Corey R. Quackenbush
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View article: Defining criteria for broadly neutralizing HIV antibodies
Defining criteria for broadly neutralizing HIV antibodies Open
Over the course of a few years, a small percentage of individuals with HIV-1 develop broadly neutralizing antibodies (bnAbs) capable of neutralizing diverse viruses. Although hundreds of antibodies with neutralizing activity against hetero…
View article: In Vitro Evolution and Computational Approaches to Predict, Prevent and Control Future Pandemics
In Vitro Evolution and Computational Approaches to Predict, Prevent and Control Future Pandemics Open
The natural tendency of virus to mutate and the under-sampling of the environment makes it difficult to become aware of the emergence of new viral strains with pandemic potential. Being able to predict what mutations make a virus more infe…
View article: Orally available nucleoside analog UMM-766 provides protection in a murine model of orthopox disease
Orally available nucleoside analog UMM-766 provides protection in a murine model of orthopox disease Open
Although smallpox has been eradicated, other orthopoxviruses continue to be a public health concern as exemplified by the ongoing Mpox (formerly monkeypox) global outbreak. While medical countermeasures (MCMs) previously approved by the Fo…
View article: A multi-tissue gene expression dataset for hibernating brown bears
A multi-tissue gene expression dataset for hibernating brown bears Open
Objectives Complex physiological adaptations often involve the coordination of molecular responses across multiple tissues. Establishing transcriptomic resources for non-traditional model organisms with phenotypes of interest can provide a…
View article: Data files for bear multi-tissue transcriptomic dataset
Data files for bear multi-tissue transcriptomic dataset Open
Supplementary data files accompanying a dataset comprised of 26 samples collected from 13 tissues of two hibernating brown bears. Raw data are available on NCBI BioProject: PRJNA835146.
View article: Epigenetic inheritance of DNA methylation changes in fish living in hydrogen sulfide–rich springs
Epigenetic inheritance of DNA methylation changes in fish living in hydrogen sulfide–rich springs Open
Significance Environmental factors can promote phenotypic variation through alterations in the epigenome and mediate adaptation of an organism to the environment. Observations suggest the adaptation of Poecilia mexicana fish to toxic, hydr…
View article: Comparative transcriptomic analysis reveals key components controlling spathe color in<i>Anthurium andraeanum</i>(Hort.)
Comparative transcriptomic analysis reveals key components controlling spathe color in<i>Anthurium andraeanum</i>(Hort.) Open
Anthurium andraeanum (Hort.) is an important ornamental in the tropical cut-flower industry. However, there is currently not enough information to establish a clear connection between the genetic model(s) proposed and the putative genes in…
View article: Antipsychotic-induced vacuous chewing movements and extrapyramidal side effects are highly heritable in mice
Antipsychotic-induced vacuous chewing movements and extrapyramidal side effects are highly heritable in mice Open
Pharmacogenomics is yet to fulfill its promise of manifestly altering clinical medicine. As one example, a predictive test for tardive dyskinesia (an adverse drug reaction consequent to antipsychotic exposure) could greatly improve the cli…
View article: The Antipsychotic Olanzapine Interacts with the Gut Microbiome to Cause Weight Gain in Mouse
The Antipsychotic Olanzapine Interacts with the Gut Microbiome to Cause Weight Gain in Mouse Open
The second-generation antipsychotic olanzapine is effective in reducing psychotic symptoms but can cause extreme weight gain in human patients. We investigated the role of the gut microbiota in this adverse drug effect using a mouse model.…
View article: Genetics of Adverse Reactions to Haloperidol in a Mouse Diallel: A Drug–Placebo Experiment and Bayesian Causal Analysis
Genetics of Adverse Reactions to Haloperidol in a Mouse Diallel: A Drug–Placebo Experiment and Bayesian Causal Analysis Open
Haloperidol is an efficacious antipsychotic drug that has serious, unpredictable motor side effects that limit its utility and cause noncompliance in many patients. Using a drug–placebo diallel of the eight founder strains of the Collabora…
View article: No association of the serotonin transporter polymorphisms 5-HTTLPR and RS25531 with schizophrenia or neurocognition
No association of the serotonin transporter polymorphisms 5-HTTLPR and RS25531 with schizophrenia or neurocognition Open
A promoter polymorphism in the serotonin transporter gene has been widely studied in neuropsychiatry. We genotyped the 5-HTTLPR/rs25531 triallelic polymorphism in 728 schizophrenia cases from the CATIE study and 724 control subjects. In a …
View article: Antipsychotic Behavioral Phenotypes in the Mouse Collaborative Cross Recombinant Inbred Inter-Crosses (RIX)
Antipsychotic Behavioral Phenotypes in the Mouse Collaborative Cross Recombinant Inbred Inter-Crosses (RIX) Open
Schizophrenia is an idiopathic disorder that affects approximately 1% of the human population, and presents with persistent delusions, hallucinations, and disorganized behaviors. Antipsychotics are the standard pharmacological treatment fo…
View article: Author Correction: Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear
Author Correction: Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear Open
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View article: Transcriptomics of Tasmanian Devil (Sarcophilus Harrisii) Ear Tissue Reveals Homogeneous Gene Expression Patterns across a Heterogeneous Landscape
Transcriptomics of Tasmanian Devil (Sarcophilus Harrisii) Ear Tissue Reveals Homogeneous Gene Expression Patterns across a Heterogeneous Landscape Open
In an era of unprecedented global change, exploring patterns of gene expression among wild populations across their geographic range is crucial for characterizing adaptive potential. RNA-sequencing studies have successfully characterized g…
View article: Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear
Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear Open
Revealing the mechanisms underlying the reversible physiology of hibernation could have applications to both human and animal health as hibernation is often associated with disease-like states. The present study uses RNA-sequencing to reve…
View article: Antipsychotic behavioral phenotypes in the mouse Collaborative Cross recombinant inbred inter-crosses (RIX)
Antipsychotic behavioral phenotypes in the mouse Collaborative Cross recombinant inbred inter-crosses (RIX) Open
Schizophrenia is an idiopathic disorder that affects approximately 1% of the human population, and presents with persistent delusions, hallucinations, and disorganized behaviors. Antipsychotics are the standard pharmacological treatment fo…
View article: Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao
Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao Open
As the source of chocolate, cacao has become one of the most important crops in the world. The identification of molecular markers to understand the demographic history, genetic diversity and population structure plays a pivotal role in ca…
View article: Ancestry informative alleles captured with reduced representation library sequencing in <i>Theobroma cacao</i>
Ancestry informative alleles captured with reduced representation library sequencing in <i>Theobroma cacao</i> Open
As the source of chocolate, cacao has become one of the most important crops in the world. The identification of molecular markers to understand the demographic history, genetic diversity and population structure plays a pivotal role in ca…
View article: Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence
Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence Open
Background Previous genomewide association studies ( GWAS s) have identified a number of putative risk loci for alcohol dependence ( AD ). However, only a few loci have replicated and these replicated variants only explain a small proporti…
View article: Additional file 3: Figure S2. of Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar
Additional file 3: Figure S2. of Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar Open
Results from differential expression analysis of female and male muscle tissue. A) MA plot for each transcript comparing the log2 fold-change versus the average transcript expression. Each dot represents a transcript and the significantly …
View article: Additional file 1: of Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar
Additional file 1: of Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar Open
Table S1. Extraction and library preparation details for each sample. Table S2. Top-matching unique BLAST alignments to SwissProt database separated by percent length coverage. Table S3. Top-matching unique BLAST alignments to SwissProt da…
View article: Additional file 2: Figure S1. of Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar
Additional file 2: Figure S1. of Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar Open
Results from differential expression analysis of female and male brain tissue. A) MA plot for each transcript comparing the log2 fold-change versus the average transcript expression. Each dot represents a transcript and the significantly d…