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 36

System / cell line: strain ✕ Assay: nucleotide ✕ Clear

Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories.

PMID 18712842 · PMC2906129 · Journal of medical virology · 2008 · 8 claims · 5 setups

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Coverage of naturally occurring BKV strains varies substantially among current PCR diagnostic assays due to primer/probe mismatches

bkv virus sequence primer cross-reactivity
HIV-1 sequence evolution in vivo after superinfection with three viral strains.

PMID 17716368 · PMC2020475 · Retrovirology · 2007 · 8 claims · 8 setups

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gag and env-V3 nucleotide evolution follows a similar pattern in all three strains: low substitution rate in the first 2-3 years of infection, then an increase driven mainly by synonymous substitutions

blood seminal pbmcs biological strain-specific bulk in-house
Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.

PMID 16700631 · PMC1463904 · PLoS medicine · 2006 · 8 claims · 6 setups

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The Indian Ocean outbreak was initiated by a strain related to East African CHIKV isolates, which subsequently evolved via a traceable microevolution history

chikv partial pseudoscutellaris mosquito nucleotide phylogenetic focus
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
Recombinant vaccine-derived poliovirus in Madagascar.

PMID 12899139 · PMC3023450 · Emerging infectious diseases · 2003 · 7 claims · 4 setups

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Five acute flaccid paralysis cases in southern Madagascar were associated with vaccine-derived poliovirus (VDPV) type 2 isolates

poliovirus genbank rflp partial sequence
Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

PMID 17784912 · PMC2169797 · Molecular microbiology · 2007 · 8 claims · 6 setups

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MG192 is highly variable among and within M. genitalium strains both in vitro and in vivo

genitalium clinical urine pairwise pcr serial
Genetic variation of St. Louis encephalitis virus.

PMID 18632961 · PMC2696384 · The Journal of general virology · 2008 · 8 claims · 4 setups

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Phylogenetic analysis of 106 SLEV E gene sequences confirms seven major lineages (I-VII) and refines them into 13 clades (IA, IB, IIA, IIB, IIC, IID, IIG, III, IV, VA, VB, VI, VII)

slev rt-pcr phylogenetic recombination
Comparing whole genomes using DNA microarrays.

PMID 18347592 · PMC7097741 · Nature reviews. Genetics · 2008 · 8 claims · 6 setups

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DNA microarrays offer a relatively inexpensive and efficient alternative to genome sequencing for comparing all known classes of genomic diversity between closely related genomes.

genome saccharomyces mitochondrial sars array comparative resequencing
Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.

PMID 19922637 · PMC2784780 · Virology journal · 2009 · 7 claims · 6 setups

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A new intragenotypic recombinant HCV strain (1b/1a), named H23, was detected in 1 of 10 hemophiliac patients studied

hcv 5'ncr serum maximum sequence recombination
Rise of the machines.

PMID 18670625 · PMC2467494 · PLoS genetics · 2008 · 8 claims · 4 setups

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New short-read sequencing platforms (Illumina Genome Analyzer, 454 FLX, ABI SOLiD) enable rapid, scalable whole-genome resequencing that was previously restricted to dedicated sequencing centers using Sanger methods.

bacillus independent subtilis whole-genome read
Tuberculosis vaccine strain Mycobacterium bovis BCG Russia is a natural recA mutant.

PMID 18637199 · PMC2483709 · BMC microbiology · 2008 · 8 claims · 5 setups

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A RecA- phenotype increases genetic stability and may help restrict ongoing genome evolution of BCG substrains while maintaining protective efficacy

bovis bcg genomic cell-free allelic southern sequencing
Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.

PMID 18992264 · PMC2682550 · Mutation research · 2009 · 8 claims · 8 setups

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A combined functional assay, bioinformatics prediction, and structural modeling approach can classify BRCA1 variants of uncertain significance

saccharomyces cerevisiae hek-293t yeast yeast β-galactosidase dual
Genetic determinants of virulence in pathogenic lineage 2 West Nile virus strains.

PMID 18258114 · PMC2600181 · Emerging infectious diseases · 2008 · 8 claims · 7 setups

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The nonstructural genes, especially NS5, are the most variable regions between highly and less neuroinvasive lineage 2 WNV strains

lineage mice patients complete phylogenetic nucleotide
Genome Sequencing of Methicillin-Resistant and Methicillin-Susceptible Mammaliicoccus sciuri from Diseased Animals.

PMID 36125295 · PMC9583799 · Microbiology resource announcements · 2022 · 7 claims · 7 setups

Has reproduction · 92

Draft genomes of a methicillin-resistant Mammaliicoccus sciuri strain (2254A, from an armadillo) and a methicillin-susceptible strain (6942A, from a cow) are reported.

sciuri bacterial assembled 2254a long-read maldi-tof genome
Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

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Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr
Comparative Genome Analysis of 16SrXII-A 'Candidatus Phytoplasma solani' POT Transmitted by Hyalesthes obsoletus.

PMID 41597744 · PMC12843639 · Microorganisms · 2026 · 7 claims · 8 setups

Has reproduction · 95

The complete 832,614 bp circular chromosome of the H. obsoletus-transmissible 'Ca. P. solani' 16SrXII-A strain POT was assembled and functionally reconstructed.

catharanthus pacbio smrt pot experimental endpoint smrt
N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

PMID 36422864 · PMC9731578 · eLife · 2022 · 8 claims · 8 setups

Has reproduction · 55

Pho92 specifically binds m6A-modified RNA via its YTH domain, both in vitro and in vivo

cerevisiae diploid yeast recombinant affinity rt-qpcr chip-seq
Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018.

PMID 36925474 · PMC10011098 · Frontiers in microbiology · 2023 · 8 claims · 8 setups

Has reproduction · 74

The STM 6018 genome contains two prophages: a complete Mu-like capsular phage and a filamentous phage that integrates into a putative dif site.

cupriavidus stm taiwanensis genome 16s average
Genetic variation of SARS coronavirus in Beijing Hospital.

PMID 15200810 · PMC3323231 · Emerging infectious diseases · 2004 · 8 claims · 4 setups

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113 sequence variations at 9 recurrent variant sites were identified in 29 full-length S-gene sequences compared to the BJ01 reference strain

clinical extracted rna-derived cloned nested screening direct
Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.

PMID 18053243 · PMC2225410 · BMC infectious diseases · 2007 · 7 claims · 5 setups

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The P120' surface-exposed N-terminal region undergoes substantial genetic variability among Tunisian M. hominis clinical isolates

cloned clinical hominis pcr culture sanger

Experiments

Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories.

HIV-1 sequence evolution in vivo after superinfection with three viral strains.

Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.

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

Recombinant vaccine-derived poliovirus in Madagascar.

Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

Genetic variation of St. Louis encephalitis virus.

Comparing whole genomes using DNA microarrays.

Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.

Rise of the machines.

Tuberculosis vaccine strain Mycobacterium bovis BCG Russia is a natural recA mutant.

Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.

Genetic determinants of virulence in pathogenic lineage 2 West Nile virus strains.

Genome Sequencing of Methicillin-Resistant and Methicillin-Susceptible Mammaliicoccus sciuri from Diseased Animals.

Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

Comparative Genome Analysis of 16SrXII-A 'Candidatus Phytoplasma solani' POT Transmitted by Hyalesthes obsoletus.

N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018.

Genetic variation of SARS coronavirus in Beijing Hospital.

Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.