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 131

System / cell line: presence ✕ Assay: alignment ✕ Clear

Presence of myocilin sequence variants in Japanese patients with open-angle glaucoma.

PMID 18334962 · PMC2268858 · Molecular vision · 2008 · 8 claims · 4 setups

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Two MYOC sequence variants were identified in Japanese POAG patients: a novel non-synonymous variant p.Gln297His and a previously reported variant p.Ala363Thr.

genomic myoc poag pcr amino clinical
Phylogenetic analysis of RhoGAP domain-containing proteins.

PMID 17127216 · PMC5054073 · Genomics, proteomics & bioinformatics · 2006 · 7 claims · 6 setups

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RhoGAP domain-containing proteins, sharing the conserved arginine residue, form a monophyletic group with a common ancestor.

rhogap aligned bayesian domain sequence maximum bayesian
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes.

PMID 19906700 · PMC2808873 · Nucleic acids research · 2010 · 7 claims · 4 setups

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NCG is a web database integrating duplicability, orthology, evolutionary appearance, and network topology data for 736 human cancer genes

cancer proteome pten genome orthology protein-protein
Computational comparison of two mouse draft genomes and the human golden path.

PMID 12537546 · PMC151282 · Genome biology · 2003 · 8 claims · 7 setups

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The Celera and public mouse genome assemblies differ in about 10% of the mouse genome, with complementary strengths (Celera higher base-pair accuracy and overall coverage; public assembly higher quality in some finished BAC regions and freely accessible)

newly genome chromosome genomic blat blastn repeat
Structural organization and interactions of transmembrane domains in tetraspanin proteins.

PMID 15985154 · PMC1190194 · BMC structural biology · 2005 · 8 claims · 5 setups

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TM1, TM2 and TM3 of human tetraspanins display a distinct heptad repeat motif (abcdefg)n, while TM4 lacks this motif.

tetraspanin cd9 gfp single-cysteine sequence cross-species fluorescence
Vertebrate gene finding from multiple-species alignments using a two-level strategy.

PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

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DOGFISH cleanly separates a multi-species alignment classifier (RVM cascade) from an HMM-based structure predictor, avoiding tight coupling of alignment complexity with HMM formalism

genomic encode entire chromosome multi-species hmm-based classifier
A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.

PMID 19043541 · PMC2580819 · PLoS computational biology · 2008 · 8 claims · 5 setups

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A general model-free methodological framework is proposed for reconstructing Contiguous Ancestral Regions (CARs) from conserved syntenies, generalizing prior computational and cytogenetic approaches

genome boreoeutherian ferungulate marker-presence whole-genome ancestral combinatorial
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups

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A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys

personal genomic pcr-validated unrelated short-read pcr sanger
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
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
Extreme conservation of noncoding DNA near HoxD complex of vertebrates.

PMID 15462684 · PMC524357 · BMC genomics · 2004 · 7 claims · 7 setups

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Three blocks of extremely conserved non-coding DNA (CR1, CR2, CR3) exist within 7 kb upstream of the HoxD complex, 3' of Evx-2, conserved from fish to human.

hoxd genomic pcr pcr-amplified comparative pcr southern
Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

PMID 16195578 · PMC1240112 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Alternative splices in 10,818 human-mouse gene pairs can be classified as conserved, novel, or diverged based on genomic and transcript-level cross-species comparison.

orthologous diverse tissues gene comparative est microarray
Human-zebrafish non-coding conserved elements act in vivo to regulate transcription.

PMID 16179648 · PMC1236720 · Nucleic acids research · 2005 · 8 claims · 4 setups

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Deeply conserved human-zebrafish non-coding elements are enriched for in vivo cis-acting transcriptional regulatory activity.

ncbi genes zebrafish comparative annotation gfp
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

PMID 15752422 · PMC555591 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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A previously unidentified fourth human SULT1A gene (SULT1A4) exists on chromosome 16 and is transcriptionally active

genome chimpanzee sult1a3 est blast-like comparative pairwise
Evolutionarily conserved human targets of adenosine to inosine RNA editing.

PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

panel brain chicken flna comparative rt-pcr homology
ECgene: genome annotation for alternative splicing.

PMID 15608289 · PMC540072 · Nucleic acids research · 2005 · 8 claims · 5 setups

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ECgene combines genome-based EST clustering with a graph-theoretic transcript assembly procedure to predict gene models including alternative splicing events.

brca2 rgs17 organs cdna genomic genome transcript
DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

PMID 15608249 · PMC539965 · Nucleic acids research · 2005 · 5 claims · 8 setups

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Comparative human-mouse genome analysis identifies conserved sequence tags (CSTs, >=70% identity over >=100bp) that frequently correspond to non-coding elements with putative regulatory or structural roles

identified cst csts comparative coding exon
Genome assembly comparison identifies structural variants in the human genome.

PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

genome ceph unrelated individuals whole-genome pcr quantitative
Systematic identification of pseudogenes through whole genome expression evidence profiling.

PMID 16945953 · PMC1636364 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Developed a novel bioinformatics method that identifies pseudogenes by profiling whole-genome transcript and protein expression evidence

genome ensembl vega celera spliced protein-to-genome pseudogene
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

Experiments

Presence of myocilin sequence variants in Japanese patients with open-angle glaucoma.

Phylogenetic analysis of RhoGAP domain-containing proteins.

Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes.

Computational comparison of two mouse draft genomes and the human golden path.

Structural organization and interactions of transmembrane domains in tetraspanin proteins.

Vertebrate gene finding from multiple-species alignments using a two-level strategy.

A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

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

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

Extreme conservation of noncoding DNA near HoxD complex of vertebrates.

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

Human-zebrafish non-coding conserved elements act in vivo to regulate transcription.

Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

Evolutionarily conserved human targets of adenosine to inosine RNA editing.

ECgene: genome annotation for alternative splicing.

DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

Genome assembly comparison identifies structural variants in the human genome.

Systematic identification of pseudogenes through whole genome expression evidence profiling.

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