Bioinformatics and Computational Molecular Biology
Algorithms and Hardware
Books
Books on Bioinformatics and Molecular Biology
Bioinformatics and Molecular Biology:
Bioinformatics: Sequence and Genome Analysis,
David W. Mount, Cold Spring Harbor Laboratory Press, 2001, ISBN 0-87969-608-7.
1. Historical Introduction and Overview 2. Collecting and Storing Sequences in the Laboratory 3. Alignment of Pairs of Sequences 4. Multiple Sequence Alignment 5. Prediction of RNA Secondary Structure 6. Phylogenetic Prediction 7. Database Searching for Similar Sequences 8. Gene Prediction 9. Protein Classification and Structure Prediction 10. Genome Analysis
Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison, Cambridge University Press, 1999, ISBN 0521629713.
1. Introduction 2. Pairwise sequence alignment 3. Multiple alignments 4. Hidden Markov models 5. Hidden Markov models applied to biological sequences 6. The Chomsky hierarchy of formal grammars 7. RNA and stochastic context-free grammars 8. Phylogenetic trees 9. Phylogeny and alignment
Philip E. Bourne, Helge Weissig, Wiley, 2003, ISBN 0-471-20200-2.
Defining Bioinformatics and Structural Bioinformatics (R. Altman & J. Dugan). Fundamentals of Protein Structure (E. Scheeff & J. Fink). Fundamentals of DNA and RNA Structure (S. Neidle, et al.). Computational Aspects of High-Throughput Crystallographic Macromolecular Structure Determination (P. Adams, et al.). Macromolecular Structure Determination by NMR Spectroscopy (J. Markley, et al.). Electron Microscopy (N. Volkmann & D. Hanein). Molecular Visualization (J. Tate). The PDB Format, mmCIF Formats, and Other Data Formats (J. Westbrook & P. Fitzgerald). The Protein Data Bank (The PDB Team). The Nucleic Acid Database (H. Berman, et al.). Other Structure-Based Databases (H. Weissig & P. Bourne). Protein Structure Evolution and the SCOP Database (B. Reddy & amp; P. Bourne). The CATH Domain Structure Database (C. Orengo, et al.). Structural Quality Assurance (R. Laskowski). All-Atom Contacts: A New Approach to Structure Validation (J. Richardson). Structure Comparison and Alignment (P. Bourne & I. Shindyalov). Secondary Structure Assignment (C. Andersen & B. Rost). Identifying Structural Domains in Proteins (L. Wernisch & S. Wodak). Inferring Protein Function from Structure (G. Bartlett, et al.). Prediction of Protein-Protein Interactions from Evolutionary Information (A. Valencia & F. Pazos). Electrostatic Interactions (N. Baker & J. McCammon). Principles and Methods of Docking and Ligand Design (J. Krumrine, et al.). Structural Bioinformatics in Drug Discovery (E. Fauman, et al.). CASP and CAFASP Experiments and Their Findings (P. Bourne). Homology Modeling (E. Krieger, et al.). Fold Recognition Methods (A. Godzik). Ab Initio Methods (D. Chivian, et al.). Prediction in 1D: Secondary Structure, Membrane Helices, and Accessibility (B. Rost). Structural Genomics (S. Burley & J. Bonanno).
Biochemistry and Molecular Biology, 2nd Edition,
William H. Elliott, Daphne C. Elliott, Oxford, 2001, ISBN 0-19-870045-8.
1. Chemistry, energy, and metabolism 2. Enzymes 3. The structure of proteins 4. The cell membrane 5. Digestion and absorption of food 6. Preliminary outline of fuel distribution and utilization by the different tissues of the body 7. Biochemical mechanisms involved in food transport, storage, and mobilization 8. Energy release from foodstuffs - a preliminary overview 9. Glycolysis, the citric acid cycle, and the electron transport system: reactions involved in these pathways 10. Energy release from fat 11. A switch from catabolic to anabolic metabolism - first the synthesis of fat and related compounds in the body 12. Synthesis of glucose in the body (gluconeogenesis) 13. Strategies for metabolic control and their application to carbohydrate and fat metabolism 14. Why should there be an alternative pathway of glucose oxidation? - the pentose phosphate pathway 15. Raising electrons of water back up the energy scale - photosynthesis 16. Amino acid metabolism 17. Cellular disposal of unwanted molecules 18. Enzymic protective mechanisms in the body 19. Nucleotide metabolism 20. DNA - its structure and arrangement in cells 21. DNA synthesis and repair 22. Gene transcription - the first step in the mechanism by which genes direct protein synthesis 23. Eukaryotic gene transcription and control 24. Gene cloning, reProtein synthesis, intracellular transport, and degradation 25. How are newly synthesised proteins delivered to their correct destinations - protein targeting 26. Cell signalling 27. The immune system 28. Viruses and viroids 29. Gene cloning, recombinant DNA technology, genetic engineering 30. Molecular biology of cancer 31. The red blood cell and role of hemoglobin 32. Muscle contraction 33. The cytoskeleton, molecular motors and intracellular transport
Protein Structure, 2nd Edition,
C. Branden, J. Toose, Garland, 1999, ISBN 0–8153–2305–0.
1. The Building Blocks 2. Motifs of Protein Structure 3. Alpha-Domain Structures 4. Alpha/Beta Structures 5. Beta Structures 6. Folding and Flexibility 7. DNA Structures 8. DNA Recognition in Procaryotes by Helix-Turn-Helix Motifs 9. DNA Recognition by Eucaryotic Transcription Factors 10. Specific Transcription Factors Belong to a Few Families 11. An Example of Enzyme Catalysis: Serine Proteinases 12. Membrane Proteins 13. Signal Transduction 14. Fibrous Proteins 15. Recognition of Foreign Molecules by the Immune System 16. The Structure of Spherical Viruses 17. Prediction, Engineering and Design of Protein Structures 18. Determination of Protein Structures
Genomes, 2nd Edition,
T. Brown, Wiley Bios Scientific, 2002, ISBN 0-471-25046-5.
1. The Human Genome 2. Genome Anatomies 3. Transcriptomes and Proteomes 4. Studying DNA 5. Mapping Genomes 6. Sequencing Genomes 7. Understanding a Genome Sequence 8. Accessing the Genome 9. Assembly of the Transcription Initiation Complex 10. Synthesis and Processing of RNA 11. Synthesis and Processing of the Proteome 12. Regulation of Genome Activity 13. Genome Replication 14. Mutation, Repair and Recombination 15. How Genomes Evolve 16. Molecular Phylogenetics
Artificial Intelligence and Molecular Biology,
L. Hunter, AAAI, ISBN 0-262-58115-9 (out of print, but full PDF text at web site).
1. Molecular Biology for Computer Scientists 2. The Computational Linguistics of Biological Sequences 3. Neural Networks, Adaptive Optimization, and RNA Secondary Structure Prediction 4. Predicting Protein Structural Features With Artificial Neural Networks 5. Developing Hierarchical Representations for Protein Structures: An Incremental Approach 6. Integrating AI with Sequence Analysis 7. Planning to Learn about Protein Structure 8. A Qualitative Biochemistry and its Application to the Regulation of the Tryptophan Operon 9. Identification of Qualitatively Feasible Metabolic Pathways 10. Knowledge-Based Simulation of DNA Metabolism: Prediction of Action and Envisionment of Pathways 11. An AI Approach to the Interpretation of the NMR Spectra of Proteins 12. Molecular Scene Analysis: Crystal Structure Determination Through Imagery 13. Afterword: The Anti-Expert System -- Thirteen Hypotheses an AI Program Should Have Seen Through
Computer Architecture: A quantitative Approach, 3rd Edition,
J. Hennessy, D. Patterson, Morgan Kaufmann, 2003, ISBN 1-55860-596-7.
1. Fundamentals of Computer Design 2. Instruction Set Principles and Examples 3. Instruction-Level Parallelism and Its Dynamic Exploitation 4. Exploiting Instruction-Level Parallelism with Software Approaches 5. Memory Hierarchy Design 6. Multiprocessors and Thread-Level Parallelism 7. Storage Systems 8. Interconnection Networks and Clusters
The Designer's Guide to VHDL, 2nd Edition,
P. Ashenden, Morgan Kaufmann, 2001, ISBN 1-55860-674-2.
1. Fundamental Concepts 2. Scalar Data Types and Operations 3. Sequential Statements 4. Composite Data Types and Operations 5. Basic Modeling Constructs 6. Case Study: A Pipelined Multiplier Accumulator 7. Subprograms 8. Packages and Use Clauses 9. Aliases 10. Case Study: A Bit-Vector Arithmetic Package 11. Resolved Signals 12. Generic Constants 13. Components and Configurations 14. Generate Statements 15. Case Study: The DLX Computer System 16. Guards and Blocks 17. Access Types and Abstract Data Types 18. Files and Input/Output 19. Case Study: Queuing Networks 20. Attributes and Groups 21. Miscellaneous Topics
Analysis and Design of Digital Integrated Circuits, 3rd Edition,
D. Hodges, H. Jackson, R. Saleh, McGraw Hill, 2004, ISBN 0-07-228365-3.
1. Introduction 2. MOS Devices 3. Fabrication and Layout 4. Invertor Design 5. Basic Gates 6. High-Speed CMOS Design 7. Dynamic Logic Circuits 8. Interconnect Design 9. Memory Design (Part I) 10. Memory Design (Part II) 11. Clocks and Power Distribution 12. Input and Output 13. Bipolar Digital Circuits
Digital Design, 3rd Edition,
M. Mano, Prentice Hall, 2002, ISBN 0-13-062121-8.
1. Binary Systems 2. Boolean Algebra and Logic Gates 3. Gate-Level Minimization 4. Combinational Logic 5. Synchronous Sequential Logic 6. Registers ad Counters 7. Memory and Programmable Logic 8. Register Transfer Level 9. Asynchronous Sequential Logic 10. Digital Integrated Circuits 11. Laboratory Experiments 12. Standard Graphic Symbols
Boise State University College of Engineering
Boise State University Department of Electrical and Computer Engineering
This page created by Dr. Scott F. Smith
This page was last updated on 01 February 2004.
Biological Sequence Analysis
Structural Bioinformatics