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The State of the Art in Transcriptome AnalysisRNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript le
An emerging, ever-evolving branch of science, bioinformatics has paved the way for the explosive growth in the distribution of biological information to a variety of biological databases, including the National Center for Biotechnology Information. For growth to continue in this field, biologists must obtain basic computer skills while computer specialists must possess a fundamental understanding of biological problems. Bridging the gap between biology and computer science, Bioinformatics: A Practical Approach assimilates current bioinformatics knowledge and tools relevant to the omics age into one cohesive, concise, and self-contained volume. Written by expert contributors from around the world, this practical book presents the most state-of-the-art bioinformatics applications. The first part focuses on genome analysis, common DNA analysis tools, phylogenetics analysis, and SNP and haplotype analysis. After chapters on microarray, SAGE, regulation of gene expression, miRNA, and siRNA, the book presents widely applied programs and tools in proteome analysis, protein sequences, protein functions, and functional annotation of proteins in murine models. The last part introduces the programming languages used in biology, website and database design, and the interchange of data between Microsoft Excel and Access. Keeping complex mathematical deductions and jargon to a minimum, this accessible book offers both the theoretical underpinnings and practical applications of bioinformatics.
Thoroughly Describes Biological Applications, Computational Problems, and Various Algorithmic Solutions Developed from the author’s own teaching material, Algorithms in Bioinformatics: A Practical Introduction provides an in-depth introduction to the algorithmic techniques applied in bioinformatics. For each topic, the author clearly details the biological motivation and precisely defines the corresponding computational problems. He also includes detailed examples to illustrate each algorithm and end-of-chapter exercises for students to familiarize themselves with the topics. Supplementary material is available at http://www.comp.nus.edu.sg/~ksung/algo_in_bioinfo/ This classroom-tested textbook begins with basic molecular biology concepts. It then describes ways to measure sequence similarity, presents simple applications of the suffix tree, and discusses the problem of searching sequence databases. After introducing methods for aligning multiple biological sequences and genomes, the text explores applications of the phylogenetic tree, methods for comparing phylogenetic trees, the problem of genome rearrangement, and the problem of motif finding. It also covers methods for predicting the secondary structure of RNA and for reconstructing the peptide sequence using mass spectrometry. The final chapter examines the computational problem related to population genetics.
Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline.
Advances in sequencing technology have allowed scientists to study the human genome in greater depth and on a larger scale than ever before – as many as hundreds of millions of short reads in the course of a few days. But what are the best ways to deal with this flood of data? Algorithms for Next-Generation Sequencing is an invaluable tool for students and researchers in bioinformatics and computational biology, biologists seeking to process and manage the data generated by next-generation sequencing, and as a textbook or a self-study resource. In addition to offering an in-depth description of the algorithms for processing sequencing data, it also presents useful case studies describing the applications of this technology.
The Beauty of Protein Structures and the Mathematics behind Structural Bioinformatics Providing the framework for a one-semester undergraduate course, Structural Bioinformatics: An Algorithmic Approach shows how to apply key algorithms to solve problems related to macromolecular structure. Helps Students Go Further in Their Study of Structural Biology Following some introductory material in the first few chapters, the text solves the longest common subsequence problem using dynamic programming and explains the science models for the Nussinov and MFOLD algorithms. It then reviews sequence alignment, along with the basic mathematical calculations needed for measuring the geometric properties of macromolecules. After looking at how coordinate transformations facilitate the translation and rotation of molecules in a 3D space, the author introduces structural comparison techniques, superposition algorithms, and algorithms that compare relationships within a protein. The final chapter explores how regression and classification are becoming more useful in protein analysis and drug design. At the Crossroads of Biology, Mathematics, and Computer Science Connecting biology, mathematics, and computer science, this practical text presents various bioinformatics topics and problems within a scientific methodology that emphasizes nature (the source of empirical observations), science (the mathematical modeling of the natural process), and computation (the science of calculating predictions and mathematical objects based on mathematical models).
In recent years there have been tremendous achievements made in DNA sequencing technologies and corresponding innovations in data analysis and bioinformatics that have revolutionized the field of genome analysis. In this book, an impressive array of expert authors highlight and review current advances in genome analysis. This volume provides an invaluable, up-to-date and comprehensive overview of the methods currently employed for next-generation sequencing (NGS) data analysis, highlights their problems and limitations, demonstrates the applications and indicates the developing trends in various fields of genome research. The first part of the book is devoted to the methods and applications that arose from, or were significantly advanced by, NGS technologies: the identification of structural variation from DNA-seq data; whole-transcriptome analysis and discovery of small interfering RNAs (siRNAs) from RNA-seq data; motif finding in promoter regions, enhancer prediction and nucleosome sequence code discovery from ChiP-Seq data; identification of methylation patterns in cancer from MeDIP-seq data; transposon identification in NGS data; metagenomics and metatranscriptomics; NGS of viral communities; and causes and consequences of genome instabilities. The second part is devoted to the field of RNA biology with the last three chapters devoted to computational methods of RNA structure prediction including context-free grammar applications. An essential book for everyone involved in sequence data analysis, next-generation sequencing, high-throughput sequencing, RNA structure prediction, bioinformatics and genome analysis.

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