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 49

System / cell line: gene ✕ Assay: exon-intron ✕ Clear

Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database.

PMID 16093549 · PMC1184218 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Created the Mammalian Orthologous Intron Database (MOID) containing orthologous introns of human, mouse and rat identified via conserved reading-frame position

introns ribosomal rrna comparative orthologous pairwise
Genome informatics: taming the avalanche of genomic data.

PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

genes arabidopsis genome vertebrate comparative conservation whole-genome
Evolution of Highly Repetitive Silk Genes in the Luna Moth, Actias luna.

PMID 41738778 · PMC12962854 · Genome biology and evolution · 2026 · 8 claims · 6 setups

Has reproduction · 89

Eight sericin genes were identified in the A. luna genome, including two clusters of closely related paralogs (serB-D and serE-G)

luna four sericin blast nhmmer manual
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
FGF: a web tool for Fishing Gene Family in a whole genome database.

PMID 17584790 · PMC1933194 · Nucleic acids research · 2007 · 6 claims · 3 setups

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FGF efficiently searches and identifies gene families in whole-genome databases and outputs visual phylogenetic trees annotated with gene structure, chromosome position, duplication fate, and selective pressure (Ka/Ks)

genome rice gene large-scale
Molecular genetics and structural genomics of the human protein kinase C gene module.

PMID 11897026 · PMC88812 · Genome biology · 2002 · 8 claims · 4 setups

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The nine human PKC genes are dispersed throughout the genome, with five isotypes (α, β, δ, ζ, ι) previously incorrectly assigned to chromosomes in the literature.

metaphase genome pkc genomic fluorescence bioinformatic snp
Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica.

PMID 18312668 · PMC2275272 · BMC genomics · 2008 · 8 claims · 5 setups

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The conventional TCR loci (TRA/D, TRB, TRG) in opossum are highly conserved in organization and complexity with those of eutherian mammals.

monodelphis 23-day-old trav trbv comparative rt-pcr phylogenetic
Homozygous P86S mutation of the human glucagon receptor is associated with hyperglucagonemia, alpha cell hyperplasia, and islet cell tumor.

PMID 19657311 · PMC2767399 · Pancreas · 2009 · 8 claims · 6 setups

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A homozygous P86S mutation in GCGR is associated with hyperglucagonemia and α cell hyperplasia in the patient

patient's hek293 pancreatic sanger radioligand camp
Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.

PMID 41629338 · PMC12966425 · Scientific data · 2026 · 8 claims · 8 setups

Has reproduction · 91

Assembled the first chromosome-level genome of G. vermiculophylla: 77.5 Mb, 22 pseudochromosomes, contig N50 2.61 Mb, scaffold N50 3.16 Mb

vermiculophylla assembled predicted genome short-read nanopore hi-c
Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3.

PMID 11454237 · PMC34549 · BMC genetics · 2001 · 6 claims · 4 setups

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The desmuslin (DMN) gene was localized to chromosome 15q26.3 via electronic screening of the human genome database, and its 5-exon genomic organization was determined.

genomic electronic pcr pcr-restriction
Frequent loss of the AXIN1 locus but absence of AXIN1 gene mutations in adenocarcinomas of the gastro-oesophageal junction with nuclear beta-catenin expression.

PMID 14970870 · PMC3215949 · British journal of cancer · 2004 · 8 claims · 7 setups

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Nuclear β-catenin expression in GEJ adenocarcinoma cell lines correlates with enhanced TCF-mediated reporter gene transcription

gej paired showing tumours tcf pcr-sscp bidirectional
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
Genomic approaches to the genetics of alcoholism.

PMID 12875046 · PMC6683845 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2002 · 8 claims · 4 setups

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Alcoholism is a complex disease that develops from a combination of numerous genetic and environmental factors, unlike single-gene disorders such as cystic fibrosis or Huntington's disease.

specified genomic gene genomic exon
Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

PMID 11991808 · PMC107843 · BMC genetics · 2002 · 6 claims · 5 setups

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The genomic organization of human CCS was characterized, with the 823 bp coding region organized into 8 exons spanning 12798 bp of genomic DNA.

bac heart ccs genomic genomic rt-pcr transcription
Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

PMID 16327884 · PMC1298935 · PLoS genetics · 2005 · 8 claims · 8 setups

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Point mutations in FOXE1, GLI2, JAG2, LHX8, MSX1, MSX2, SATB2, SKI, SPRY2, and TBX10 may be rare causes of isolated CL/P

family additional unrelated mutant direct linkage targeted
The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

genomic predicted cdna tissues genomic sequence pcr
Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.

PMID 17038195 · PMC1618849 · BMC genomics · 2006 · 8 claims · 6 setups

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EXPOLDB is a novel database integrating human gene expression variability data (including monozygotic twin comparisons) with (TG/CA)n repeat polymorphism information

blood genomic genes housekeeping microarray repeat est-based
Designating eukaryotic orthology via processed transcription units.

PMID 18445630 · PMC2425467 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Existing ortholog databases discard/ignore alternative splicing via all-against-all protein comparisons, causing ambiguous ortholog calls and misclassification of AS isoforms as in-paralogs

ortholog blat exon-intron blast-based
Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance.

PMID 35931984 · PMC9356423 · BMC genomics · 2022 · 8 claims · 8 setups

Has reproduction

114 CNGC genes were identified across the genomes of four cotton species (G. arboreum, G. raimondii, G. barbadense, G. hirsutum)

arboreum cotton hirsutum ghcngc genome-wide phylogenetic gene
Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

Has reproduction · 78

73 IQD gene family members were identified in the wheat genome and classified into six phylogenetic groups

triticum taiqd wheat rice genome-wide phylogenetic gene

Experiments

Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database.

Genome informatics: taming the avalanche of genomic data.

Evolution of Highly Repetitive Silk Genes in the Luna Moth, Actias luna.

SVC: structured visualization of evolutionary sequence conservation.

FGF: a web tool for Fishing Gene Family in a whole genome database.

Molecular genetics and structural genomics of the human protein kinase C gene module.

Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica.

Homozygous P86S mutation of the human glucagon receptor is associated with hyperglucagonemia, alpha cell hyperplasia, and islet cell tumor.

Chromosome-level genome assembly of agar-producing red seaweed Gracilaria vermiculophylla.

Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3.

Frequent loss of the AXIN1 locus but absence of AXIN1 gene mutations in adenocarcinomas of the gastro-oesophageal junction with nuclear beta-catenin expression.

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

Genomic approaches to the genetics of alcoholism.

Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.

Designating eukaryotic orthology via processed transcription units.

Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance.

Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.