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 1.7k

Assay: sequence ✕ Clear

Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

PMID 36129291 · PMC9584332 · Microbiology resource announcements · 2022 · 7 claims · 4 setups

Has reproduction · 81

A complete 30,616-nucleotide genome of Cervid atadenovirus A was determined from lung tissue of black-tailed deer that died of AHD in British Columbia in 2020

lung sequencing assembled deer high-throughput metagenomic reference
What the Phage: a scalable workflow for the identification and analysis of phage sequences.

PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups

Has reproduction · 76

WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow

assembled illumina phage-predicted predicted multitool metagenome gene
Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

PMID 10449521 · PMC2195597 · The Journal of experimental medicine · 1999 · 7 claims · 8 setups

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A novel C→A point mutation at nucleotide 850 of GCSFR cDNA causes a Pro→His substitution at position 206 (P206H) in the proline-rich hinge of the CRH domain of the G-CSF receptor extracellular domain in an SCN patient hyporesponsive to G-CSF.

bone fibroblast 32d.cl8.6 32d rt-pcr genomic flow
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
Clues to the etiology of autoimmune diseases through analysis of immunoglobulin genes.

PMID 11879542 · PMC128918 · Arthritis research · 2002 · 8 claims · 6 setups

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Antibody sequences that violate normal ontogenic/developmental constraints indicate a failure of B-cell regulation

peripheral diseased rheumatoid autoimmune immunoglobulin single-cell cloning
Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3.

PMID 11454237 · PMC34549 · BMC genetics · 2001 · 6 claims · 4 setups

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The desmuslin (DMN) gene was localized to chromosome 15q26.3 via electronic screening of the human genome database, and its 5-exon genomic organization was determined.

genomic electronic pcr pcr-restriction
Variation in the E2-binding domain of HPV 16 is associated with high-grade squamous intraepithelial lesions of the cervix.

PMID 11308254 · PMC2363853 · British journal of cancer · 2001 · 8 claims · 6 setups

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E2 gene disruption in the analysed regions is significantly more frequent in high-grade SILs than low-grade SILs

paraffin-embedded hpv16-positive representative cervical pcr restriction bidirectional
In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

PMID 12537567 · PMC151180 · Genome biology · 2002 · 6 claims · 4 setups

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Strain-specific mouse genome sequence databases can be used in a high-throughput in silico pipeline to discover gene-coding variants within murine QTLs, without de novo sequencing.

strains genomic celera blast-based targeted phred
Species-specific protein sequence and fold optimizations.

PMID 12487631 · PMC139977 · BMC bioinformatics · 2002 · 7 claims · 7 setups

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Environmental niche is a significant factor explaining variability in amino acid composition across 100 complete genomes

predicted mean over orf principal hierarchical domain-based
Finding signals that regulate alternative splicing in the post-genomic era.

PMID 12429065 · PMC244920 · Genome biology · 2002 · 8 claims · 8 setups

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Alternative splicing generates protein and regulatory diversity from a limited number of genes and modulates isoform levels in a cell-context-specific manner

intron-containing genome brain-specific cell-free computational comparative selex
Molecular archeology of L1 insertions in the human genome.

PMID 12372140 · PMC134481 · Genome biology · 2002 · 8 claims · 4 setups

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TSDfinder, a new algorithm, refines RepeatMasker-identified L1 boundaries by locating poly(A) tails, TSDs, and inversion breakpoints

genome tsd 50-nt full-length repeat sequence repeat-content
Comparative genomics.

PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups

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Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences

caenorhabditis yeast mammalian vertebrate whole-genome comparative interspecies-similarity-informed
Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

PMID 13678422 · PMC222960 · BMC bioinformatics · 2003 · 8 claims · 8 setups

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The human genome encodes at least 71 kelch-repeat proteins

genome yeast kelch-repeat full-length blast blastp cross-referencing
Recent segmental and gene duplications in the mouse genome.

PMID 12914656 · PMC193640 · Genome biology · 2003 · 8 claims · 8 setups

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33.6 Mb (1.2%) of the February 2003 mouse genome assembly (2,695 Mb) is involved in recent segmental duplications

genome gene ensembl-annotated chromosome pairwise gene blat
Getting positive about selection.

PMID 12914654 · PMC193638 · Genome biology · 2003 · 8 claims · 4 setups

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Purifying selection is the predominant form of molecular evolution, preserving fitness by eliminating deleterious mutations, while positive selection is rare but critical for adaptation.

genome chimpanzee human-chimpanzee humans whole-genome ratio maximum-likelihood
Identifying related L1 retrotransposons by analyzing 3' transduced sequences.

PMID 12734010 · PMC156586 · Genome biology · 2003 · 8 claims · 6 setups

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L1 elements with transduction-derived 3' sequence (L1-TDs) can be computationally identified using RepeatMasker/TSDfinder and grouped into families sharing a common progenitor via BLAST comparison of downstream sequences.

genome database l1-td ncbi genome-wide blast pairwise
Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence.

PMID 12702206 · PMC154576 · Genome biology · 2003 · 8 claims · 6 setups

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Segmental duplications comprise 3.53% (107.4/3,043.1 Mb) of the June 2002 human genome assembly

genome refseq-annotated chromosome chromosome-wide e-pcr ambsnp
Chromosomal phenotypes and submicroscopic abnormalities.

PMID 15601540 · PMC3525070 · Human genomics · 2004 · 8 claims · 8 setups

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Microdeletion syndromes are flanked by region-specific low-copy repeats (LCRs), and non-allelic homologous recombination (NAHR) between these LCRs, via interchromosomal or intrachromosomal mechanisms, causes the deletions.

patients parents vegf164 zebrafish breakpoint parental inversion
Genome-wide analysis of the human Alu Yb-lineage.

PMID 15588477 · PMC3525081 · Human genomics · 2004 · 8 claims · 6 setups

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1,733 Alu Yb-lineage elements are present on human autosomal chromosomes

genome genomic non-human yb7 computational pcr-based pcr
Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

bac genome metaphase overlapping manual repeat fluorescence

Experiments

Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

What the Phage: a scalable workflow for the identification and analysis of phage sequences.

Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

Comparative genomics and understanding of microbial biology.

Clues to the etiology of autoimmune diseases through analysis of immunoglobulin genes.

Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3.

Variation in the E2-binding domain of HPV 16 is associated with high-grade squamous intraepithelial lesions of the cervix.

In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

Species-specific protein sequence and fold optimizations.

Finding signals that regulate alternative splicing in the post-genomic era.

Molecular archeology of L1 insertions in the human genome.

Comparative genomics.

Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

Recent segmental and gene duplications in the mouse genome.

Getting positive about selection.

Identifying related L1 retrotransposons by analyzing 3' transduced sequences.

Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence.

Chromosomal phenotypes and submicroscopic abnormalities.

Genome-wide analysis of the human Alu Yb-lineage.

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.