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 76

System / cell line: flanking ✕ Assay: genome ✕ Clear

ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

PMID 16845048 · PMC1538778 · Nucleic acids research · 2006 · 6 claims · 4 setups

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ProMiR II improves on the original ProMiR by integrating free energy, G/C ratio, conservation score and entropy for more controllable miRNA prediction

genome cytomegalovirus six probabilistic 5-fold directional
Adequate use of allele frequencies in Hispanics--a problem elucidated in nephrotic syndrome.

PMID 19876656 · PMC2899680 · Pediatric nephrology (Berlin, Germany) · 2010 · 7 claims · 3 setups

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Self-identified Hispanic SRNS patients in the USA are genetically heterogeneous, being of either Caucasian or Mesoamerican (Native-American) descent

genomic same healthy direct genome-wide
A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population.

PMID 16904005 · PMC1779589 · Genome biology · 2006 · 8 claims · 7 setups

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Eight SNPs with extreme European-branch locus-specific branch length (LSBL) were selected from a genome-wide FST dataset as candidates for selection in Europe.

snp irish french fst-based microsatellite genome-wide
Dissecting microregulation of a master regulatory network.

PMID 18294391 · PMC2289817 · BMC genomics · 2008 · 8 claims · 6 setups

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143 human miRNAs (termed p53-miRs) each contain at least one putative p53 binding site within 10 kb flanking sequence and are predicted to target at least one known gene

genome mirnas mirna-target predicted p53 mirna cross-referencing
Molecular archeology of L1 insertions in the human genome.

PMID 12372140 · PMC134481 · Genome biology · 2002 · 8 claims · 4 setups

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TSDfinder, a new algorithm, refines RepeatMasker-identified L1 boundaries by locating poly(A) tails, TSDs, and inversion breakpoints

genome tsd 50-nt full-length repeat sequence repeat-content
Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

PMID 19329065 · PMC5054122 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 8 setups

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Nucleotide preference at CpG flanking sites transitions from 5' T (invertebrates) to 5' A (vertebrates) at the invertebrate-vertebrate boundary

genomes same pufferfish elegans nucleotide genome-wide kruskal-wallis
Identifying synonymous regulatory elements in vertebrate genomes.

PMID 15980499 · PMC1160227 · Nucleic acids research · 2005 · 7 claims · 4 setups

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SynoR is a tool that performs de novo genome-wide identification of synonymous regulatory elements (SREs) using evolutionarily conserved TFBS modules as seeds

genome genes genome-wide gene tissue-specificity
Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.

PMID 15817567 · PMC1074747 · Nucleic acids research · 2005 · 8 claims · 8 setups

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966 pseudogenes derived from the four human Y (hY) RNAs were characterized in the human genome

genome chimpanzee pseudogenes genomic megablast blat sequence
Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach.

PMID 15673711 · PMC548376 · Nucleic acids research · 2005 · 8 claims · 6 setups

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A new technique combining whole-genome selective PCR amplification and subtractive hybridization can experimentally identify polymorphic retroelement insertions without prior knowledge of RE evolutionary history or sequence

genomic driver coli individual whole-genome subtractive cloning
Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

PMID 17175533 · PMC1802619 · Nucleic acids research · 2007 · 8 claims · 6 setups

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202 novel box H/ACA RNA-related sequences were identified in the human genome

genome chimpanzee aca flanking megablast comparative sequence
Intronic alternative splicing regulators identified by comparative genomics in nematodes.

PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

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Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

elegans database transgenic comparative est cross-species
Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

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Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr
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
Evolution of the NANOG pseudogene family in the human and chimpanzee genomes.

PMID 16469101 · PMC1457002 · BMC evolutionary biology · 2006 · 7 claims · 5 setups

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The NANOG gene and all pseudogenes except NANOGP8 occupy orthologous chromosomal positions in the chimpanzee genome, indicating they originated before the human-chimpanzee divergence.

chimpanzee megablast pcr flanking-sequence
Comparative genomics of multidrug resistance in Acinetobacter baumannii.

PMID 16415984 · PMC1326220 · PLoS genetics · 2006 · 7 claims · 5 setups

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A. baumannii strain AYE contains an 86-kb genomic resistance island (AbaR1) clustering 45 of its 52 resistance genes, the largest resistance island described to date

baumannii resistance clinical whole-genome comparative sequence
How accurately is ncRNA aligned within whole-genome multiple alignments?

PMID 17963514 · PMC2206062 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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MULTIZ does a fairly accurate job of aligning ncRNA regions across 17 vertebrate genomes, but better alignments exist in some regions.

genome vertebrate nonhuman genomic sequence whole-genome covariance
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
Analysis of recent segmental duplications in the bovine genome.

PMID 19951423 · PMC2796684 · BMC genomics · 2009 · 8 claims · 6 setups

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Recently duplicated sequence (≥1 kb, ≥90% identity) comprises 3.11% (94.4 Mb) of the bovine genome assembly (Btau_4.0)

bos bovine genes cattle genome fluorescent repeat
Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

genome rhesus vega-annotated tpas transcript-to-genome same synteny
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

ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

Adequate use of allele frequencies in Hispanics--a problem elucidated in nephrotic syndrome.

A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population.

Dissecting microregulation of a master regulatory network.

Molecular archeology of L1 insertions in the human genome.

Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

Identifying synonymous regulatory elements in vertebrate genomes.

Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.

Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach.

Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

Intronic alternative splicing regulators identified by comparative genomics in nematodes.

Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

Human SNPs resulting in premature stop codons and protein truncation.

Evolution of the NANOG pseudogene family in the human and chimpanzee genomes.

Comparative genomics of multidrug resistance in Acinetobacter baumannii.

How accurately is ncRNA aligned within whole-genome multiple alignments?

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

Analysis of recent segmental duplications in the bovine genome.

Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

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