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 37

System / cell line: high ✕ Assay: nucleotide ✕ Clear

Intronic alternative splicing regulators identified by comparative genomics in nematodes.

PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

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Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

elegans database transgenic comparative est cross-species
Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema.

PMID 17895298 · PMC2533592 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 7 setups

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Nucleotide and amino acid substitution trends between human-mouse orthologs are highly asymmetric and polarized in opposite directions for high-GC versus low-GC gene groups.

human-mouse high aarm orthologous content pairwise
Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

PMID 36129291 · PMC9584332 · Microbiology resource announcements · 2022 · 7 claims · 4 setups

Has reproduction · 81

A complete 30,616-nucleotide genome of Cervid atadenovirus A was determined from lung tissue of black-tailed deer that died of AHD in British Columbia in 2020

lung sequencing assembled deer high-throughput metagenomic reference
Frequency of single nucleotide polymorphisms in NOD1 gene of ulcerative colitis patients: a case-control study in the Indian population.

PMID 19723304 · PMC2748065 · BMC medical genetics · 2009 · 7 claims · 4 setups

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Three NOD1 Exon 6 SNPs (W219R, L349P, L370R) show statistically significant association with ulcerative colitis compared to controls

genomic pcr patients dhplc cloning pcr-rflp
Rbfox2 controls autoregulation in RNA-binding protein networks.

PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups

Has reproduction · 48

Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.

v6.5 fhfox2 top introns iclip sequencing rt-pcr
Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

PMID 19329065 · PMC5054122 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 8 setups

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Nucleotide preference at CpG flanking sites transitions from 5' T (invertebrates) to 5' A (vertebrates) at the invertebrate-vertebrate boundary

genomes same pufferfish elegans nucleotide genome-wide kruskal-wallis
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

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Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

embryonic neural t-cells mm8 chip-seq chip-chip pwm
High-density SNP genotyping to define beta-globin locus haplotypes.

PMID 18829352 · PMC4251776 · Blood cells, molecules & diseases · 2009 · 8 claims · 5 setups

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RFLP analysis lacks sufficient site density/coverage to accurately reflect the genomic complexity of the β-locus

genomic rflp subset rflp high-density haploview
High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies.

PMID 18495026 · PMC2408599 · BMC cancer · 2008 · 8 claims · 4 setups

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HRM correctly identified all 73 EGFR-mutation-positive FFPE samples previously found by sequencing, giving 100% sensitivity and 90% specificity

ffpe single high direct hrm
Positive selection for the male functionality of a co-retroposed gene in the hominoids.

PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups

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PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives

african chimpanzee orangutan reconstructed population hka comparative
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
Molecular and clinical analyses of 84 patients with tuberous sclerosis complex.

PMID 16981987 · PMC1592085 · BMC medical genetics · 2006 · 8 claims · 6 setups

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Mutations were identified in 64 of 84 (76%) TSC probands, comprising 9 TSC1 and 55 TSC2 mutations

genomic pcr-amplified tsc healthy dhplc direct pcr
In silico promoters: modelling of cis-regulatory context facilitates target predictio.

PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

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An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

serca2 rantes genes podocyte-associated literature-based promoter cross-referenced
A restricted spectrum of NRAS mutations causes Noonan syndrome.

PMID 19966803 · PMC3118669 · Nature genetics · 2010 · 8 claims · 6 setups

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Germline NRAS mutations (T50I, G60E) cause a subset of Noonan syndrome cases via enhanced MAPK activation

cohort cos-7 recombinant nras mutation western ras
EDAR mutation in autosomal dominant hypohidrotic ectodermal dysplasia in two Swedish families.

PMID 17125505 · PMC1684249 · BMC medical genetics · 2006 · 6 claims · 3 setups

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A nonsense mutation c.1072C>T (p.Arg358X) in exon 12 of EDAR was identified in affected individuals from both Swedish families and is disease-specific

genomic patients dhplc pcr clinical
MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.

PMID 34172000 · PMC8235852 · BMC genomics · 2021 · 8 claims · 8 setups

Has reproduction · 74

MicroPIPE, an end-to-end Nextflow/Singularity-based pipeline built from systematically validated tool choices, produces high-quality complete bacterial genome assemblies without manual intervention.

coli sequences nanopore basecalling demultiplexing
SVC: structured visualization of evolutionary sequence conservation.

PMID 15991338 · PMC1160265 · Nucleic acids research · 2005 · 7 claims · 5 setups

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SVC aligns protein-coding sequences of orthologous gene pairs and maps them back onto their encoding exons/introns to generate a scaffold of conserved gene structure.

orthologous exonic tblastx blastn sliding-window
Discrimination of three mutational events that result in a disruption of the R122 primary autolysis site of the human cationic trypsinogen (PRSS1) by denaturing high performance liquid chromatography.

PMID 11734061 · PMC60523 · BMC genetics · 2001 · 7 claims · 3 setups

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DHPLC can readily discriminate the two known mutational events (c.365G>A and c.365~366GC>AT) that both cause the R122H mutation

genomic pcr independently pcr denaturing direct
Three novel mutations in KIF21A highlight the importance of the third coiled-coil stalk domain in the etiology of CFEOM1.

PMID 17511870 · PMC1888713 · BMC genetics · 2007 · 8 claims · 5 setups

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Most individuals with CFEOM1 and rare individuals with CFEOM3 harbor heterozygous mutations in KIF21A

genomic pedigree proband pcr denaturing dhplc
Comparison of the mismatch-specific endonuclease method and denaturing high-performance liquid chromatography for the identification of HBB gene mutations.

PMID 18694524 · PMC2525636 · BMC biotechnology · 2008 · 8 claims · 4 setups

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The mismatch-specific endonuclease method achieved 100% sensitivity and specificity for identifying HBB gene mutations in the study sample.

genomic pcr mismatch-specific dhplc direct

Experiments

Intronic alternative splicing regulators identified by comparative genomics in nematodes.

Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema.

Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

Frequency of single nucleotide polymorphisms in NOD1 gene of ulcerative colitis patients: a case-control study in the Indian population.

Rbfox2 controls autoregulation in RNA-binding protein networks.

Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

High-density SNP genotyping to define beta-globin locus haplotypes.

High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies.

Positive selection for the male functionality of a co-retroposed gene in the hominoids.

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

Molecular and clinical analyses of 84 patients with tuberous sclerosis complex.

In silico promoters: modelling of cis-regulatory context facilitates target predictio.

A restricted spectrum of NRAS mutations causes Noonan syndrome.

EDAR mutation in autosomal dominant hypohidrotic ectodermal dysplasia in two Swedish families.

MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.

SVC: structured visualization of evolutionary sequence conservation.

Discrimination of three mutational events that result in a disruption of the R122 primary autolysis site of the human cationic trypsinogen (PRSS1) by denaturing high performance liquid chromatography.

Three novel mutations in KIF21A highlight the importance of the third coiled-coil stalk domain in the etiology of CFEOM1.

Comparison of the mismatch-specific endonuclease method and denaturing high-performance liquid chromatography for the identification of HBB gene mutations.