This book offers a gripping introduction to the fastest growing field of biology with easy-to-follow examples and a well-prepared appendix for the reader to cook up and experience everything right away.
The book gets the reader started with the basics, such as how to easily find sequence information and then analyze it. In further chapters, the authors go into the various analysis options from RNA, DNA and proteins to entire metabolic pathways. Exciting examples from biology are chosen in each chapter to illustrate the analysis. Each chapter concludes with an exercise section that immediately puts what has been learned to use.
The subject of this book is a must for any biology student, whether undergraduate or graduate, as bioinformatics is now unearthing amazing insights into the molecular basis of all living things. Computer science students and other students from related sciences will get a good introduction to bioinformatics, as biology and current topics (e.g. AI) are systematically introduced step by step alongside the software.
Discover the key to life together with the authors and learn to understand the language of life.
This book is a translation of the original German 2nd edition Bioinformatik by Thomas Dandekar and Meik Kunz, published by Springer-Verlag GmbH Germany, part of Springer Nature in 2021. The translation was done with the help of artificial intelligence (machine translation by the service DeepL.com). A subsequent human revision was done primarily in terms of content, so that the book will read stylistically differently from a conventional translation. Springer Nature works continuously to further the development of tools for the production of books and on the related technologies to support the authors.
Author(s): Thomas Dandekar, Meik Kunz
Edition: 1
Publisher: Springer
Year: 2023
Language: English
Commentary: PDF Quality: 99.99 % || [[trace-bullet]]
Pages: 366
City: Berlin, Heidelberg
Tags: Bioinformatics; Biomedicine; Computer; Information; Life; Systems Biology
Contents
Part I: How Does Bioinformatics Work?
Access
Short Instructions for Usage of the Book
1: Sequence Analysis: Deciphering the Language of Life
1.1 How Do I Start My Bioinformatics Analysis? Useful Links and Tools
1.2 Protein Analysis Is Easy with the Right Tool
1.3 Exercises for Chap. 1
Literature
Further Reading
2: Magic RNA
2.1 RNA Sequences Are Biologically Active
2.2 Analysis of RNA Sequence, Structure and Function
2.3 Exercises for Chap. 2
Literature
Own RNA Analysis Examples Together with Method Protocols
3: Genomes: Molecular Maps of Living Organisms
3.1 Sequencing Genomes: Spelling Genomes
3.2 Deciphering the Human Genome
3.3 A Profile of the Human Genome
3.4 Exercises for Chap. 3
Literature
4: Modeling Metabolism and Finding New Antibiotics
4.1 How Can I Model Metabolism Bioinformatically?
4.2 Useful Tools for Metabolic Modelling
4.3 Exercises for Chap. 4
Literature
5: Systems Biology Helps to Discover Causes of Disease
5.1 Application Example: How Does Phosphorylation Cause Heart Failure?
5.2 Generalization: How to Build a Systems Biology Model?
5.3 Exercises for Chap. 5
Literature
Application Examples
Part II: How Do I Understand Bioinformatics?
From a Computer-Technical (Informatics) Point of View, Three Points Are Interesting
From a Biological Point of View, the Following Points Are Generally Important
6: Extremely Fast Sequence Comparisons Identify All the Molecules That Are Present in the Cell
6.1 Fast Search: BLAST as an Example for a Heuristic Search
6.2 Maintenance of Databases and Acceleration of Programs
6.3 Exercises for Chap. 6
Literature
7: How to Better Understand Signal Cascades and Measure the Encoded Information
7.1 Coding with Bits
7.2 The Different Levels of Coding
7.3 Understanding Coding Better
7.4 Exercises for Chap. 7
Literature
8: When Does the Computer Stop Calculating?
8.1 When Does It Become a Challenge for the Computer?
8.2 Complexity and Computing Time of Some Algorithms
8.3 Informatic Solutions for Computationally Intensive Bioinformatics Problems
Other Possibilities Include
8.4 NP Problems Are Not Easy to Grasp
8.5 Exercises for Chap. 8
Literature
9: Complex Systems Behave Fundamentally in a Similar Way
9.1 Complex Systems and Their Behaviour
9.2 Opening Up Complex Systems Using Omics Techniques
9.3 Typical Behaviour of Systems
9.4 System Credentials: Emergence, Modular Construction, Positive and Negative Signal Return Loops
9.5 Pioneers of Systems Science
9.6 Which Systems Biology Software Can I Use?
9.7 Exercises for Chap. 9
Literature
10: Understand Evolution Better Applying the Computer
10.1 A Brief Overview of Evolution from the Origin of Life to the Present Day
10.2 Considering Evolution: Conserved and Variable Areas
10.3 Measuring Evolution: Sequence and Secondary Structure
10.4 Describing Evolution: Phylogenetic Trees
10.5 Protein Evolution: Recognizing Domains
10.6 Exercises for Chap. 10
Evolution Tasks
Phylogeny Tasks
Literature
11: Design Principles of a Cell
11.1 Bioinformatics Provides an Overview of the Design of a Cell
11.2 Bioinformatics Provides Detailed Insights into the Molecular Biology of the Cell
11.3 Exercises for Chap. 11
Literature
Part III: What Is Catching and Fascinating About Bioinformatics?
3.1 No Black and White: Fascinating Shades of Individuality
12: Life Continuously Acquires New Information in Dialogue with the Environment
12.1 Molecular Words Only Ever Make Sense in the Context of the Cell
12.2 Printing Errors Are Constantly Selected Away in the Cell
12.3 Exercises for Chap. 12
Literature
13: Life Invents Ever New Levels of Language
13.1 The Different Languages and Codes in a Cell
13.2 New Molecular, Cellular and Intercellular Levels and Types of Language Are Emerging All the Time
13.3 Innovation: Synthetic Biology
13.4 New Levels of Communication Through Technology
13.5 The Internet – A New Level of Communication
13.6 A Parallel Language Level: Natural and Analogue Computation
13.7 Future Level of Communication: The Nanocellulose Chip
13.8 Using the Language of Life Technically with the Help of Synthetic Biology
Synthetic Biology: Important Links and Applications for Bioinformatics
Emerging Technology Competition
13.9 Exercises for Chap. 13
Literature
14: We Can Think About Ourselves – The Computer Cannot
14.1 People Question, Computers Follow Programs
14.2 Artificial Intelligence
14.3 Current Applications of Artificial Intelligence in Bioinformatics
14.4 Biological Intelligence
14.5 Exercises for Chap. 14
Literature
15: How Is Our Own Extremely Powerful Brain Constructed?
15.1 Modular Construction Leads to Ever New Properties – Up to Consciousness
15.2 Bioinformatics Helps to Better Describe the Brain
15.3 Brain Blueprints
Brain Complexity Directly Mapped Digitally
15.4 Possible Objectives
15.5 Exercises for Chap. 15
Literature
16: Bioinformatics Connects Life with the Universe and All the Rest
16.1 Solving Problems Using Bioinformatics
16.2 Model and Mitigate Global Problems
Global Warming
16.3 Global Digitalisation and Personal Space
16.4 What Are the Tasks for Modern Bioinformatics in the Internet Age?
16.5 Exercises for Chap. 16
Literature
17: Conclusion and Summary
Part IV: Glossary, Tutorial, Solutions and Web Links
18: Glossary
19: Tutorial: An Overview of Important Databases and Programs
19.1 Genomic Data: From Sequence to Structure and Function
19.2 RNA: Sequence, Structure Analysis and Control of Gene Expression
19.3 Proteins: Information, Structure, Domains, Localization, Secretion and Transport
19.4 Cellular Communication, Signalling Cascades, Metabolism, Shannon Entropy
19.5 Life Always Invents New Levels of Language
19.6 Introduction to Programming (Meta Tutorial)
Programming Languages and Tutorials
20: Solutions to the Exercises
20.1 Sequence Analysis: Deciphering the Language of Life
20.2 Magic RNA
20.3 Genomes – Molecular Maps of Living Organisms
20.4 Modeling Metabolism and Finding New Antibiotics
20.5 Systems Biology Helps to Discover the Causes of Disease
20.6 Extremely Fast Sequence Comparisons Identify all the Molecules that Are Present in the Cell
20.7 How to Better Understand Signal Cascades and Measure the Encoded Information
20.8 When Does the Computer Stop Calculating?
20.9 Complex Systems Behave Fundamentally in a Similar Way
20.10 Understand Evolution Better Applying the Computer
20.11 Design Principles of a Cell
20.12 Life Continuously Acquires New Information in Dialogue with the Environment
20.13 Life Always Invents New Levels of Language
20.14 We Can Think About Ourselves – The Computer Cannot
20.15 How Is Our Own Extremely Powerful Brain Constructed?
20.16 Bioinformatics Connects Life with the Universe and all the Rest
Literature
Further Reading
Overview of Important Databases and Programs and Their General Use
Alignment/Tribes
Datasets on Biological Quantities/Biotechnology/Synthetic Biology
Dotplot
Functional Databases
Brain Blueprints
Genome Annotation/Sequence Analysis/Online Libraries/Experimental Datasets
Graphics Programs, Modeling and Network Analysis
Interaction Database, Drug Interaction Database
Localization/Motive Prediction
Programming Languages
Promoter Analysis
Protein Analysis
RNA Analysis
