This book presents the foundations of key problems in computational molecular biology and bioinformatics. It focuses on computational and statistical principles applied to genomes, and introduces the mathematics and statistics that are crucial for understanding these applications. The book features a free download of the R software statistics package and the text provides great crossover material that is interesting and accessible to students in biology, mathematics, statistics and computer science. More than 100 illustrations and diagrams reinforce concepts and present key results from the primary literature. Exercises are given at the end of chapters.
The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background.
Li, R., et al. (2009). SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966–1967. Li, Z., et al. (2014). Vindel: A simple pipeline for checking indel redundancy. BMC Bioinformatics, 15, 359.
[209] Köhler S., et al. (2014) The Human Phenotype Ontology project: Linking molecular biology and disease through phenotype data. Nucleic Acids Research 42:D966–D974. [210] Köhler S., et al. (2013) Construction and accessibility of a ...
Fraser, C. M., J. D. Gocayne, O. White, M. D. Adams, R. A. Clayton, R. D. Fleischmann, C. J. Bult, A. R. Kerlavage, G. Sutton, J. M. Kelley, R. D. Fritchman, J. F. Weidman, K. V. Small, M. Sandusky, J. Fuhrmann, D. Nguyen, ...
METHODS OF COMPUTATIONAL GENOME ANALYSIS.
Programmed cell death in bacterial populations. Science 267: 836-837. 933. Yeo JP, Alderuccio F, Toh BH. 1994. A new chromosomal protein essential for mitotic spindle assembly. Nature 367: 288-291. 934. Yeo JP, Alderuccio F, Toh BH.
This decision was motivated by several factors. Firstly, the main focus of this book is computational and statistical approaches in genomics research. Thus, the main emphasis is on methods rather than on applications.
Computational Genome Analysis: An Introduction
... genome-wide scans by Kui Zhang, Howard Wiener, T. Mark Beasley, Christopher I. Amos, and David B. Allison 5.1 5.2 5.3 5.4 Introduction Methods Results Discussion 33 33 34 40 42 43 44 46 46 49 49 51 54 58 63 67 67 69 72 79 Part II.
From sequencing genomes to discovering motifs in large collections of functionally equivalent sequences of nucleic acids and proteins, the value of powerful computational tools has become abundantly clear. The Compact Hand