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 115

System / cell line: pcr ✕ Assay: species ✕ Clear

Initial characterization of Chlamydophila (Chlamydia) pneumoniae cultured from the late-onset Alzheimer brain.

PMID 18829386 · PMC2730674 · International journal of medical microbiology : IJMM · 2009 · 6 claims · 7 setups

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C. pneumoniae was cultured from two late-onset AD brain tissue samples (Tor-1 from hippocampus, Phi-1 from temporal cortex) from different North American regions.

tor-1 brain hep-2 pcr culture immunofluorescence
Plasmodium vivax dhfr and dhps mutations in isolates from Madagascar and therapeutic response to sulphadoxine-pyrimethamine.

PMID 18302746 · PMC2268703 · Malaria journal · 2008 · 6 claims · 7 setups

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pvdhfr and pvdhps mutations are common in Malagasy P. vivax isolates, with pvdhfr mutants far more prevalent than pvdhps mutants

vivax vivax-infected paired patients gene real-time microsatellite
Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

PMID 16725047 · PMC1482685 · Virology journal · 2006 · 6 claims · 4 setups

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Mouse liver mRNA cross-hybridizes to corresponding human gene probes on the Agilent Human 22K oligonucleotide microarray

liver genomic hcv-infected agilent two-color semi-quantitative real-time
Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

PMID 16805923 · PMC1779541 · Genome biology · 2006 · 8 claims · 6 setups

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The chimpanzee genome contains at least 42 separate families of endogenous retroviruses, 9 newly identified

chimpanzee domains genomic hg16 genome-wide sequence ltr-ltr
RPS4Y gene family evolution in primates.

PMID 18477388 · PMC2397393 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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The duplication event giving rise to RPS4Y2 occurred after the divergence of New World monkeys, about 35 million years ago.

primate chromosomes rps4x concatenated pcr fluorescence repeat
Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.

PMID 40990923 · PMC12687342 · Evolution; international journal of organic evolution · 2025 · 8 claims · 5 setups

Has reproduction · 64

The LWS opsin gene was identified in 13 species of caecilians spanning 8 of 10 recognized families

caecilian caecilia archival lws pcr eye histology
Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

PMID 15269786 · PMC479043 · PLoS biology · 2004 · 7 claims · 6 setups

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APOBEC3G has been under strong, recurrent positive selection throughout primate evolution (~33 million years)

apobec3g pairwise human-chimpanzee apobec1 pcr phylogenetic sliding
Genomic signatures of human versus avian influenza A viruses.

PMID 17073083 · PMC3294750 · Emerging infectious diseases · 2006 · 8 claims · 6 setups

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52 validated 'species-associated' amino acid positions distinguish human from avian influenza A viruses

throat clinical 401-genome avian rt-pcr immunofluorescent sequence
Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

PMID 17029642 · PMC1635982 · BMC genomics · 2006 · 8 claims · 7 setups

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The number of index-species (IS) mismatches in a primer pair significantly reduces amplification success, with an estimated 6-8% decrease in success rate per additional mismatch.

dog hamster pcr primer pcr blast sequence
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

PMID 17299583 · PMC1797623 · PloS one · 2007 · 6 claims · 4 setups

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5′-tagged PCR primers enable pooling of homologous PCR products from multiple sources into a single GS20 run with accurate post-hoc assignment of sequences to source

extracts pooled same non-assigned pcr parallel conventional
The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

PMID 19094205 · PMC2637867 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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AR was duplicated into two paralogs, AR-A and AR-B, during a teleost-specific whole genome duplication (WGD), after the split of Acipenseriformes but before the divergence of Osteoglossiformes.

fish full-length tetraodon rt-pcr database molecular
Sequencing of 16S rRNA gene: a rapid tool for identification of Bacillus anthracis.

PMID 12396926 · PMC2730316 · Emerging infectious diseases · 2002 · 7 claims · 4 setups

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All 86 B. anthracis isolates tested share an identical 16S rRNA gene sequence, designated 16S type 6

bacillus clinical additional 16s nested comparative
Spotted-fever group Rickettsia in Dermacentor variabilis, Maryland.

PMID 15496254 · PMC3320417 · Emerging infectious diseases · 2004 · 8 claims · 6 setups

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SFG Rickettsia infection prevalence in Maryland D. variabilis was 3.8% (15/392)

dermacentor tick-derived glta field pcr single sequencing
Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription.

PMID 26618080 · PMC4655093 · PeerJ · 2015 · 8 claims · 8 setups

Has reproduction · 68

Siphonophorae is the first diverging clade within Hydroidolina.

hydroidolinan nanomia liriope assembled long-range rna-seq dna-seq
Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.

PMID 35044202 · PMC8768832 · Microbiology spectrum · 2022 · 8 claims · 7 setups

Has reproduction · 79

AgrVATE, a novel kmer-based BLASTn and in silico PCR/Snippy pipeline, enables fast, standardized agr group typing and frameshift/null mutation detection from genome assemblies

aureus complete extracted agr kmer-based sheep mash
Genetic diversity and distribution of Peromyscus-borne hantaviruses in North America.

PMID 10081674 · PMC2627704 · Emerging infectious diseases · 1999 · 8 claims · 5 setups

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SNV-like hantaviruses are widely distributed in Peromyscus species rodents throughout North America

hantavirus-infected aligned phylogenetic archival rt-pcr maximum bootstrap
Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease.

PMID 18974839 · PMC2572839 · PloS one · 2008 · 7 claims · 6 setups

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Pseudomonas 16S rDNA is significantly more prevalent in ileal biopsies of CD patients than non-IBD patients

ileal p16s otu pseudomonas nested cloning
Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

vertebrate cdna pedf complete genomic rt-pcr phylogenetic
Mixed Cryptosporidium infections and HIV.

PMID 16707069 · PMC3373040 · Emerging infectious diseases · 2006 · 7 claims · 5 setups

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Mixed Cryptosporidium infections were detected in 7 of 21 patients originally diagnosed with only C. canis or C. felis

stool nested ssu sequencing
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous

Experiments

Initial characterization of Chlamydophila (Chlamydia) pneumoniae cultured from the late-onset Alzheimer brain.

Plasmodium vivax dhfr and dhps mutations in isolates from Madagascar and therapeutic response to sulphadoxine-pyrimethamine.

Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

RPS4Y gene family evolution in primates.

Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.

Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

Genomic signatures of human versus avian influenza A viruses.

Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

Sequencing of 16S rRNA gene: a rapid tool for identification of Bacillus anthracis.

Spotted-fever group Rickettsia in Dermacentor variabilis, Maryland.

Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription.

Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.

Genetic diversity and distribution of Peromyscus-borne hantaviruses in North America.

Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease.

Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

Mixed Cryptosporidium infections and HIV.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.