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 23

System / cell line: sequences ✕ Assay: exact ✕ Clear

The most frequent short sequences in non-coding DNA.

PMID 19966278 · PMC2831315 · Nucleic acids research · 2010 · 8 claims · 2 setups

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Short frequent sequences (9-14 bases) in non-coding DNA may play a role in maintaining chromosome structure and function

whole-genome genome-wide
A computational study of off-target effects of RNA interference.

PMID 15800213 · PMC1072799 · Nucleic acids research · 2005 · 8 claims · 5 setups

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The chance of RNAi off-target effects is considerable, ranging from 5% to 80% depending on organism and parameters, when using exact sequence identity between siRNA and transcripts.

schizosaccharomyces caenorhabditis homo pombe off-target mismatch-tolerant rational
Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements.

PMID 20008508 · PMC2836564 · Nucleic acids research · 2010 · 8 claims · 6 setups

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Most TEs insert within specific 'hotspots' along the targeted TE rather than uniformly.

genome sequences unique nested chi-square position-specific
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

user-supplied ranked gene fasta-formatted functional gene novo
The distribution of SNPs in human gene regulatory regions.

PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

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SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

gene mammalian promoter experimentally genome-wide computational binding
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
HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments.

PMID 18215327 · PMC2265691 · Virology journal · 2008 · 8 claims · 6 setups

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N-linked glycosylation of HIV-1 gp120 differs between plasma and leukocyte compartments

plasma hiv-1 nlg presence env phylogenetic signature
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
Ensembl 2006.

PMID 16381931 · PMC1347495 · Nucleic acids research · 2006 · 8 claims · 5 setups

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Ensembl now provides annotation for 19 genomes, up from 4 the previous year, including new mammalian (Rhesus macaque, Opossum), chordate (Ciona intestinalis), and yeast genomes.

cow ensembl snps genome gene whole-genome pairwise
SLDMS: A Tool for Calculating the Overlapping Regions of Sequences.

PMID 35046988 · PMC8761809 · Frontiers in plant science · 2021 · 8 claims · 5 setups

Has reproduction · 80

SLDMS is a novel method for computing overlapping regions of sequencing reads using suffix array (SA), longest common prefix (LCP) array, document array (DA), and a monotonic stack.

sequencing concatenated pacbio-hifi third-generation running-time suffix overlap
Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

myeloid reference selected genome-localized microarray promoter k-medoids
Predicting failure rate of PCR in large genomes.

PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

genomic genome pcr combined large-scale exact-match mismatch-tolerant
CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity.

PMID 15507145 · PMC526769 · BMC medical genetics · 2004 · 8 claims · 7 setups

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PCR amplification and sequencing of CLC-2 revealed 1 SNP in the promoter, 4 SNPs in intron 1, and none in exon 20

nasal genomic ib3-1 western pcr fisher's
Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

PMID 16925841 · PMC1810556 · Genome biology · 2006 · 8 claims · 5 setups

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Exogean is a framework using directed acyclic coloured multigraphs (DACMs) to represent biological objects (mRNA, ESTs, protein alignments, exons) and iteratively combine them into complex protein-coding transcript models.

genome sequences automatic manual sequence
Gene losses during human origins.

PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

pseudogene chimpanzee human-specific population comparative phylogenetic fisher's
BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

PMID 18234728 · PMC2564862 · Journal of medical genetics · 2008 · 8 claims · 7 setups

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BHD germline mutation detection rate was 88% (51/58 families) using direct DNA sequencing

peripheral blood-derived folliculin chest direct subcloning sequence
Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

PMID 19005564 · PMC2579325 · PloS one · 2008 · 8 claims · 7 setups

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Doublet mutations are significantly more frequent in EGFR (6.0%) and TP53 (2.3%) in human lung cancer than spontaneous doublets in mouse lacI (0.7%), about 8-fold and 3-fold higher respectively.

egfr tp53 laci lung literature comparative statistical
Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

PMID 18405369 · PMC2359762 · BMC microbiology · 2008 · 8 claims · 5 setups

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emm type is often a poor marker for clonal genetic background across the global S. pyogenes collection

streptococcus pyogenes emm values multilocus emm comparative
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

genome h-invdb gene sets genome transcript-to-genome coding
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

user-supplied gene predicted interactome gene kegg transcription

Experiments

The most frequent short sequences in non-coding DNA.

A computational study of off-target effects of RNA interference.

Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements.

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

The distribution of SNPs in human gene regulatory regions.

Designating eukaryotic orthology via processed transcription units.

HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments.

Database resources of the National Center for Biotechnology Information.

Ensembl 2006.

SLDMS: A Tool for Calculating the Overlapping Regions of Sequences.

Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

Predicting failure rate of PCR in large genomes.

CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity.

Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

Gene losses during human origins.

BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.