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 31

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

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
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
Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

PMID 18439302 · PMC2432081 · BMC genomics · 2008 · 8 claims · 7 setups

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Adjacent cassette exon pairs can be categorized by EST-derived correlation coefficient into three groups: mutually exclusive (ME, r<=-0.7), independent (IND, -0.2<=r<=0.2), and linked (LNK, r>=0.7)

human-mouse adjacent est genome splice
The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

Has reproduction · 100

44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

tetramorium bicarinatum vpg venom whole-genome blast gene
GeneSeer: a sage for gene names and genomic resources.

PMID 16176584 · PMC1266031 · BMC genomics · 2005 · 7 claims · 4 setups

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GeneSeer aggregates gene name synonyms from GenBank, FlyBase, ExPASy, HUGO, ENSEMBL, UCSC and Gene Ontology into a name-translation database that maps any familiar name to a reference (SOFAR) identifier.

sofar clusters rnai gene blast sequence shrna
Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups

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A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.

genomes longin plant phytolongin iterative phylogenetic genomic
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
TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation.

PMID 15345028 · PMC517934 · BMC medical genetics · 2004 · 8 claims · 4 setups

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No disease-associated mutations were found in TM4SF10 in 16 XLMR patients from 14 families with linkage to the TM4SF10 locus.

genomic dog sage pcr northern sage
Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

vertebrate cdna pedf complete genomic rt-pcr phylogenetic
MRX87 family with Aristaless X dup24bp mutation and implication for polyAlanine expansions.

PMID 17480217 · PMC1868705 · BMC medical genetics · 2007 · 8 claims · 7 setups

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The MRX87 disease locus maps to the Xp22-p21 interval, a known hot spot region for mental handicap

peripheral genomic pcr leukocytes two-point direct pcr
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
Mutation analysis of the ATR gene in breast and ovarian cancer families.

PMID 15987455 · PMC1175065 · Breast cancer research : BCR · 2005 · 8 claims · 5 setups

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ATR mediates the DNA damage response by phosphorylating tumor suppressors such as p53, BRCA1 and CHK1, making it a plausible candidate breast/ovarian cancer susceptibility gene

index atr variant mutation direct variant
Human SNPs resulting in premature stop codons and protein truncation.

PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

genome transcripts validated x-snp-encoded database blast exon-intron
Distribution and effects of nonsense polymorphisms in human genes.

PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups

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Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.

genome genes nonsense snps genome-wide snp codon
Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

PMID 18500987 · PMC2426694 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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Sequences homologous to the CIDE-N domain/NCD show a wide phylogenetic distribution, from hydra and sea anemone to mammals, while true Cide proteins are restricted to vertebrates.

organisms cide cideb hmmer tblastn sequence
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
Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

PMID 10389971 · PMC2363009 · British journal of cancer · 1999 · 6 claims · 5 setups

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Microsatellite instability is common in sporadic pancreatic cancer but occurs at a uniformly low rate and is not accompanied by hMLH1/hMSH2 alterations, suggesting it does not drive pancreatic tumorigenesis.

sporadic msi-positive tumour unstable microsatellite denaturing sequencing
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

full-length deduced alternative panel cdna-to-genome manual motif
Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

PMID 16719907 · PMC1513570 · BMC genomics · 2006 · 8 claims · 5 setups

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A 2 Mb BAC contig of 78 clones was assembled covering the entire bovine FHIT locus

bovine pcr-based comparative rt-pcr

Experiments

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

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

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

GeneSeer: a sage for gene names and genomic resources.

Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

Genomic approaches to the genetics of alcoholism.

TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation.

Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

MRX87 family with Aristaless X dup24bp mutation and implication for polyAlanine expansions.

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

SVC: structured visualization of evolutionary sequence conservation.

Mutation analysis of the ATR gene in breast and ovarian cancer families.

Human SNPs resulting in premature stop codons and protein truncation.

Distribution and effects of nonsense polymorphisms in human genes.

Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

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

Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.