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 14

System / cell line: sequenced ✕ Assay: region ✕ Clear

Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

PMID 17062162 · PMC1635044 · Virology journal · 2006 · 8 claims · 6 setups

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VACV-DUKE is most similar to VACV-ACAM2000 and VACV-CLONE3, confirming it as a Dryvax-derived isolate

vacv-duke whole-genome phylogenetic comparative
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

PMID 19796657 · PMC3568755 · Journal of microbiological methods · 2009 · 8 claims · 6 setups

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The 16S rRNA V5 hypervariable region, amplified as a short ~82-base segment, provides reliable taxonomic identification of oral bacteria against public databases like HOMD.

pooled 16s sequenced topo 16s primer taxonomic
Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

PMID 16847467 · PMC3099416 · The pharmacogenomics journal · 2007 · 8 claims · 6 setups

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NAT2 variants are homogeneously distributed across native populations of the American continent

chromosomes same inferred american pcr statistical haplotype
Genomic regions and candidate genes selected during the breeding of rice in Vietnam.

PMID 35899250 · PMC9309459 · Evolutionary applications · 2022 · 8 claims · 7 setups

Has reproduction · 75

XP-CLR and FST scans identify genomic regions with distorted allele frequency/differentiation patterns resulting from differential selective pressures between Vietnamese rice subpopulations

vietnamese indica subpopulation whole-genome whole-genome xp-clr fst
Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

PMID 19788805 · PMC2819883 · Emerging infectious diseases · 2009 · 8 claims · 7 setups

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A 7-locus MLST scheme selected from conserved housekeeping genes shared across 4 Chlamydiaceae species (7 genomes) can genotype diverse C. trachomatis reference and clinical isolates.

genome-sequenced trachomatis same concatenated whole-genome multilocus ompa
Mutation patterns of mtDNA: empirical inferences for the coding region.

PMID 18518963 · PMC2438339 · BMC evolutionary biology · 2008 · 5 claims · 3 setups

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Heteroplasmy was detected in 6.5% (3/46) of Azorean families analyzed, all caused by new point mutations with no insertions/deletions.

extended-family same direct electropherogram molecular
Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 82

An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

exemplar paired-end cleaned assembled transcriptome read novo
Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

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aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

pediatric tumor eight desmoplastic aprimes bisulfite quantitative
PCR-free method detects high frequency of genomic instability in prostate cancer.

PMID 19797393 · PMC2794161 · Nucleic acids research · 2009 · 7 claims · 6 setups

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A novel PCR-free random cloning/sequencing method can detect genomic variants that PCR-based approaches miss in heterogeneous tumor genomes.

blood normal prostate matched pcr-free degenerate-pcr blastn
Comparative genomics and understanding of microbial biology.

PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

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GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

completed same sequenced mycobacterium whole-genome comparative phylogenomic
A distinct epigenetic signature at targets of a leukemia protein.

PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups

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Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve

32d sequence gene bioinformatic real-time
Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design.

PMID 18515352 · PMC2447791 · Nucleic acids research · 2008 · 7 claims · 7 setups

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Uprobe provides new predesigned whole-genome universal overgo probe sets for screening marsupial, rodent, and carnivore BAC libraries.

wallaby squirrel deer clouded overgo bac comparative
OptiType: precision HLA typing from next-generation sequencing data.

PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

Has reproduction · 95

OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome
ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

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Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

ductal same sporadic paired cdna quantitative genotyping

Experiments

Genomic sequence and analysis of a vaccinia virus isolate from a patient with a smallpox vaccine-related complication.

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

Genomic regions and candidate genes selected during the breeding of rice in Vietnam.

Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

Mutation patterns of mtDNA: empirical inferences for the coding region.

Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

PCR-free method detects high frequency of genomic instability in prostate cancer.

Comparative genomics and understanding of microbial biology.

A distinct epigenetic signature at targets of a leukemia protein.

Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design.

OptiType: precision HLA typing from next-generation sequencing data.

ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.