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 22

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

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

genome genomic kinase psi-blast comparative genscan
Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.

PMID 17554261 · PMC2628541 · Nature genetics · 2007 · 8 claims · 8 setups

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IRGM SNPs (rs13361189, rs4958847) show strong replicated association with Crohn disease; IRGM induces autophagy and control of intracellular bacteria

wtccc replication population cases genome-wide taqman snp
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
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
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
A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population.

PMID 16904005 · PMC1779589 · Genome biology · 2006 · 8 claims · 7 setups

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Eight SNPs with extreme European-branch locus-specific branch length (LSBL) were selected from a genome-wide FST dataset as candidates for selection in Europe.

snp irish french fst-based microsatellite genome-wide
Transcriptome annotation using tandem SAGE tags.

PMID 17709346 · PMC2034470 · Nucleic acids research · 2007 · 8 claims · 7 setups

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A novel algorithm pairs tandem SAGE tags anchored on two different restriction sites (CATG and GATC) to define tag-delimited genomic sequences (TDGS)

monocyte-derived unigene genome macrophage sage modified virtual
Rats go genomic.

PMID 16522223 · PMC1431730 · Genome biology · 2006 · 7 claims · 8 setups

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A systems biology approach combining genome-wide expression profiling with expression QTL (eQTL) mapping can identify candidate genes underlying complex-disease QTLs

recombinant genes serotonin adenomatous genome-wide targeted knockout
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
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
Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection.

PMID 19109909 · PMC2630178 · Neuron · 2008 · 8 claims · 8 setups

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MEF2 directly regulates a genome-wide program of 182 activity-dependent target genes in hippocampal neurons

e18 hippocampal forebrain profiling rt-qpcr chip-chip
Genetic and functional association of FAM5C with myocardial infarction.

PMID 18430236 · PMC2383879 · BMC medical genetics · 2008 · 8 claims · 5 setups

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SNPs within FAM5C show genetic linkage to and association with myocardial infarction in the GENECARD family-based sample

genecard cathgen donor aortic genome-wide case-control expression
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
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
Adequate use of allele frequencies in Hispanics--a problem elucidated in nephrotic syndrome.

PMID 19876656 · PMC2899680 · Pediatric nephrology (Berlin, Germany) · 2010 · 7 claims · 3 setups

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Self-identified Hispanic SRNS patients in the USA are genetically heterogeneous, being of either Caucasian or Mesoamerican (Native-American) descent

genomic same healthy direct genome-wide
Gene function in the mammalian genome, courtesy of the mouse.

PMID 12537544 · PMC151280 · Genome biology · 2003 · 8 claims · 8 setups

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Mosaicism of Mus musculus domesticus and Mus musculus musculus haplotypes exists across the inbred laboratory mouse genome, and genome-wide haplotype mapping can enhance positional cloning

inbred genome mice model genome-wide large-scale phenotypic
Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups

Has reproduction · 63

>700 tissue-specific transcriptomes generated from w1118 and 141 DGRP Drosophila lines, forming a circadian gene expression atlas

w1118 dgrp drosophila dgrp-796 bulk high uas-rnai
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
Population genomics: diversity and virulence in the Neisseria.

PMID 18822386 · PMC2612085 · Current opinion in microbiology · 2008 · 8 claims · 8 setups

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Horizontal genetic exchange (recombination) plays a central role in shaping bacterial speciation and population structure in Neisseria

neisseria meningitidis meningococcal multi-locus microarray 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.

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

Experiments

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

Molecular characterization of retinitis pigmentosa in Saudi Arabia.

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

A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population.

Transcriptome annotation using tandem SAGE tags.

Rats go genomic.

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

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

Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection.

Genetic and functional association of FAM5C with myocardial infarction.

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

Systems biology of gene regulation fulfills its promise.

Adequate use of allele frequencies in Hispanics--a problem elucidated in nephrotic syndrome.

Gene function in the mammalian genome, courtesy of the mouse.

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

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.

Population genomics: diversity and virulence in the Neisseria.

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.