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 34

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

In silico meets in vivo.

PMID 18304380 · PMC2374716 · Genome biology · 2008 · 8 claims · 8 setups

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About 10% of positions in multiple sequence alignments of the human genome with other vertebrate genomes are likely incorrect.

genome lines prokaryotic genomes genome genome-wide gene
Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

PMID 37853325 · PMC10583454 · Genetics, selection, evolution : GSE · 2023 · 5 claims · 6 setups

Has reproduction

SLDP selects a subset of WGS variants using GWAS prior information (P-value threshold) combined with LD pruning (r2) to improve genomic prediction accuracy.

duroc discovery training real low-coverage genome-wide genomic
Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing.

PMID 36401180 · PMC9673297 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 8 setups

Has reproduction · 50

BaseVar + STITCH at 1.0X sequencing depth with a sample size >300 achieves the highest genotyping accuracy among tested imputation strategies (genotype concordance >98.8%, genotype accuracy >0.97).

angora domesticated candidate low-coverage multivariate principal
Population genomics of human gene expression.

PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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Gene expression levels in lymphoblastoid cell lines are a heritable trait

ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl
A sequence-based survey of the complex structural organization of tumor genomes.

PMID 18364049 · PMC2397511 · Genome biology · 2008 · 8 claims · 6 setups

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End sequencing profiling (ESP) can identify all classes of genome rearrangements in tumor genomes by paired-end sequencing of BAC clones

tumors breast bac bt474 bac low-coverage fluorescence
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

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A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

breast computational array-cgh gene bac
A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae.

PMID 19917080 · PMC2784802 · BMC genomics · 2009 · 8 claims · 4 setups

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Genome-wide deletion screening identified 149 genes whose deletion causes NiSO4 sensitivity and 119 genes whose deletion confers NiSO4 resistance.

cerevisiae lists yeast genome-wide functional protein-protein
HITS-CLIP yields genome-wide insights into brain alternative RNA processing.

PMID 18978773 · PMC2597294 · Nature · 2008 · 8 claims · 8 setups

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HITS-CLIP, combining CLIP with high-throughput sequencing, provides a genome-wide, unbiased method to map protein-RNA interactions in vivo.

neocortex brain 293t hits-clip traditional exon
Sequencing the regulatory genome.

PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

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Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

interphase nine beta-globin drosophila nuclear digital chip
Discovery and validation of new molecular targets in treating dyslipidemia: the role of human genetics.

PMID 20211435 · PMC3328807 · Trends in cardiovascular medicine · 2009 · 8 claims · 8 setups

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Mendelian randomization uses genetic variants as a 'randomized trial of nature' to assess causal relationships between lipid biomarkers and CHD, overcoming confounding and reverse causality limitations of observational epidemiology.

population myocardial individuals animal genome-wide case-control gene
The impact of new research technologies on our understanding of environmental causes of disease: the concept of clinical vulnerability.

PMID 19948053 · PMC2793242 · Environmental health : a global access science source · 2009 · 8 claims · 8 setups

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GWAS-identified genetic variants confer only modest relative risks (1.15-1.5), comparable in magnitude to weak/contested environmental exposures

polish cohort nonsmokers low genome-wide biomarker epidemiological
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

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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
A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups

Has reproduction · 61

T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.

tuber ectomycorrhizal melanosporum rna-seq whole-genome sequencing guided
Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.

PMID 36864379 · PMC9979506 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups

Has reproduction · 100

French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population.

boars lwd lws pig whole-genome genetic genome-wide
From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.

PMID 33960035 · PMC9292448 · Molecular ecology · 2021 · 7 claims · 6 setups

Has reproduction · 59

382 (over 383) genomic regions contain SNPs that are consistently zonated across all surveyed intertidal habitats spanning the North Atlantic.

semibalanus individual rocky barnacles pool-seq sanger temperature
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
Systems biology of gene regulation fulfills its promise.

PMID 16719937 · PMC1779525 · Genome biology · 2006 · 8 claims · 8 setups

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Suz12, a Polycomb Group complex component, has DNA targets identifiable by ChIP-chip and can silence large genomic regions in a cell-type-specific manner.

unspecified embryonic five yeast chip-chip chip-pet computational
The changing face of genomics.

PMID 15128443 · PMC416465 · Genome biology · 2004 · 8 claims · 8 setups

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Genome-wide ChIP-chip mapping of ~200 yeast transcriptional regulators across environmental conditions reveals general principles of promoter architecture and regulatory response types

yeast drosophila zebrafish elegans chip-chip comparative insertional
GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update.

PMID 19910367 · PMC2808900 · Nucleic acids research · 2010 · 7 claims · 7 setups

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GenomeRNAi is a database integrating RNAi phenotypes, reagents, and gene annotations from cell-based screens in Drosophila and human cells

drosophila hela genome-scale image-based rna-seq
Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

bac genome metaphase overlapping manual repeat fluorescence

Experiments

In silico meets in vivo.

Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing.

Population genomics of human gene expression.

A sequence-based survey of the complex structural organization of tumor genomes.

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae.

HITS-CLIP yields genome-wide insights into brain alternative RNA processing.

Sequencing the regulatory genome.

Discovery and validation of new molecular targets in treating dyslipidemia: the role of human genetics.

The impact of new research technologies on our understanding of environmental causes of disease: the concept of clinical vulnerability.

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

A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.

From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.

Identifying cis-regulatory sequences by word profile similarity.

Systems biology of gene regulation fulfills its promise.

The changing face of genomics.

GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update.

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.