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 483

System / cell line: variants ✕ Clear

Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

PMID 19759830 · PMC2736399 · PloS one · 2009 · 8 claims · 7 setups

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Statistical evidence of genetic compartmentalization between lung and blood HIV-1 env sequences was found in 10 of 18 subjects.

paired lung tissue-pair pooled hiv-1 maximum statistical
Application of proteomics methods for pathogen discovery.

PMID 19751767 · PMC7119679 · Journal of virological methods · 2010 · 8 claims · 6 setups

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Proteomic techniques can detect and characterize unknown infectious agents in cell culture without prior knowledge of the pathogen

hlf sequences synthetic conventional 2d-dige gelc-ms
Disease-causing mutations in the CLRN1 gene alter normal CLRN1 protein trafficking to the plasma membrane.

PMID 19753315 · PMC2742642 · Molecular vision · 2009 · 8 claims · 5 setups

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Wild-type HA-tagged CLRN1 is correctly trafficked to the plasma membrane in transfected BHK-21 cells

bhk-21 genomic ush confocal western cycloheximide
Genomic views of distant-acting enhancers.

PMID 19741700 · PMC2923221 · Nature · 2009 · 8 claims · 8 setups

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Meta-analysis of ~1200 top GWAS SNPs found that in 40% of cases (472/1170) no known exons overlap the linked SNP or its haplotype block, implying noncoding variation causally contributes to many traits.

genome patients embryos ret gwas targeted transgenic
A MANBA mutation resulting in residual beta-mannosidase activity associated with severe leukoencephalopathy: a possible pseudodeficiency variant.

PMID 19728872 · PMC2745377 · BMC medical genetics · 2009 · 8 claims · 7 setups

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A novel homozygous missense mutation, c.1922G>A (p.Arg641His), in MANBA was identified in a patient with severe neurological disease featuring pyramidal and cerebellar involvement, a phenotype not previously reported in β-mannosidosis.

family hek293t lymphoid pcr-amplified fluorometric site-directed western
Frequency of single nucleotide polymorphisms in NOD1 gene of ulcerative colitis patients: a case-control study in the Indian population.

PMID 19723304 · PMC2748065 · BMC medical genetics · 2009 · 7 claims · 4 setups

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Three NOD1 Exon 6 SNPs (W219R, L349P, L370R) show statistically significant association with ulcerative colitis compared to controls

genomic pcr patients dhplc cloning pcr-rflp
Severe insulin resistance and intrauterine growth deficiency associated with haploinsufficiency for INSR and CHN2: new insights into synergistic pathways involved in growth and metabolism.

PMID 19720790 · PMC2780873 · Diabetes · 2009 · 7 claims · 8 setups

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INSR is disrupted by the chromosome 19 breakpoint, causing INSR haploinsufficiency (monoallelic expression) that explains the insulin resistance/dysglycemia phenotype

metaphase genomic ebv-transformed serum fluorescence multiplex sanger
Congenital bovine spinal dysmyelination is caused by a missense mutation in the SPAST gene.

PMID 19714378 · PMC2854348 · Neurogenetics · 2010 · 8 claims · 5 setups

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A missense mutation (R560Q) in the SPAST gene's ATPase domain causes bovine spinal dysmyelination

cattle bovine coli affinity-purified snp reverse cdna
A novel gammaD-crystallin mutation causes mild changes in protein properties but leads to congenital coralliform cataract.

PMID 19668596 · PMC2722711 · Molecular vision · 2009 · 8 claims · 6 setups

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A novel heterozygous CRYGD mutation c.43C>A (R15S) causes congenital coralliform cataract in Family A

family genomic crygd lens two-point microsatellite direct
Single-molecule sequencing of an individual human genome.

PMID 19668243 · PMC4117198 · Nature biotechnology · 2009 · 8 claims · 7 setups

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Single-molecule sequencing without cloning, amplification or ligation can sequence an individual human genome on one instrument by a single operator in four runs

genome staphylococcus single-molecule snp sanger
Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.

PMID 40281430 · PMC12032694 · BMC genomics · 2025 · 7 claims · 8 setups

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A large repository of nascent run-on RNA-seq samples (DBNascent) was assembled and uniformly processed to identify sites of bidirectional transcription genome-wide.

bidirectional across high-quality nascent comparative eqtl
polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.

PMID 36792366 · PMC9985148 · Genome biology and evolution · 2023 · 8 claims · 8 setups

Has reproduction · 71

polishCLR is a reproducible, containerized Nextflow workflow that implements best practices for polishing PacBio CLR genome assemblies.

helicoverpa alternate contigs assemblies long-read short-read duplicate
A workflow reproducibility scale for automatic validation of biological interpretation results.

PMID 37150537 · PMC10164546 · GigaScience · 2022 · 8 claims · 4 setups

Has reproduction · 100

Comparing output files by checksum alone is insufficient to verify reproducibility, since checksums can differ even when the underlying biological interpretation is unchanged

nf-core sam vcf workflow checksum biological workflow
Discrimination of three mutational events that result in a disruption of the R122 primary autolysis site of the human cationic trypsinogen (PRSS1) by denaturing high performance liquid chromatography.

PMID 11734061 · PMC60523 · BMC genetics · 2001 · 7 claims · 3 setups

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DHPLC can readily discriminate the two known mutational events (c.365G>A and c.365~366GC>AT) that both cause the R122H mutation

genomic pcr independently pcr denaturing direct
High frequency of mitochondrial genome instability in human endometrial carcinomas.

PMID 12915881 · PMC2376924 · British journal of cancer · 2003 · 7 claims · 3 setups

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56% (28 out of 50) of endometrial carcinoma cases carry one or more somatic mtDNA changes (deletion, point mutation, or mtMSI) compared with matched normal tissue

endometrial paraffin-embedded long-range pcr polyacrylamide
Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13).

PMID 15234325 · PMC7129141 · International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2004 · 7 claims · 3 setups

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Human aminopeptidase N (APN/CD13/ANPEP) is the receptor for human coronavirus 229E (HCoV-229E)

genomic cloned consensus pcr molecular sequence
BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools.

PMID 15757512 · PMC555852 · Retrovirology · 2005 · 8 claims · 3 setups

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BioAfrica's HIV-1 Proteomics Resource integrates protein structure, gene expression, post-translational modification, functional activity and protein-macromolecule interaction data with bioinformatics tools in a single website.

hiv-1 motif sequence literature-derived
PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

PMID 16620382 · PMC1459209 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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PedGenie is a valid, flexible statistical tool for genetic association analysis in pedigrees of arbitrary size and structure using Monte Carlo significance testing

simulated gaw12 breast monte pedigree-based genetic
Rare germline mutations in the BRCA2 gene are associated with early-onset prostate cancer.

PMID 17700570 · PMC2360390 · British journal of cancer · 2007 · 8 claims · 3 setups

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Germline protein-truncating BRCA2 mutations confer an elevated relative risk (~7.8-fold) of early-onset prostate cancer in Caucasian men

peripheral population-based same germline epidemiological genotype-phenotype
Absence of mutations in NR2E1 and SNX3 in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes.

PMID 17655765 · PMC1950490 · BMC medical genetics · 2007 · 8 claims · 3 setups

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No coding mutations were found in NR2E1 or SNX3 in five patients with MMEP or related phenotypes

patients unaffected sanger restriction

Experiments

Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

Application of proteomics methods for pathogen discovery.

Disease-causing mutations in the CLRN1 gene alter normal CLRN1 protein trafficking to the plasma membrane.

Genomic views of distant-acting enhancers.

A MANBA mutation resulting in residual beta-mannosidase activity associated with severe leukoencephalopathy: a possible pseudodeficiency variant.

Frequency of single nucleotide polymorphisms in NOD1 gene of ulcerative colitis patients: a case-control study in the Indian population.

Severe insulin resistance and intrauterine growth deficiency associated with haploinsufficiency for INSR and CHN2: new insights into synergistic pathways involved in growth and metabolism.

Congenital bovine spinal dysmyelination is caused by a missense mutation in the SPAST gene.

A novel gammaD-crystallin mutation causes mild changes in protein properties but leads to congenital coralliform cataract.

Single-molecule sequencing of an individual human genome.

Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.

polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.

A workflow reproducibility scale for automatic validation of biological interpretation results.

Discrimination of three mutational events that result in a disruption of the R122 primary autolysis site of the human cationic trypsinogen (PRSS1) by denaturing high performance liquid chromatography.

High frequency of mitochondrial genome instability in human endometrial carcinomas.

Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13).

BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools.

PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

Rare germline mutations in the BRCA2 gene are associated with early-onset prostate cancer.

Absence of mutations in NR2E1 and SNX3 in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes.