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Article
Open AccessInvestigating the effects of chronic low-dose radiation exposure in the liver of a hypothermic zebrafish model
Mankind’s quest for a manned mission to Mars is placing increased emphasis on the development of innovative radio-protective countermeasures for long-term space travel. Hibernation confers radio-protective eff...
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Article
Novelty-induced locomotor behavior predicts heroin addiction vulnerability in male, but not female, rats
The ongoing rise in opioid use disorder (OUD) has made it imperative to better model the individual variation within the human population that contributes to OUD vulnerability. Using animal models that capture...
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Article
Open AccessTreatment with soluble CD24 attenuates COVID-19-associated systemic immunopathology
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19) through direct lysis of infected lung epithelial cells, which releases damage-associated molecular patter...
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Article
Open AccessPALMER: improving pathway annotation based on the biomedical literature mining with a constrained latent block model
In systems biology, it is of great interest to identify previously unreported associations between genes. Recently, biomedical literature has been considered as a valuable resource for this purpose. While clas...
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Protocol
Molecular Profiling of RNA Tumors Using High-Throughput RNA Sequencing: From Raw Data to Systems Level Analyses
RNAseq is a powerful technique enabling global profiles of transcriptomes in healthy and diseased states. In this chapter we review pipelines to analyze the data generated by sequencing RNA, from raw data to a...
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Chapter
Identification of Pathway-Modulating Genes Using the Biomedical Literature Mining
Although biomedical literature is considered as a valuable resource to investigate the relationship among genes, it still remains challenging to effectively use it for the identification of the relationships a...
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Chapter
MOSAiCS-HMM: A Model-Based Approach for Detecting Regions of Histone Modifications from ChIP-Seq Data
Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) experiments are routinely utilized for studying epigenomics of transcriptional regulation. We review some of the important statis...
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Protocol
Statistical Analysis of ChIP-seq Data with MOSAiCS
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is invaluable for identifying genome-wide binding of transcription factors and map** of epigenomic profiles. We present a stati...
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Chapter
eQTL Map** for Functional Classes of Saccharomyces cerevisiae Genes with Multivariate Sparse Partial Least Squares Regression
The availability of high-throughput genoty** technologies and microarray assays has enabled investigation of genetic variations that influence levels of gene expression. Expression Quantitative Trait Loci (e...
