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 15

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

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
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
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
Adaptively inferring human transcriptional subnetworks.

PMID 16760900 · PMC1681499 · Molecular systems biology · 2006 · 8 claims · 7 setups

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A multivariate linear spline (MARS-based) model correlating PWM binding scores with log expression ratios can identify active cis-motif combinations in mammalian promoters without requiring gene clustering.

liver proximal hela predicted microarray computational novo
Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

PMID 18927607 · PMC2559870 · PloS one · 2008 · 8 claims · 5 setups

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No pathogenic mutations were found in LRRK2, PRKN, or ATXN3 in a Nigerian cohort of apparently sporadic PD patients.

nigerian same novel sanger targeted repeat
Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

PMID 18622261 · PMC2680356 · Pharmacogenetics and genomics · 2008 · 7 claims · 7 setups

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UGT2B7 haplotype 4 is associated with increased enzyme activity (M3G and M6G formation)

liver caucasian ugt2b7 gene snp enzymatic
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

Has reproduction · 50

330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

brassica r500 rapa genomic bulk reference-based snp
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

Has reproduction · 86

RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

ccds glioblastoma experimental simulated simulated bulk quality
Genetic and functional association of FAM5C with myocardial infarction.

PMID 18430236 · PMC2383879 · BMC medical genetics · 2008 · 8 claims · 5 setups

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SNPs within FAM5C show genetic linkage to and association with myocardial infarction in the GENECARD family-based sample

genecard cathgen donor aortic genome-wide case-control expression
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
Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

PMID 20057903 · PMC2802291 · Molecular vision · 2009 · 7 claims · 8 setups

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BEST1 mutations are not correlated with the severity of functional and clinical data in Best VMD patients

genomic unrelated best1 best1-4 direct chromosome pathogenicity
A near complete genome for goat genetic and genomic research.

PMID 34507524 · PMC8434745 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

Has reproduction · 89

Saanen_v1 is a high-quality de novo goat genome assembly from a male Saanen buck, including the first goat Y chromosome scaffold.

saanen goat testicular saanen_v1 pacbio illumina hi-c
A third approach to gene prediction suggests thousands of additional human transcribed regions.

PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

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A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

genome 4.4-mb known nucleotide repeat polyadenylation
Linkage disequilibrium mapping of a breast cancer susceptibility locus near RAI/PPP1R13L/iASPP.

PMID 18588689 · PMC2474586 · BMC medical genetics · 2008 · 8 claims · 6 setups

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A region spanning the gene RAI and the 5' portion of XPD is associated with postmenopausal breast cancer

peripheral genomic genotype independent linkage targeted genotyping
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

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

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

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

Adaptively inferring human transcriptional subnetworks.

Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

Genetic and functional association of FAM5C with myocardial infarction.

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

Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

A near complete genome for goat genetic and genomic research.

A third approach to gene prediction suggests thousands of additional human transcribed regions.

Linkage disequilibrium mapping of a breast cancer susceptibility locus near RAI/PPP1R13L/iASPP.

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.