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"Methods for extraction, manipulation, and characterization of nucleic acids, peptides, and proteins have been rapidly developed. Extraction from a variety of tissues and samples have become routine and automated. Next generation sequencing (NGS) methods have been developed. This book focuses on medically-focused methods"--

Nucleotide sequence. --- Nucleotide sequence --- Data processing.

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This book evaluates and comprehensively summarizes the scientific findings that have been achieved through RNA-sequencing (RNA-Seq) technology. RNA-Seq transcriptome profiling of healthy and diseased tissues allows FOR understanding the alterations in cellular phenotypes through the expression of differentially spliced RNA isoforms. Assessment of gene expression by RNA-Seq provides new insight into host response to pathogens, drugs, allergens, and other environmental triggers. RNA-Seq allows us to accurately capture all subtypes of RNA molecules, in any sequenced organism or single-cell type, under different experimental conditions. Merging genomics and transcriptomic profiling provides novel information underlying causative DNA mutations. Combining RNA-Seq with immunoprecipitation and cross-linking techniques is a clever multi-omics strategy assessing transcriptional, post-transcriptional and post-translational levels of gene expression regulation.

Nucleotide sequence. --- Cyclic nucleotides.

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Pocket gophers --- Nucleotide sequence

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One strategy cells use for regulation is modifying proteins, DNA, and RNA to control their structure, function, and stability. For years, research has focused on the reversible modifications to proteins and DNA. However, RNA can also be highly modified, and more than 170 types of modification to RNA have been identified so far. Current methods for mapping and sequencing RNA and its modifications -- also known as the epitranscriptome -- are limited, partly because available sequencing technologies can detect only a small number of them. This limits the understanding of different molecular processes and leaves a gap in knowledge related to human diseases and disorders. To address these limitations and develop a roadmap for the sequencing of RNA with the epitranscriptome, the National Academies of Sciences, Engineering, and Medicine convened an ad hoc committee to provide a consensus report. A workshop held on March 14-15, 2023 was one part of an information-gathering effort by the committee and is summarized in this proceedings.

RNA --- Nucleotide sequence. --- Analysis.

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Presenting the fundamental algorithms and data structures that power bioinformatics workflows, this book covers a range of topics from the foundations of sequence analysis (alignments and hidden Markov models) to classical index structures (k-mer indexes, suffix arrays, and suffix trees), Burrows-Wheeler indexes, graph algorithms, network flows, and a number of advanced omics applications. The chapters feature numerous examples, algorithm visualizations, and exercises, providing graduate students, researchers, and practitioners with a powerful algorithmic toolkit for the applications of high-throughput sequencing. An accompanying website (www.genome-scale.info) offers supporting teaching material. The second edition strengthens the toolkit by covering minimizers and other advanced data structures and their use in emerging pangenomics approaches.

Genomics. --- Nucleotide sequence.