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 14

System / cell line: fraction ✕ Assay: genome-wide ✕ Clear

Long-range regulation is a major driving force in maintaining genome integrity.

PMID 19682388 · PMC2741452 · BMC evolutionary biology · 2009 · 7 claims · 5 setups

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Long-range transcriptional regulation is a major driving force in maintaining genome integrity by constraining where chromosomal breakpoints can become fixed.

opossum genome comparative identification statistical
Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

PMID 35028613 · PMC8714941 · Cell reports. Medicine · 2021 · 8 claims · 5 setups

Has reproduction · 75

Stage-stratified molecular subclassification of Ta and T1 tumors provides greater biological understanding and more clinically meaningful information than subtypes derived from all NMIBCs combined.

stage tumors copy genome-wide whole-exome
Diversity of tRNA genes in eukaryotes.

PMID 17088292 · PMC1693877 · Nucleic acids research · 2006 · 8 claims · 6 setups

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The number of tRNA genes having the same anticodon but different sequences elsewhere (isodecoder genes) varies significantly (10–246) across 11 eukaryotes despite isoacceptor numbers being similar (41–55)

eukaryotic bacterial genome synthetic genome-wide sequence manual
Duplication count distributions in DNA sequences.

PMID 19256873 · PMC3121164 · Physical review. E, Statistical, nonlinear, and soft matter physics · 2008 · 8 claims · 8 setups

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Duplication count distributions N(c) for complex 40-mers show power-law-like decay for c roughly 3 to 50 (or higher) across human, C. elegans, A. thaliana, and D. melanogaster genomes.

genome elegans thaliana melanogaster genome-wide transposable homogeneous
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

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Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

aml tumor novo additional genome snp comparative
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.

PMID 18053250 · PMC2246260 · Genome biology · 2007 · 8 claims · 4 setups

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Loss-of-function phenotypes in yeast are predictable from a gene's connections in a functional gene network via guilt-by-association.

saccharomyces guilt-by-association comparison network-guided
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

PMID 19728866 · PMC2768980 · Genome biology · 2009 · 6 claims · 6 setups

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Integrating 16 genomic features (32 sub-features) via a naïve Bayes classifier produces a genome-scale FLN of 21,657 human genes and 22,388,609 weighted links that outperforms any individual data source for inferring functional linkages.

genome gene omim known naïve linkage disease-centric
Genomic mutation rates: what high-throughput methods can tell us.

PMID 19644920 · PMC2952423 · BioEssays : news and reviews in molecular, cellular and developmental biology · 2009 · 8 claims · 8 setups

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High-throughput DNA analyses yield genome mutation rate estimates markedly higher than those obtained with pre-genomic strategies

cerevisiae elegans melanogaster mammals fluctuation mutation indirect
Genomics and proteomics of immune modulatory effects of a butanol fraction of echinacea purpurea in human dendritic cells.

PMID 18847511 · PMC2571112 · BMC genomics · 2008 · 8 claims · 8 setups

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[BF/S+L/Ep] butanol fraction from E. purpurea enhances maturation of human immature dendritic cells (increased CD83 expression)

immature idcs [bf phytocompounds flow mtt lal
Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

hgmd refseq aligned svm svm reciprocal inter-species
Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice.

PMID 27655631 · PMC5175363 · Nucleic acids research · 2016 · 8 claims · 8 setups

Has reproduction · 10

Embryonic ATZ exposure affects meiosis, spermiogenesis and reduces spermatozoa number in F3 generation male mice

testis dissociated epididymis chip-seq strand-specific h&e
Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.

PMID 33170850 · PMC7654773 · PloS one · 2020 · 8 claims · 4 setups

Has reproduction · 68

Yeast cells activate a rapid transcriptional reprogramming process following acute lethal ethanol stress that is likely adaptive for post-stress survival.

cerevisiae colony-forming-unit bulk pooled
Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

PMID 23516341 · PMC3597545 · PLoS computational biology · 2013 · 8 claims · 7 setups

Has reproduction · 44

Local sequence context strongly determines position-specific polymerase kinetic rate: roughly 80% of IPD variation is explained by a 10 bp context (7 bases upstream, 2 bases downstream of the incorporation site), saturating at 7 bases upstream.

plasmid coli wild-type artificial smrt read-mixing distributional
Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

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The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis

Experiments

Long-range regulation is a major driving force in maintaining genome integrity.

Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

Diversity of tRNA genes in eukaryotes.

Duplication count distributions in DNA sequences.

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

Genomic mutation rates: what high-throughput methods can tell us.

Genomics and proteomics of immune modulatory effects of a butanol fraction of echinacea purpurea in human dendritic cells.

Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice.

Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.

Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.