BIOS Instant Notes in Bioinformatics

J Howard Parish, Richard M Twyman, Charlie Hodgman, Andrew French, David Westhead

• Publisher: Taylor & Francis
• Year: 2009
• eBook ISBN: 9781134158867
• Edition: 2
• Topic: Biological Sciences
• Subtopic: Biology
• Index: Biological Sciences

The second edition of Instant Notes in Bioinformatics introduced the readers to the themes and terminology of bioinformatics. It is divided into three parts: the first being an introduction to bioinformatics in biology; the second covering the physical, mathematical, statistical and computational basis of bioinformatics, using biological examples wherever possible; the third describing applications, giving specific detail and including data standards. The applications covered are sequence analysis and annotation, transcriptomics, proteomics, metabolite study, supramolecular organization, systems biology and the integration of-omic data, physiology, image analysis, and text analysis.

INDEX

0-D data 30

1-D data 30

2-D data 31

2D-NMR 31, 270

3D-data 32

454 sequencing 107, 113

80–20 rule 46

abstraction 41, 69, 71

ACeDB 109, 120, 121, 128, 132, 138

adaptive method 87

adjacency list 72, 75

adjacency matrix 74, 75

alpha release 42

analysis of variance (ANOVA) 61, 65

arcs 72

annealing 13, 15–17, 103, 105

annotation 132

arithmetic mean 62, 169

arithmetic logic unit 37–39

ArMeT 270

array 3, 4, 19, 22, 23, 29, 32, 35–40, 50, 67, 73, 75, 94, 103, 114, 181–191, 194–196, 199–201, 205, 279, 299, 302–305, 311

artificial intelligence 89, 90, 168, 253

ASCII 19, 21, 22

bad 327

base calling 113

Bayesian belief network 196

Bayesian inference 57, 91, 92, 197

Bayesian networks 93, 94

Bayesian reasoning 91, 93

Bayesian statistics 57, 91, 93, 194, 196, 204

Bayes’ rule 57–59, 92, 93

Benjamini-Hochberg correction 61, 67

beta release 42

bifurcational analysis 283, 286

binomial distribution 49, 51, 52

biochemical pathway 76, 109, 125, 276, 277

Bioconductor 187–190

biological replicate 200, 201

biological system 4, 5, 10, 13, 14, 69, 79, 262, 275, 289

bipartite graph 77

bit 20–22, 35, 39, 43, 102, 103, 264, 265, 300–302

bit depth 299, 300

Bonferroni correction 67

Boolean network 194, 197

Boundary-element analysis 86

byte 4, 20–23, 31, 32, 40, 41

bytecode 40

C++ 25, 37, 39, 40, 75

Canny operator 315

cellular automata 78

central limit theorem 54, 311

central processing unit 20, 37, 38

chain termination sequencing 111

CheBI 277

ChIP-chip 181, 183

chi-squared 65

cladograms 165

cliques 73, 74, 219, 278

cluster 10, 90, 103, 113, 123, 126, 161, 168–171, 178, 182, 188–190, 194–196, 201, 203–205, 209, 219, 220, 255, 260, 311, 319, 320, 325

clustering 90, 109, 161, 168–171, 178, 188–190, 194–196, 201, 203, 209, 319, 320, 325

color images 301, 302

compiler 40

compression 302, 303

Computable Plant project 293

computing power 45, 273, 291, 296, 297, 327

conditional probability 49...

Table of contents

• BIOS INSTANT NOTES
• CONTENTS
• ABBREVIATIONS
• PREFACE
• Section A The changing face of research biology
• Section B Definitions of bioinformatics
• Section C Essentials of physics
• Section D Data and databases
• Section E Data categories
• Section F Computation
• Section G Probability and statistics
• Section H Modeling and mathematical techniques
• Section I Artificial intelligence and machine learning
• Section J Genomes and other sequences
• Section K Transcriptomics
• Section L Proteins and proteomics
• Section M Metabolomics
• Section N Supramolecular organization
• Section O Biochemical dynamics
• Section P Physiology
• Section Q Image analysis
• Section R Textual analysis
• FURTHER READING
• INDEX