widespread, previously hidden ribosome collisions across endogenous coding sequences in fast-proliferating yeast cells.

exponentially yeast sucrose disome-seq cryo-electron
Similarities and differences in genome-wide expression data of six organisms.

PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

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Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental
The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

PMID 16733552 · PMC1464830 · PLoS genetics · 2006 · 8 claims · 7 setups

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Human and chimp genomes differ by ~35 million single nucleotide substitutions, corresponding to ~1.06% divergence after removing polymorphic sites

chimpanzee chimp population non-human genome snp high-density
F-SNP: computationally predicted functional SNPs for disease association studies.

PMID 17986460 · PMC2238878 · Nucleic acids research · 2008 · 6 claims · 8 setups

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F-SNP is a database integrating functional effect predictions for SNPs from 16 bioinformatics tools/databases across four categories: splicing, transcription, translation, and post-translation

genome protein-coding genomic genome-wide non-synonymous exonic nonsense
Molecular characterization of retinitis pigmentosa in Saudi Arabia.

PMID 19956407 · PMC2786884 · Molecular vision · 2009 · 8 claims · 7 setups

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The causative mutation was identified in 51 of 52 (94%/98%) Saudi RP patients, including seven novel mutations.

blood-derived families pcr-amplified ethnically genome-wide linkage bidirectional
Identifying cis-regulatory sequences by word profile similarity.

PMID 19730735 · PMC2731932 · PloS one · 2009 · 8 claims · 8 setups

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WPH-finder identifies putative co-regulated CRMs by scanning the genome for sequences with word profiles similar to a known CRM, without explicitly defining binding sites

stripe pair-rule nrsf-bound eve genome-wide chip-chip chip-seq
Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter.

PMID 17720713 · PMC2034477 · Nucleic acids research · 2007 · 8 claims · 4 setups

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The native 22-nt c-kit87 sequence occurs only once in the entire human genome.

genome synthetic c-kit87 c-kit genome-wide circular molecular
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

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Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

unigene shuffled real genomes genome-wide alignment gene
Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

PMID 18187510 · PMC2275096 · Nucleic acids research · 2008 · 8 claims · 6 setups

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G-richness downstream of the TSS is strand-biased, concentrated on the nontemplate strand, with a peak at +200 to +300 bp

refseq chicken random genome-wide quadparser regulatory
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

PMID 19822575 · PMC2794179 · Nucleic acids research · 2009 · 8 claims · 6 setups

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ChIP-seq identified 3064 GABP peaks, 7266 FOXA2 peaks and 18783 HNF4a peaks in HepG2 cells

hepg2 liver chip-seq quantitative co-immunoprecipitation
Investigating epigenetic biomarkers of age, sex, and disease in captive South African cheetahs (Acinonyx jubatus jubatus).

PMID 41528985 · PMC12798976 · PloS one · 2026 · 8 claims · 7 setups

Has reproduction · 58

A cheetah-specific epigenetic clock (CheetahClock) built from 52 CpG sites predicts age across blood and liver samples with r=0.97 and MAE=0.86 years

cheetah genes methylation elastic epigenome-wide
Genetic architecture of natural variation of cardiac performance from flies to humans.

PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups

Has reproduction · 74

Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines

drosophila dgrp gene induced high-speed genome-wide epistasis
A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females.

PMID 35471187 · PMC9113746 · eLife · 2022 · 8 claims · 5 setups

Has reproduction · 73

Created Aegypti-Atlas, an online RNAseq resource covering Ae. aegypti body parts, gut regions, and a blood meal digestion time course

dissected five anterior midguts rnaseq rt-qpcr

Experiments

QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.

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

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

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

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

A third approach to gene prediction suggests thousands of additional human transcribed regions.

Translating genome sequences into biological understanding.

Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding.

Similarities and differences in genome-wide expression data of six organisms.

The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

F-SNP: computationally predicted functional SNPs for disease association studies.

Molecular characterization of retinitis pigmentosa in Saudi Arabia.

Identifying cis-regulatory sequences by word profile similarity.

Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter.

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

Investigating epigenetic biomarkers of age, sex, and disease in captive South African cheetahs (Acinonyx jubatus jubatus).

Genetic architecture of natural variation of cardiac performance from flies to humans.

A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females.