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Acorn: an R package for de novo variant analysis
BackgroundThe study of de novo variation is important for assessing biological characteristics of new variation and for studies related to human...
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Transcriptome Data Analysis Using a De Novo Assembly Approach
Characterization and profiling of the gene expression data or, more formally, called transcriptome are crucial steps in revealing the involvement of...
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Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions
Existing methods for analysis of spatial transcriptomic data focus on delineating the global gene expression variations of cell types across the...
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GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership
Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell...
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De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms – a brief guide
Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the...
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Mass Spectrometric De Novo Sequencing of Natural Peptides
Natural peptides secreted under stress conditions by many organisms are bioactive molecules with a broad spectrum of activities. These molecules...
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The Production of Space in the Frontiers of Tourism: Critical Analysis of the Huella de Glaciares Circuit Between El Chaltén, Argentina, and Villa O’Higgins, Chile
Nature-based tourism (NBT) has been positioned as being aligned with conservationconservation objectives and capable of contributing to socialsocial...
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De-Insertion Current Analysis of Pore-Forming Peptides and Proteins Using Gold Electrode-Supported Lipid Bilayer
Analysis of the pore formation mechanisms of transmembrane peptides and proteins potentially provides an insight into cellular biology because of...
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Differential expression of miRNAs associated with pectoral myopathies in young broilers: insights from a comparative transcriptome analysis
IntroductionWhite Stri** (WS) and Wooden Breast (WB) pectoral myopathies are relevant disorders for contemporary broiler production worldwide....
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Expression analysis suggests that DNMT3L is required for oocyte de novo DNA methylation only in Muridae and Cricetidae rodents
BackgroundDuring early mammalian development, DNA methylation undergoes two waves of reprogramming, enabling transitions between somatic cells,...
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Identification and co-expression analysis of temperature responsive circRNAs in tea plant
Circular RNAs (circRNAs) are recently known to regulate various biological processes associated with developmental transitions and stress condition...
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An External Memory Approach for Large Genome De Novo Assembly
De novo genome assembly of sequenced reads is a fundamental problem in bioinformatics. When there is no reference genome sequence to guide the...
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On two-stage analysis of multi-environment trials
Two-stage analysis methods are often used in multi-environment trials (MET) for plant variety selection, when a single-stage approach is not feasible...
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Classifying breast cancer subtypes on multi-omics data via sparse canonical correlation analysis and deep learning
BackgroundClassifying breast cancer subtypes is crucial for clinical diagnosis and treatment. However, the early symptoms of breast cancer may not be...
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Large-scale analysis of de novo mutations identifies risk genes for female infertility characterized by oocyte and early embryo defects
BackgroundOocyte maturation arrest and early embryonic arrest are important reproductive phenotypes resulting in female infertility and cause the...
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Comparative de novo transcriptome analysis and random UV mutagenesis: application in high biomass and astaxanthin production enhancement for Haematococcus pluvialis
BackgroundAstaxanthin is a natural carotenoid with strong antioxidant capacity. The high demand on astaxanthin by cosmetic, food, pharmaceutical and...
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Mitochondrial DNA Sequencing and BLAST Analysis Reveal Visual Misidentification of Nonhuman Primates Suspected to have Died of Yellow Fever in Brazil in 2017–2020
Epidemics have significant impacts on primate populations. In 2016, yellow fever spread rapidly to the most densely populated states of Brazil,...
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Integrated analysis of lncRNA/circRNA–miRNA–mRNA in the proliferative phase of liver regeneration in mice with liver fibrosis
BackgroundNon-coding RNAs play important roles in liver regeneration; however, their functions and mechanisms of action in the regeneration of...
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Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome
BackgroundRecent studies uncovered pervasive transcription and translation of thousands of noncanonical open reading frames (nORFs) outside of...
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RNA-Seq Data Analysis
RNA-Seq data analysis stands as a vital part of genomics research, turning vast and complex datasets into meaningful biological insights. It is a...