Introduction to bioinformatics 4th Edition by M Lesk ISBN 0199651566 9780199651566

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ISBN 10: 0199651566 
ISBN 13: 9780199651566
Author: M Lesk

Introduction to bioinformatics 4th Table of contents:

CHAPTER 1: Introduction
Life in space and time
Phenotype = genotype + environment + life history + epigenetics
Evolution is the change over time in the world of living things
Biological classification and nomenclature
Dogmas: central and peripheral
The structure of DNA
Transcription and translation
The structures of proteins
Statics and dynamics
Systems biology
The human genome
Variation in human genome sequences
The human genome and medicine
Databases in molecular biology
Observables and data archives
A database without effective modes of access is merely a data graveyard
Information flow in bioinformatics
Curation, annotation, and quality control
The World Wide Web
Electronic publication
Computers and computer science
Programming
Après moi, le déluge? Sorry—too late!
How much sequencing power is there in the world?
How does the amount of data in bioinformatics compare with other large scientific information archives?
Recommended reading
Exercises and Problems
CHAPTER 2: From genetics to genomes
The classical genetics background
DNA embodies genes
Maps and tour guides
Linkage maps
Linkage
Chromosome banding
High-resolution maps, based directly on DNA sequences
Restriction maps
DNA sequencing
Frederick Sanger and the development of DNA sequencing
DNA sequencing by termination of chain replication
Automation of DNA sequencing
Next-generation sequencing
Paired-end reads
Life in the fast lane
Assembly—computational aspects
Pattern matching
Suffix trees
Fragment assembly
Genomics in personal identification
DNA ‘fingerprinting’
Personal identification by amplification of specific regions has superseded the RFLP approach
Mitochondrial DNA
Analysis of non-human DNA sequences
Parentage testing
Ethical, legal, and social issues
Databases containing human DNA sequence information
Use of DNA sequencing in research on human subjects
Recommended reading
Exercises and Problems
CHAPTER 3: The panorama of life
Genomes, transcriptomes, and proteomes
Genes
Proteomics and transcriptomics
Eavesdropping on the transmission of genetic information
Genome-sequencing projects
Genomes of prokaryotes
The genome of the bacterium Escherichia coli
The genome of the archaeon Methanocaldococcus jannaschii
The genome of one of the simplest organisms: Mycoplasma genitalium
Metagenomics: the collection of genomes in a coherent environmental sample
The human microbiome
Genomes of eukarya
Gene families
The genome of Saccharomyces cerevisiae (Baker’s yeast)
The genome of Caenorhabditis elegans
The genome of Drosophila melanogaster
The genome of Arabidopsis thaliana
The genome of Homo sapiens (the human genome)
Protein-coding genes
Repeat sequences
RNA
Single-nucleotide polymorphisms and haplotypes
Systematic measurements and collections of single-nucleotide polymorphisms
Genetic diversity in anthropology
DNA sequences and languages
Evolution of genomes
Please pass the genes: horizontal gene transfer
Comparative genomics of eukarya
Recommended reading
Exercises and Problems
CHAPTER 4: Alignments and phylogenetic trees
Introduction to sequence alignment
Dotplots and sequence alignments
Measures of sequence similarity
Scoring schemes
Derivation of substitution matrices: PAM matrices
Computing the alignment of two sequences
Variations and generalizations
Approximate methods for quick screening of databases
The dynamic programming algorithm for optimal pairwise sequence alignment
Significance of alignments
Multiple sequence alignment
Applications of multiple sequence alignments to database searching
Profiles
PSI-BLAST
Complete pairwise sequence alignment of human PAX-6 protein and Drosophila melanogaster eyeless
Hidden Markov Models
Phylogeny
Determination of taxonomic relationships from molecular properties
Use of sequences to determine phylogenetic relationships
Use of SINES and LINES to derive phylogenetic relationships
Phylogenetic trees
Clustering methods
The maximum-likelihood method
Reconstruction of ancestral sequences
Pyruvate decarboxylase: synthesis, activity, and crystal structure of predicted ancestor
The problem of varying rates of evolution
Bayesian methods
Are trees the correct way to present phylogenetic relationships?
Computational considerations
Putting it all together
Recommended reading
Exercises and Problems
CHAPTER 5: Structural bioinformatics and drug discovery
Introduction
Protein stability and folding
The Sasisekharan–Ramakrishnan–Ramachandran plot describes allowed mainchain conformations
The sidechains
Protein stability and denaturation
Protein folding as a process
Applications of hydrophobicity
Coiled-coiled proteins
Description of the variety of protein structures
Superposition of structures, and structural alignments
Evolution of protein structures
Classifications of protein structures
SCOP
Protein structure prediction and modelling
A priori and empirical methods
Critical Assessment of Structure Prediction
Secondary structure prediction
Homology modelling
Fold recognition
Conformational energy calculations and molecular dynamics
ROSETTA
Protein structure prediction from contact maps derived from correlated mutations in multiple sequence alignments
Design of novel proteins
Drug discovery and development
The lead compound
Improving on the lead compound: quantitative structure–activity relationships
Bioinformatics in drug discovery and development
Molecular modelling in drug discovery
Recommended reading
Exercises and Problems
CHAPTER 6: Scientific publications and archives: media, content, access, and presentation
The scientific literature
Access to scholarly publications
Open access
The Public Library of Science
Traditional and digital libraries
How to populate a digital library
The information explosion
The web: higher dimensions
New media: video, sound
Searching the scientific literature
Bibliography management
Databases
Database contents
Database quality control
The literature as a database
Database organization
Annotation
Markup languages
Database access
Links
Database interoperability
Data mining
Programming languages and tools for database construction and access
Traditional programming languages
Scripting languages
Program libraries specialized for molecular biology
Java—computing over the web
Natural language processing
Natural language processing in mining the biomedical literature
Biomedical applications of text mining
Hypothesis generation
A glaucoma-related network derived by text mining
Recommended reading
Exercises and Problems
CHAPTER 7: Artificial intelligence and machine learning
What are artificial intelligence and machine learning?
Classification and clustering
Binary classifier
Receiver Operating Characteristic (ROC) curves
Artificial neural networks
Self-organizing maps
Decision trees
Support vector machines (SVMs)
Kernel methods
Clustering
Clustering by graph spectral theory
Recommended reading
Exercises and Problems
CHAPTER 8: Introduction to systems biology
Introduction
Networks and graphs
Connectivity in networks
Dynamics, stability, and robustness
Some sources of ideas for systems biology
Complexity of sequences
Shannon’s definition of entropy
Complexity of sequences
The relationship between complexity, randomness, and compressibility
The Burrows-Wheeler Transform
Inverting the Burrows-Wheeler Transform
The Burrows-Wheeler Transform brings repeats together, facilitating compression
Use of the Burrows-Wheeler transform for searching for patterns in strings
Complexity of other types of biological data
Static and dynamic complexity
Predictability and chaos
Analysis and comparison of networks
Analysis of graphs by matrix algebra
Graph isomorphism
Recommended reading
Exercises and Problems
CHAPTER 9: Metabolic pathways
Introduction
Classification of protein function
The Enzyme Commission
The Gene OntologyTM Consortium protein function classification
Prediction of protein function
Catalysis by enzymes
Active sites
Cofactors
Protein–ligand binding equilibria
Enzyme kinetics
Measures of effectiveness of enzymes
How do enzymes evolve new functions?
Control over enzyme activity
Structural mechanisms of evolution of altered or novel protein functions
Pathways and limits in the divergence of sequence, structure, and function
Evolution by gene duplication
Databases of metabolic pathways
The Kyoto Encyclopedia of Genes and Genomes (KEGG)
Evolution and phylogeny of metabolic pathways
Pathway comparison
Alignment of metabolic pathways
Comparing linear metabolic pathways
Comparing non-linear metabolic pathways: The pentose phosphate pathway and the Calvin-Benson cycle
Dynamics of metabolic networks
Robustness of metabolic networks
Dynamic modelling of metabolism
Simulation of metabolic pathways in Plasmodium falciparum
The Human Metabolome Database supports clinical applications to the study of inborn errors of metabolism, and to cancer
Recommended reading
Exercises and Problems
CHAPTER 10: Control of organization and organization of control
Transcriptomics
The ENCODE Project
Determination of RNA sequences
RNAseq v. microarrays
DNA microarrays
RNAseq
The Genotype-Tissue Expression (GTEx) project
Expression patterns in different physiological states
Variation of expression patterns during the life cycle of Drosophila melanogaster
Different life stages make different demands on different genes
Protein complexes and aggregates
Properties of protein–protein complexes
Protein interaction networks
Components of the primosome assembly in Bacillus subtilis
Regulatory networks
Signal transduction and transcriptional control
Structural biology of regulatory networks
Examples of relatively simple regulatory control networks
Regulation of the lactose operon in E. coli
The genetic switch of bacteriophage λ
The diauxic shift in Saccharomyces cerevisiae
Logical structure of regulatory networks
The transcriptional regulatory network of E. coli
The transcriptional regulatory network of Saccharomyces cerevisiae
Adaptability of the yeast regulatory network
Recommended reading
Exercises and Problems

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