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 19

System / cell line: novel ✕ Assay: test ✕ Clear

Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

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Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.

hiv-1 four simulated population-based maximum bayesian
Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

PMID 19706363 · PMC3525194 · Human genomics · 2009 · 8 claims · 6 setups

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A novel HPV type (HPV-85) was identified and phylogenetically characterized, showing closest relatedness to HPV-70/39/18/45/59 within the A7 genital HPV group

novel hpv gene h5n1 whole-genome intrinsic statistical
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous
FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

Has reproduction · 65

FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

simulated four rna-seq randomly simulated paired-end read-mappability
Catechol-O-methyltransferase (COMT) gene variants: possible association of the Val158Met variant with opiate addiction in Hispanic women.

PMID 18270997 · PMC2909109 · American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2008 · 8 claims · 5 setups

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The G/A and A/A genotypes of G472A (Val158Met) are point-wise significantly associated with opiate addiction in Hispanic women but not men (P=0.049)

genomic opioid-dependent subjects direct taqman statistical
Cystic fibrosis in Korean children:a case report identified by a quantitative pilocarpine iontophoresis sweat test and genetic analysis.

PMID 15716623 · PMC2808565 · Journal of Korean medical science · 2005 · 8 claims · 8 setups

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CF should be suspected in Korean/Asian children with chronic respiratory symptoms despite its rarity in Asian populations

korean family bronchial quantitative sweat cftr
EGASP: the human ENCODE Genome Annotation Assessment Project.

PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

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Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

encode computational manual rt-pcr
Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

PMID 17535437 · PMC1892558 · BMC microbiology · 2007 · 8 claims · 6 setups

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Cjd strains are phylogenetically distinct from Cjj strains based on MLST and CGI analysis

geographically cjd novel jejuni multilocus comparative phenotypic
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
A distinct clinical, neuropsychological and radiological phenotype is associated with progranulin gene mutations in a large UK series.

PMID 18234697 · PMC2577762 · Brain : a journal of neurology · 2008 · 8 claims · 7 setups

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Five different pathogenic GRN mutations (frameshift/premature termination) were identified in 25 affected members of a large UK FTLD cohort, with no whole-gene deletions detected

ftld grn genomic post-mortem clinical volumetric direct
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
Exome sequencing in 38 patients with intracranial aneurysms and subarachnoid hemorrhage.

PMID 32367296 · PMC7419486 · Journal of neurology · 2020 · 8 claims · 6 setups

Has reproduction · 78

Sequence variants in PCNT, RNF213 and THSD1 support a role as susceptibility factors for cerebrovascular disease (UIA/aSAH)

unrelated affected additional 75-patient exome sanger gene
Genome informatics: taming the avalanche of genomic data.

PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

genes arabidopsis genome vertebrate comparative conservation whole-genome
Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups

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CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed

cerevisiae cycle reanalysis statistical optimal
Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.

PMID 38594607 · PMC11003151 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 8 setups

Has reproduction · 100

H3K27ac ChIP-seq and RNA-seq were used to construct eRNA expression profiles across multiple tissues in Enshi Black (ES) and Duroc pigs, revealing tissue-level eRNA regulatory landscapes

longissimus muscle snps pig h3k27ac strand-specific starr-seq
Ab initio identification of human microRNAs based on structure motifs.

PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

genome mirna hairpins chromosome secondary linear five-fold
Phylogeography of mtDNA haplogroup R7 in the Indian peninsula.

PMID 18680585 · PMC2529308 · BMC evolutionary biology · 2008 · 8 claims · 7 setups

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R7a1, a recently derived sub-branch of haplogroup R7, is particularly frequent among Munda-speaking tribal groups

mtdnas haplogroup genetic geographic complete hvs-i reduced-median
Prevalence of A2143G mutation of H. pylori-23S rRNA in Chinese subjects with and without clarithromycin use history.

PMID 18507832 · PMC2427034 · BMC microbiology · 2008 · 7 claims · 6 setups

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A2143G point mutation of the H. pylori 23S rRNA gene causes clarithromycin resistance

fasting subjects serum pylori pcr 13c-urea elisa
Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

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Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

european african individuals nondiabetic snp variant direct

Experiments

Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

Catechol-O-methyltransferase (COMT) gene variants: possible association of the Val158Met variant with opiate addiction in Hispanic women.

Cystic fibrosis in Korean children:a case report identified by a quantitative pilocarpine iontophoresis sweat test and genetic analysis.

EGASP: the human ENCODE Genome Annotation Assessment Project.

Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

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

A distinct clinical, neuropsychological and radiological phenotype is associated with progranulin gene mutations in a large UK series.

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

Exome sequencing in 38 patients with intracranial aneurysms and subarachnoid hemorrhage.

Genome informatics: taming the avalanche of genomic data.

Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.

Ab initio identification of human microRNAs based on structure motifs.

Phylogeography of mtDNA haplogroup R7 in the Indian peninsula.

Prevalence of A2143G mutation of H. pylori-23S rRNA in Chinese subjects with and without clarithromycin use history.

Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.