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 45

System / cell line: sequence ✕ Assay: junction ✕ Clear

Continued colonization of the human genome by mitochondrial DNA.

PMID 15361937 · PMC515365 · PLoS biology · 2004 · 7 claims · 6 setups

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NUMT insertion into nuclear chromosomes is an ongoing process shaped by double-strand-break repair (as shown in yeast) and continuing in humans.

homo genomic chimpanzee genome genome-wide pcr sanger
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

elegans pooled pcr known semi-nested cloning initio
Sequence context affects the rate of short insertions and deletions in flies and primates.

PMID 18291026 · PMC2374710 · Genome biology · 2008 · 8 claims · 6 setups

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The rate of insertion or deletion of specific lengths can vary by more than 100-fold depending on the surrounding sequence context

chimpanzee simulans chimp primate comparative direct nucleotide
IMGT, the international ImMunoGeneTics information system.

PMID 15608269 · PMC540019 · Nucleic acids research · 2005 · 8 claims · 6 setups

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IMGT is a high-quality integrated knowledge resource for immunoglobulins (IG), T cell receptors (TR), MHC, and related proteins of the immune system (RPI) across vertebrate species

igh mhc pairs automated junction structure
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
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
PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays.

PMID 19906711 · PMC2808952 · Nucleic acids research · 2010 · 6 claims · 4 setups

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PLANdbAffy is a database of Affymetrix probe alignments to the human genome for five widely used arrays (HG-U133A, HG-U133B, HG-U133 Plus 2.0, Human Exon 1.0, Human Gene 1.0)

hg-u133a ucsc dbsnp probe blat est snp
iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes.

PMID 18974167 · PMC2639305 · Bioinformatics (Oxford, England) · 2008 · 6 claims · 3 setups

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iMapper is a web application for automated analysis and mapping of insertional mutagenesis sequence data against vertebrate and invertebrate Ensembl genomes (human, mouse, rat, zebrafish, Drosophila, S. cerevisiae).

piggybac splinkerette-pcr-derived sequence splinkerette genome throughput
Splicing bioinformatics to biology.

PMID 16732900 · PMC1779529 · Genome biology · 2006 · 8 claims · 8 setups

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Mutually exclusive selection of Dscam exon 6 variants is governed by base pairing between a conserved intronic docking site and selector sequences adjacent to each alternative exon.

dscam alternative heterologous expressing comparative dicodon reporter
Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

PMID 17012280 · PMC1636463 · Nucleic acids research · 2006 · 7 claims · 5 setups

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DSBs induced at the TRS/vector junction (EcoRV site) generate numerous mutagenic events in flanking sequences, whereas DSBs within the repeat tract (EcoRI site) produce no such mutants

coli plasmids plasmid white plasmid sequencing non-b
LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

PMID 24709818 · PMC4079972 · Genome research · 2014 · 8 claims · 8 setups

Has reproduction · 68

LaSSO (Lariat Sequence Site Origin) identifies intronic lariat reads and pinpoints branch points genome-wide from RNA-seq data by considering every intronic base as a potential branch point and including all possible exon-skipping lariats.

schizosaccharomyces pombe rna-seq lasso lariat-specific
A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.

PMID 19087293 · PMC2636810 · BMC bioinformatics · 2008 · 6 claims · 6 setups

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A theoretical exon-exon junction protein database accounting for all in-phase (frame-preserving) exon combinations can be built from the Ensembl Core Database using Perl/Bioperl/MySQL/Ensembl API.

ensembl liver candidate same database tandem decoy
Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

PMID 17003057 · PMC1635253 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Stepwise directed evolution using chimeric FLRT (FRT/genomic hybrid) intermediate sites can generate Flp variants capable of recombining native genomic FRT-like sequences from the human IL10 gene (FL-IL10A, FL-IL10B).

coli flp il10 flp-holliday recombination site-specific computational
Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains.

PMID 18590534 · PMC2481270 · BMC genomics · 2008 · 8 claims · 6 setups

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B. pertussis strains carrying the ptxP3 allele gradually replaced ptxP1 strains and became predominant from 1998, coinciding with the Dutch pertussis resurgence

dutch additional pertussis ptxp3 multi-locus multiple-locus microarray-based
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

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Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

unigene shuffled real genomes genome-wide alignment gene
Analysis of virulence factors of Helicobacter pylori isolated from a Vietnamese population.

PMID 19698173 · PMC2739534 · BMC microbiology · 2009 · 8 claims · 5 setups

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Three distinct deletion patterns (39-bp, 18-bp, no deletion) exist upstream of the cagA EPIYA repeat region (pre-EPIYA region), providing a novel genotyping marker.

pylori gastric pcr sequence comparative
Large genomic rearrangements in the CFTR gene contribute to CBAVD.

PMID 17448246 · PMC1876208 · BMC medical genetics · 2007 · 7 claims · 6 setups

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Large genomic rearrangements in CFTR contribute to CBAVD and should be systematically investigated alongside point mutation screening

genomic pcr cftr semi-quantitative junction direct
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

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High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

lncap lncap-derived r1881-treated massively blast blat
GENCODE: producing a reference annotation for ENCODE.

PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

tissues encode rt-pcr comparative automated
Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.

PMID 16872520 · PMC1553449 · BMC genomics · 2006 · 8 claims · 7 setups

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Native Peruvian H. pylori strains comprise two lineages: predominant hp-Europe and ~20% hsp-Amerind (Amerindian ancestry, closer to Alaska strains)

pylori peruvian spanish fluorescent multilocus oipa

Experiments

Continued colonization of the human genome by mitochondrial DNA.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

Sequence context affects the rate of short insertions and deletions in flies and primates.

IMGT, the international ImMunoGeneTics information system.

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

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

PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays.

iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes.

Splicing bioinformatics to biology.

Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.

Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.

Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains.

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

Analysis of virulence factors of Helicobacter pylori isolated from a Vietnamese population.

Large genomic rearrangements in the CFTR gene contribute to CBAVD.

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

GENCODE: producing a reference annotation for ENCODE.

Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.