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 20

System / cell line: variants ✕ Assay: bioinformatic ✕ Clear

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

genome poly est cdna est blast cdna
Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

PMID 19674479 · PMC2743674 · Molecular brain · 2009 · 7 claims · 8 setups

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R125M, R127L, and R125M/R127L BDNF SNP variants are poorly cleaved, resulting in predominant secretion of proBDNF (CR-proBDNF)

bdnf hippocampal cortical cerebellar bioinformatic western immunoprecipitation
Missense variants in human forkhead transcription factors reveal determinants of forkhead DNA bispecificity.

PMID 41124077 · PMC12795473 · Cell reports · 2025 · 6 claims · 5 setups

Has reproduction · 92

Non-DNA-contacting residues, especially in the loop between helices 2 and 3 and in wing 2, control mono- vs. bispecificity of FH domains for the FKH and FHL motifs

reference chimeric foxn3 foxk1 universal pbm chip-seq
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

PMID 17338820 · PMC1839109 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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EVDB is a comprehensive, non-redundant relational database of known human splice variants built from NCBI Entrez Gene and Evidence Viewer data

genome affymetrix probe database microarray interactive
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups

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Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR

testis panel genome 5'-race non-quantitative
Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

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A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

gbs clinical bioinformatic eburst kinetic
Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms.

PMID 16614446 · PMC1435984 · Nucleic acids research · 2006 · 8 claims · 5 setups

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A core termination signal of 4 nt (stop codon plus the following nucleotide) is preferred across most prokaryotic and eukaryotic genomes

orf coli rabbit cos-7 bioinformatic codon prokaryotic
Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.

PMID 18842124 · PMC2569949 · BMC genomics · 2008 · 7 claims · 7 setups

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GS-FLX pyrosequencing of pooled amplicons detects sequence variants with high specificity (99.95%) and no false negatives at ≥30× coverage

pools pcr genomic gs-flx massively sanger pcr
Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes.

PMID 18948297 · PMC2602764 · Nucleic acids research · 2008 · 6 claims · 8 setups

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Incorporating a biotin tag into the HTA probe enables purification of labeled heteroduplexes and direct sequencing of the separated query strand, allowing recovery of minor variant sequences

hiv-1 biotin-hta-purified original recovered heteroduplex rt-pcr sanger
Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

PMID 36721781 · PMC9884472 · PeerJ · 2023 · 8 claims · 4 setups

Has reproduction · 50

Kallisto was the most accurate VCE on simulated data, having the lowest RRMSE, followed by Freyja

sars-cov-2 publicly simulated simulated amplicon-based variant
Evaluating sequence data quality from the Swift Accel-Amplicon CFTR Panel.

PMID 31913291 · PMC6949293 · Scientific data · 2020 · 6 claims · 7 setups

Has reproduction · 89

The Accel-Amplicon CFTR panel generates sequencing data with high coverage depth and near 100% on-target reads.

genomic adapted aligned pcr amplicon multiplex qpcr
Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.

PMID 17442112 · PMC1863428 · BMC cancer · 2007 · 7 claims · 5 setups

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CYYR1 mRNA undergoes a 'subtle' alternative splicing event generating two isoforms (CAG- and CAG+) differing by a single alanine codon at the exon3/exon4 junction

neuroendocrine tumors normal cyyr1 rt-pcr quantitative psti
The estrogen hypothesis of schizophrenia implicates glucose metabolism: association study in three independent samples.

PMID 18460190 · PMC2391158 · BMC medical genetics · 2008 · 8 claims · 4 setups

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A novel candidate-gene selection strategy combining unbiased schizophrenia expression/linkage data with the estrogen hypothesis as a biological filter identifies glycolysis as a candidate pathway network for schizophrenia

case-control same compilation snp haplotype pairwise
Melusin gene (ITGB1BP2) nucleotide variations study in hypertensive and cardiopathic patients.

PMID 20017903 · PMC2803168 · BMC medical genetics · 2009 · 6 claims · 5 setups

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Only three nucleotide variations in ITGB1BP2 were found among 928 screened subjects, indicating a high degree of conservation of the gene in the populations analyzed

genomic hela itgb1bp2 melusin direct minigene in-silico
Exome sequencing of a multigenerational human pedigree.

PMID 20011588 · PMC2788131 · PloS one · 2009 · 8 claims · 6 setups

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Microarray-based exome capture combined with 454 GS FLX NGS is an efficient and reliable method to enrich for chromosomal regions of interest, validated on eight individuals from a three-generation pedigree

genomic eluted captured pcr microarray-based qpcr next-generation
Genetic variation in PARL influences mitochondrial content.

PMID 19862556 · PMC2829432 · Human genetics · 2010 · 7 claims · 5 setups

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PARL is a key regulator of mitochondrial integrity and function and plays a role in cellular apoptosis

genomic nuclear parl pcr snp real-time
Flanking p10 contribution and sequence bias in matrix based epitope prediction: revisiting the assumption of independent binding pockets.

PMID 18925947 · PMC2600787 · BMC structural biology · 2008 · 8 claims · 3 setups

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The extended matrix PP10 (built from a proline-containing peptide library) shows significant improvement in binding prediction over the original nine-residue matrix P9

recombinant peptides awcsdealplgsprcd peptide-mhc quantitative x-ray
Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation.

PMID 15867095 · PMC2213188 · The Journal of experimental medicine · 2005 · 7 claims · 6 setups

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IgVH genes have evolved precise placement of coding-strand Cs so that AID-induced C-to-T mutations are predominantly silent, especially in the CDRs.

igvh germline non-igv immunogenetics flow cdna bioinformatic
COMP mutation screening as an aid for the clinical diagnosis and counselling of patients with a suspected diagnosis of pseudoachondroplasia or multiple epiphyseal dysplasia.

PMID 15756302 · PMC2673054 · European journal of human genetics : EJHG · 2005 · 8 claims · 4 setups

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COMP mutations were identified in 78% of families referred with PSACH

genomic sequence subset pcr bidirectional sequence
Arrhythmogenic right ventricular cardiomyopathy type 6 (ARVC6): support for the locus assignment, narrowing of the critical region and mutation screening of three candidate genes.

PMID 16569242 · PMC1444927 · BMC medical genetics · 2006 · 7 claims · 4 setups

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Linkage and haplotype analysis in the South African family are highly suggestive of linkage to the ARVC6 locus on chromosome 10p12-p14

south genomic family genetic direct bioinformatic

Experiments

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

Missense variants in human forkhead transcription factors reveal determinants of forkhead DNA bispecificity.

SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms.

Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.

Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes.

Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

Evaluating sequence data quality from the Swift Accel-Amplicon CFTR Panel.

Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.

The estrogen hypothesis of schizophrenia implicates glucose metabolism: association study in three independent samples.

Melusin gene (ITGB1BP2) nucleotide variations study in hypertensive and cardiopathic patients.

Exome sequencing of a multigenerational human pedigree.

Genetic variation in PARL influences mitochondrial content.

Flanking p10 contribution and sequence bias in matrix based epitope prediction: revisiting the assumption of independent binding pockets.

Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation.

COMP mutation screening as an aid for the clinical diagnosis and counselling of patients with a suspected diagnosis of pseudoachondroplasia or multiple epiphyseal dysplasia.

Arrhythmogenic right ventricular cardiomyopathy type 6 (ARVC6): support for the locus assignment, narrowing of the critical region and mutation screening of three candidate genes.