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 31

System / cell line: prediction ✕ Assay: fragment ✕ Clear

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.

PMID 15980510 · PMC1160247 · Nucleic acids research · 2005 · 8 claims · 2 setups

Full-text index only

The GeneMark website provides web interfaces to the GeneMark family of ab initio gene-finding programs for prokaryotic, eukaryotic and viral genomic sequences

escherichia arabidopsis initio
Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

Full-text index only

Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

msi-h computational rb1cc1 normal pcr nonlinear real-time
Prediction and assessment of splicing alterations: implications for clinical testing.

PMID 18951448 · PMC2832470 · Human mutation · 2008 · 8 claims · 5 setups

Full-text index only

Bioinformatic prediction alone is insufficient; in vitro analysis is needed to confirm or establish splicing aberrations for clinical variant classification

brca1 lymphocytes mammalian large bioinformatic cycloheximide mini-gene
Automatic annotation of eukaryotic genes, pseudogenes and promoters.

PMID 16925832 · PMC1810547 · Genome biology · 2006 · 8 claims · 6 setups

Full-text index only

Fgenesh++ gene prediction pipeline identifies 91% of coding nucleotides with 90% specificity

encode regions genes chromosome computational pseudogene promoter
Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

Full-text index only

Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

genomic phylogenetic direct high
Mutation analysis in a German family identified a new cataract-causing allele in the CRYBB2 gene.

PMID 17653036 · PMC2774456 · Molecular vision · 2007 · 8 claims · 4 setups

Full-text index only

A novel heterozygous mutation (383A>T; D128V) in exon 5 of CRYBB2 cosegregates with congenital cataract in all three affected family members and is absent in unaffected relatives.

genomic pcr-amplified computational pcr restriction pcr-rflp
Large genomic rearrangements in the CFTR gene contribute to CBAVD.

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

Full-text index only

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

genomic pcr cftr semi-quantitative junction direct
Identification of five novel mutations in the long isoform of the USH2A gene in Chinese families with Usher syndrome type II.

PMID 19023448 · PMC2584772 · Molecular vision · 2008 · 8 claims · 7 setups

Full-text index only

Mutations in USH2A are responsible for most cases of USH2

genomic family probands ush2a direct restriction single
Mutation analysis of congenital cataract in a Basotho family identified a new missense allele in CRYBB2.

PMID 19649175 · PMC2718852 · Molecular vision · 2009 · 8 claims · 6 setups

Full-text index only

A heterozygous missense mutation c.607G>A in exon 6 of CRYBB2, causing p.Val187Met, is the probable causative mutation for congenital nuclear cataract in this family

genomic basotho pcr restriction secondary
The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.

PMID 18778482 · PMC2563025 · Retrovirology · 2008 · 8 claims · 7 setups

Full-text index only

Intra-host nucleotide diversity of the HIV-2 C2V3C3 region increases over the course of chronic infection in most patients

pbmcs clonal env deduced nested maximum-likelihood positive
Evaluating native-like structures of RNA-protein complexes through the deep learning method.

PMID 36828844 · PMC9958188 · Nature communications · 2023 · 8 claims · 7 setups

Has reproduction · 67

DRPScore identifies native-like RNA-protein structures with higher success rates than ITScore-PR, DARS-RNP, and 3dRPC across bound and unbound testing sets.

bound-bound unbound-bound unbound-unbound bacillus structure interface secondary
Large-scale molecular analysis of a 34 Mb interval on chromosome 6q: major refinement of the RP25 interval.

PMID 18510646 · PMC2689154 · Annals of human genetics · 2008 · 7 claims · 5 setups

Full-text index only

Direct sequencing of 43 candidate genes in 7 Spanish arRP families identified 244 sequence variants (76 novel), none pathogenic, excluding these genes as disease-causing.

spanish rp5 population candidate direct comparative pcr
Functional analysis of novel SNPs and mutations in human and mouse genomes.

PMID 19091009 · PMC2638150 · BMC bioinformatics · 2008 · 8 claims · 7 setups

Full-text index only

FANS streamlines functional analysis of novel SNPs and mutations into a simplified, few-click, four-step procedure.

apoe 11-nucleotide sequence genomic manual automated exonic
Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

PMID 18842128 · PMC2572040 · Biology direct · 2008 · 8 claims · 6 setups

Full-text index only

The Turmoil-1 transposable element in C. elegans incorporated two unrelated protein-coding sequences into its inverted terminal repeats (ITRs)

turmoil-1 rrm elegans predicted pairwise maximum genome-wide
Autosomal dominant hereditary spastic paraplegia: novel mutations in the REEP1 gene (SPG31).

PMID 18644145 · PMC2492855 · BMC medical genetics · 2008 · 8 claims · 6 setups

Full-text index only

Pathogenic REEP1 mutations were identified in 4.3% (7/162) of autosomal dominant 'pure' HSP cases

genomic pcr-amplified reep1 pcr dhplc direct
A novel GJA8 mutation causing a recessive triangular cataract.

PMID 18483562 · PMC2375854 · Molecular vision · 2008 · 8 claims · 6 setups

Full-text index only

A homozygous single base-pair insertion (c.776insG) in GJA8 causes a recessive triangular nuclear cataract in two affected siblings.

proband's blood-derived genomic family rt-pcr pcr restriction
Sequence variations of GRM6 in patients with high myopia.

PMID 19862333 · PMC2765235 · Molecular vision · 2009 · 7 claims · 8 setups

Full-text index only

Three novel GRM6 variations with predicted functional consequences (c.67-82delCAGGCGGGCCTGGCGCinsT, c.858-5a>g, c.1537G>A) were found in high myopia patients but absent in 96 controls

genomic pcr mglur6 grm6 pcr heteroduplex pcr-restriction
Bases and spaces: resources on the web for accessing the draft human genome.

PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

Full-text index only

By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

bac whole-genome draft submitted bac radiation initio
Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads.

PMID 38940130 · PMC11256924 · Bioinformatics (Oxford, England) · 2024 · 7 claims · 5 setups

Has reproduction · 87

Forseti is the first probabilistic model for resolving the splicing status of exonic scRNA-seq reads by scoring putative fragments linking read alignments to proximate priming sites

training simulated held-out paired-end cubic mlp
Common variants of the beta and gamma subunits of the epithelial sodium channel and their relation to plasma renin and aldosterone levels in essential hypertension.

PMID 15661075 · PMC547905 · BMC medical genetics · 2005 · 8 claims · 7 setups

Full-text index only

Heterozygous carriage of common βENaC/γENaC variants (G589S, i12-17CT, V546I) is significantly more prevalent in essential hypertension patients (9.2%) than in normotensive males (2.9%) or blood donors (3.0%)

hypertensive lymphocytes βenac xenopus targeted pcr-rflp plasma

Experiments

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.

Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

Prediction and assessment of splicing alterations: implications for clinical testing.

Automatic annotation of eukaryotic genes, pseudogenes and promoters.

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

Mutation analysis in a German family identified a new cataract-causing allele in the CRYBB2 gene.

Large genomic rearrangements in the CFTR gene contribute to CBAVD.

Identification of five novel mutations in the long isoform of the USH2A gene in Chinese families with Usher syndrome type II.

Mutation analysis of congenital cataract in a Basotho family identified a new missense allele in CRYBB2.

The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.

Evaluating native-like structures of RNA-protein complexes through the deep learning method.

Large-scale molecular analysis of a 34 Mb interval on chromosome 6q: major refinement of the RP25 interval.

Functional analysis of novel SNPs and mutations in human and mouse genomes.

Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

Autosomal dominant hereditary spastic paraplegia: novel mutations in the REEP1 gene (SPG31).

A novel GJA8 mutation causing a recessive triangular cataract.

Sequence variations of GRM6 in patients with high myopia.

Bases and spaces: resources on the web for accessing the draft human genome.

Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads.

Common variants of the beta and gamma subunits of the epithelial sodium channel and their relation to plasma renin and aldosterone levels in essential hypertension.