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 33

System / cell line: exon ✕ Assay: blast ✕ Clear

Leveraging human genomic information to identify nonhuman primate sequences for expression array development.

PMID 16288651 · PMC1314899 · BMC genomics · 2005 · 8 claims · 6 setups

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Human genomic DNA sequence can be leveraged to obtain 3' end sequence of NHP orthologs, which can then be used to generate NHP oligonucleotide microarrays

refseq macaca genomic rhesus exon pcr molecular
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
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups

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Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR

testis panel genome 5'-race non-quantitative
Evolution of Highly Repetitive Silk Genes in the Luna Moth, Actias luna.

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

Has reproduction · 89

Eight sericin genes were identified in the Actias luna genome, including two clusters of closely related paralogs.

actias genomes translated luna genome hmm manual
Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

PMID 18673550 · PMC2533329 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.

redundant mammalian genomic vertebrates blast pattern-hit tblastn
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

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Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

species genomic jmjd6 jmjc reciprocal comparative est
Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

genome poly est cdna est blast cdna
Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

PMID 19747392 · PMC2754481 · BMC evolutionary biology · 2009 · 8 claims · 5 setups

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The coding sequence of FGF5 is not the critical determinant of hair length differences among elephantids, including the woolly mammoth.

asian fgf5 woolly savanna pcr structural blast
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
Non-EST based prediction of exon skipping and intron retention events using Pfam information.

PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

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A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

refseq dbest genome pfam initio est comparative
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
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
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
Improved tagging strategy for protein identification in mammalian cells.

PMID 16138932 · PMC1250225 · BMC genomics · 2005 · 7 claims · 7 setups

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EGFP tagging via the artificial exon did not affect the subcellular localization of the tagged endogenous proteins

osteosarcoma hos 293t lentiviral flow confocal
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
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
SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.

PMID 18174224 · PMC2238826 · Nucleic acids research · 2008 · 6 claims · 5 setups

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Standard genome annotation pipelines misannotate selenoprotein genes because they rely on UGA as a universal stop codon, failing to recognize its dual role as the selenocysteine-recoding codon.

genomic cdna known sequence homology transcript
Database resources of the National Center for Biotechnology Information.

PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

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NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

genbank genomic eukaryotic completely sequence rapid est
A novel de novo PAX6 mutation in an Ashkenazi-Jewish family with aniridia.

PMID 18334930 · PMC2255027 · Molecular vision · 2008 · 7 claims · 5 setups

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A novel heterozygous de novo PAX6 frameshift mutation (c.577_578insG, insG@Gly72) in exon 6 causes autosomal dominant aniridia with congenital cataract, nystagmus, and glaucoma in this family.

genomic pax6 direct microsatellite blast
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

Experiments

Leveraging human genomic information to identify nonhuman primate sequences for expression array development.

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

Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

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

Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

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

Non-EST based prediction of exon skipping and intron retention events using Pfam information.

GeneSeer: a sage for gene names and genomic resources.

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

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

Improved tagging strategy for protein identification in mammalian cells.

Human SNPs resulting in premature stop codons and protein truncation.

Designating eukaryotic orthology via processed transcription units.

SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.

Database resources of the National Center for Biotechnology Information.

A novel de novo PAX6 mutation in an Ashkenazi-Jewish family with aniridia.

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