Systems biology and bioinformatics: a computational approach
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| Main Authors: | , , , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Boca Raton ; London ; New York
CRC Press, Taylor & Francis Group
[2009]
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | xxiii, 166 Seiten Diagramme |
| ISBN: | 9781420046502 |
Staff View
MARC
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| 010 | |a 2009009352 | ||
| 020 | |a 9781420046502 |c hardcover : alk. paper |9 978-1-4200-4650-2 | ||
| 035 | |a (OCoLC)312625448 | ||
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| 100 | 1 | |a Najarian, Kayvan |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Systems biology and bioinformatics |b a computational approach |c Kayvan Najarian, Siamak Najarian, Shahriar Gharibzadeh, Christopher N. Eichelberger |
| 264 | 1 | |a Boca Raton ; London ; New York |b CRC Press, Taylor & Francis Group |c [2009] | |
| 264 | 4 | |c © 2009 | |
| 300 | |a xxiii, 166 Seiten |b Diagramme | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 505 | 8 | |a Includes bibliographical references and index | |
| 650 | 4 | |a Bio-informatique | |
| 650 | 4 | |a Biologie systémique | |
| 650 | 4 | |a Bioinformatics | |
| 650 | 4 | |a Systems biology | |
| 650 | 4 | |a Computational biology | |
| 650 | 4 | |a Computational Biology | |
| 650 | 4 | |a Systems Biology | |
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| 700 | 1 | |a Najarian, Siamak |e Verfasser |0 (DE-588)1067772138 |4 aut | |
| 700 | 1 | |a Gharibzadeh, Shahriar |e Verfasser |0 (DE-588)1107777968 |4 aut | |
| 700 | 1 | |a Eichelberger, Christopher N. |e Verfasser |0 (DE-588)1107779499 |4 aut | |
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Record in the Search Index
| _version_ | 1827020033711144961 |
|---|---|
| adam_text |
Contents
Preface
.xv
Acknowledgment
.xxi
Authors
.xxiii
Chapter
1
Cell Biology
.1
1.1
Introduction and Overview
.1
1.2
An Introduction to Cell Structure
.1
1.2.1
Plasma Membrane
.1
1.2.1.1
Membrane Phospholipids
.1
1.2.1.2
Proteins
.1
1.2.1.3
Fluidity
.2
1.2.1.4
Stability
.2
1.2.1.5
Capacitive
Property
.2
1.2.1.6
Surface for Protein Attachment
.2
1.2.1.7
Control of Passage of Different Substances
.2
1.2.2
Cytoplasm
.3
1.2.2.1
Mitochondria
.3
1.2.2.2
Endoplasmic
Retícula
.3
1.2.2.3
Golgi Apparatus
.3
1.2.2.4
Lysosomes
.3
1.2.2.5
Ribosomes
.3
1.2.3
Nucleus
.3
1.3
Proteins as Tools of the Cell
.4
1.3.1
Structure of Proteins
.4
1.3.1.1
Higher Levels of Protein Organization
.4
1.3.2
Functions of Different Proteins
.4
1.3.2.1
Structural Proteins
.4
1.3.2.2
Transport Proteins
.5
1.3.2.3
Receptors
.5
1.3.2.4
Immunological Proteins
.5
1.3.2.5
Blood Carrier Proteins
.6
1.3.2.6
Enzymes
.6
1.4
Genes: Directors of the Cell
.6
1.4.1
Introduction to Inheritance
.6
1.4.2
The Structure of Genes
.6
1.4.2.1
Chromosomes and Chromatin
.7
1.4.2.2
Genetic Code
.8
1.4.3 DNA
Replication
.8
1.4.3.1
Initiation
.8
VII
viii Contents
1.4.3.2
Elongation
.9
1.4.3.3
Termination
.
Ю
1.4.4
Transcription
.
Ю
1.4.4.1
Three Kinds of
RNA
.
H
1.4.4.2
tRNA Anticodons
.
H
1.4.5
Translation
.12
1.5
Cell Cycle
.12
1.5.1
Cell Cycle: An Overview
.12
1.5.2
Mitosis
.12
1.5.2.1
Mitotic Apparatus
.12
1.5.2.2
Four Stages of Mitosis
.13
1.6
Summary
.13
1.7
Problems
.13
Chapter
2
Bioassays
.15
2.1
Introduction and Overview
.15
2.2
Southern Blotting
.15
2.3
Fluorescent In Situ Hybridization
.15
2.4 Sanger (Dideoxy)
Method
.16
2.5
Polymerase Chain Reaction
.16
2.6
Analyzing Protein Structure and Function
.17
2.6.1
X-ray Crystallography
.17
2.6.2
NMR Spectroscopy
.17
2.6.3
Affinity Chromatography
.17
2.6.4
Immunoprecipitation
.17
2.6.5
Two-Hybrid Systems
.18
2.6.6
Phage Display Method
.18
2.6.7 DNA
Footprint Analysis
.18
2.7
Studying Gene Expression and Function
—DNA Microarrays.18
2.7.1
Spotted Microarrays
.19
2.7.2
Oligonucleotide Microarrays
.19
2.7.3
SNP
Microarrays
.19
2.8
Summary
.19
2.9
Problems
.20
Chapter
3
Review of Some Computational Methods
.21
3.1
Introduction and Overview
.21
3.2
Introduction to Probability and Stochastic Processes Theories
.21
3.2.1
Metrics for Stochastic Processes
.22
3.2.1.1
Probability Density Function
.22
3.2.1.2
Mean and Variance
.23
3.2.1.3
Expectation Function
.23
Contents
¡x
3.2.3
Gaussian
Distribution.24
3.2.4
Correlation Function
.24
3.2.5
Stationary and Ergodic Stochastic Processes
.26
3.3
Bayesian Theory
.28
3.3.1
From Binary Networks to Bayesian Networks
.28
3.4
Test of Hypothesis
.29
3.4.1
ŕ
Test
.30
3.5
Expectation Maximization Method
.31
3.6
Maximum Likelihood Theory
.31
3.6.1
Kullback-Leibler Distance
.32
3.6.2
Log-Likelihood Function
.32
3.6.3
Akaike's Information Criterion
.33
3.6.4
Bayesian Information Criterion
.33
3.7
System Identification Theory
.34
3.7.1
Autoregressive
Exogenous Model
.34
3.7.2
Least Square Estimation
.37
3.8
Summary
.38
3.9
Problems
.39
Chapter
4
Computational Structural Biology. Protein Structure Prediction
.41
4.1
Introduction and Overview
.41
4.2
Protein Structure Prediction Methods
.42
4. 2.1
Ab Initio
Methods: Molecular Dynamics
.42
4.2.2
Comparative Methods
.42
4.2.2.1
Homology-Based Methods
.43
4.2.2.2
Threading Methods
.43
4.2.3
Hybrid/Informed Methods
.43
4.2.3.1
Artificial Neural Networks
.43
4.2.3.2
Hidden Markov Models
.44
4.2.3.3
Support Vector Machines
.45
4.2.3.4
Clustering Methods
.45
4.2.3.5
Blended Methods
.45
4.3
Data Resources
.46
4.3.1
Protein Sequence and Raw Structure Databases
.46
4.3.2
Protein Structure Classification Databases
.47
4.3.2.1
The SCOP Database
.47
4.3.2.2
Class, Architecture, Topology, and Homologous
Superfamily
.-.47
4.3.2.3
Molecular Modeling Database
.48
4.3.2.4
Fold Classification Based on Structure-Structure
Alignment of Proteins (FSSP/DALI) Database
.48
4.3.2.5
Spatial Arrangement of Backbone Fragments
Database
.49
4.3.2.6
InterPro
.49
x
Contents
4.4
Summary
.50
4.5
Problems
.50
References
.50
Chapter
5
Computational Structural Biology: Protein Sequence Analysis
.51
5.1
Introduction
.51
5.2
Pairwise Sequence Matching
.52
5.2.1
Pairwise Background
.52
5.2.2
Sequence Matching Methods
.52
5.2.2.1
Dot Plot Visualization Method
.53
5.2.2.2
Dynamic Programming
.53
5.2.2.3
Word Methods
.54
5.2.2.4
Bayesian Methods
.55
5.2.3
Statistical Significance
.55
5.3
Multiple Sequence Alignment
.55
5.3.1
Dynamic Programming
.56
5.3.2
Progressive Methods
.56
5.3.3
Iterative Strategies
.56
5.4
Summary
.56
5.5
Problems
.57
Chapter
6
Genomics and Proteomics
.59
6.1
Introduction and Overview
.59
6.2
Genomics
.59
6.2.1
Genetic Sequence Data
.59
6.2.2
Genetic Annotations
.60
6.2.3
Genomic Analysis
.60
6.2.4
Metagenomics
.61
6.3
Proteomics
.61
6.3.1
Protein Sequence Data
.62
6.3.2
Protein Annotations
.62
6.3.3
Proteomic Analysis
.63
6.4
Summary
.63
6.5
Problems
.64
Chapter
7
Methods for Identification of Differentially
Expressed Genes or Proteins
.65
7.1
Introduction and Overview
.65
7.2
Why
f
Test Is Not Enough?
.65
7.3
Mixture Model Method
.66
Contents xi
7.3.1 Basic
Formulations
.66
7.3.2
More
Advanced
Versions
.68
7.4 Genes
Involved in Leukemia: A Case Study
.70
7.5
Summary
.72
7.6
Problems
.72
References
.72
Chapter
8
Binary and Bayesian Networks as Static Models of
Regulatory Pathways
.73
8.1
Introduction and Overview
.73
8.2
Binary Regulator Pathways
.73
8.3
Bayesian Networks: Algorithm
.73
8.4
Applications and Practical Considerations
.74
8.5
Summary
.76
8.6
Problems
.76
Chapter
9
Metabolic Control Theory for Static Modeling of Metabolic Pathways
.77
9.1
Introduction and Overview
.77
9.2
Basic Ideas
.77
9.3
Main Concepts in Metabolic Control Theory
.79
9.3.1
Stepl
.79
9.3.2
Step
2.81
9.3.3
Step
3.82
9.4
Mason Method
.83
9.5
Metabolic Control Model for
Galactose
Regulation Pathway: A Case
Study
.86
9.6
Summary
.92
9.7
Problems
.93
References
.93
Chapter
10
System Identification and Control Theory for Dynamic Modeling of
Biological Pathways
.95
10.1
Introduction and Overview
.95
10.2
Methodology
.95
10.2.1
Nonlinear Factor Analysis
.97
10.2.2
ARX Model
.98
10.2.3
Linearized Model: Extracting Pathway Links from
Nonlinear Model
.101
10.3
Modeling of Cell Cycle: A Case Study
.102
10.3.1
Stability Analysis of System
.103
x¡¡
Contents
10.4
Summary
.106
10.5
Problems
.106
References
.107
Chapter
11
Gene Silencing for Systems Biology
.109
11.1
Introduction and Overview
.109
11.2
A Brief Review of
RNA
Interference, Small Interfering
RNA,
and Gene Silencing Mechanisms
.109
11.2.1
Pretranscriptional Gene Silencing
.109
11.2.2
Posttranscriptional Gene Silencing
.110
11.2.3
RNA
Interference
.110
11.3
Pathway Perturbation Using Gene Silencing
.
Ill
11.3.1
Overexpression
.
Ill
11.3.2
Gene Silencing
.112
11.3.3
Model Improvement and Validation
.112
11.4
Summary
.113
11.5
Problems
.113
References
.113
Chapter
12
Simulation and Systems Biology
.115
12.1
Introduction and Overview
.115
12.2
What Is Simulation?
.115
12.2.1
Power of Expression
.116
12.2.2
Economy of Form
.116
12.3
Challenges to Effective Simulation
.117
12.3.1
Identifying Meaningful Themes
.117
12.3.2
Detail Selection and Rejection
.118
12.3.3
Validation
.119
12.3.3.1
Measuring Quality Once
.119
12.3.3.2
Handling Stochastic Results
.119
12.4
CaseStudies
.120
12.4.1
Simulated Protein Folding: Rosetta@Home
.120
12.4.1.1
Generally How It Works
.121
12.4.1.2
Details to Use or Discard
.121
12.4.1.3
Computing Power
.122
12.4.1.4
Future Goals
.123
12.4.2
Simulated Protein Computing
.124
12.4.2.1
Generally How It Works
.124
12.4.2.1
Details to Use or Discard
.125
12.4.2.3
Computing Power
.128
12.4.2.4
Future Goals
.128
Contents xüi
12.5
Summary
.129
12.6 Problems.129
References
and Notes.129
Chapter
13
Software, Databases, and Other Resources for Systems Biology
.131
13.1
Introduction and Overview
.131
13.2
Databases
.132
13.2.1
Nucleotide Databases
.132
13.2.1.1
GenBank
.132
13.2.1.2 DNA Data
Bank of Japan
.132
13.2.1.3
European Molecular Biology Laboratory
.132
13.2.1.4
International Sequence Database
.132
13.2.2
Protein Database
.133
13.2.2.1
Swiss-Prot
.133
13.2.2.2
Protein Information Resource
.133
13.2.2.3
Translated EMBL
.133
13.2.2.4
Universal Protein Resource
.133
13.3
Scoring Matrix
.134
13.3.1
Point Accepted Mutation
.134
13.3.2
Blocks Substitution Matrix
.134
13.4
Analysis Software
.135
13.4.1
FASTA
.135
13.4.1.1
FASTA
Algorithm
.135
13.4.1.2
FASTA
Variants
.137
13.4.2
BLAST
.138
13.4.2.1
BLAST Algorithm
.138
13.4.2.2
BLAST Variants
.140
13.5
Bioinformatics in
MATLAB
.140
13.5.1
Sequence Analysis
.140
13.5.2
Sequence Alignment
.141
13.6
Summary
.141
13.7
Problems
.141
References
.141
Chapter
14
Future Directions
.143
14.1
Introduction and Overview
.143
14.2
Single-Cell Microarray and Systems Biology
.143
14.2.1
Microarrays to Identify Single Cells
.143
14.2.2
Microarray Analysis of a Single Cell
.145
14.3
High-Throughput Protein Assays and Systems Biology
.146
14.4
Integration of Molecular Data with Higher-Level
Datasets
.147
xiv Contents
14.4.1
Higher-Level Data Sets and Publishers
.148
14.4.2
Tools to Navigate Metadata
.149
14.4.3
Role of Higher-Level Data in Systems Biology
.149
14.5
Identifying Genes Controlling Macrolevel Changes
.150
14.5.1
Generate Candidate Markers
.151
14.5.2
Correlate Markers with Phenotype
.151
14.5.3
Infer Genes or Gene Expression Patterns
.152
14.6
Molecular-Level Image Systems and Systems Biology
.153
14.6.1
Molecular-Level Imaging
.153
14.6.2
Visual Analytics
.154
14.7
Summary
.155
14.8
Problems
.155
References and Notes
.156
Index
.159 |
| any_adam_object | 1 |
| author | Najarian, Kayvan Najarian, Siamak Gharibzadeh, Shahriar Eichelberger, Christopher N. |
| author_GND | (DE-588)1067772138 (DE-588)1107777968 (DE-588)1107779499 |
| author_facet | Najarian, Kayvan Najarian, Siamak Gharibzadeh, Shahriar Eichelberger, Christopher N. |
| author_role | aut aut aut aut |
| author_sort | Najarian, Kayvan |
| author_variant | k n kn s n sn s g sg c n e cn cne |
| building | Verbundindex |
| bvnumber | BV035814196 |
| callnumber-first | Q - Science |
| callnumber-label | QH324 |
| callnumber-raw | QH324.2 |
| callnumber-search | QH324.2 |
| callnumber-sort | QH 3324.2 |
| callnumber-subject | QH - Natural History and Biology |
| classification_rvk | WC 7700 |
| contents | Includes bibliographical references and index |
| ctrlnum | (OCoLC)312625448 (DE-599)BVBBV035814196 |
| dewey-full | 570.285 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 570 - Biology |
| dewey-raw | 570.285 |
| dewey-search | 570.285 |
| dewey-sort | 3570.285 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| format | Book |
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| genre | Einführung gnd |
| genre_facet | Einführung |
| id | DE-604.BV035814196 |
| illustrated | Not Illustrated |
| indexdate | 2025-03-19T11:01:21Z |
| institution | BVB |
| isbn | 9781420046502 |
| language | English |
| lccn | 2009009352 |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-018673063 |
| oclc_num | 312625448 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-578 |
| owner_facet | DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-578 |
| physical | xxiii, 166 Seiten Diagramme |
| publishDate | 2009 |
| publishDateSearch | 2009 |
| publishDateSort | 2009 |
| publisher | CRC Press, Taylor & Francis Group |
| record_format | marc |
| spelling | Najarian, Kayvan Verfasser aut Systems biology and bioinformatics a computational approach Kayvan Najarian, Siamak Najarian, Shahriar Gharibzadeh, Christopher N. Eichelberger Boca Raton ; London ; New York CRC Press, Taylor & Francis Group [2009] © 2009 xxiii, 166 Seiten Diagramme txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Bio-informatique Biologie systémique Bioinformatics Systems biology Computational biology Computational Biology Systems Biology Mathematische Methode (DE-588)4155620-3 gnd rswk-swf Systembiologie (DE-588)4809615-5 gnd rswk-swf Bioinformatik (DE-588)4611085-9 gnd rswk-swf Einführung gnd rswk-swf Systembiologie (DE-588)4809615-5 s Mathematische Methode (DE-588)4155620-3 s Einführung f DE-604 Bioinformatik (DE-588)4611085-9 s b DE-604 Najarian, Siamak Verfasser (DE-588)1067772138 aut Gharibzadeh, Shahriar Verfasser (DE-588)1107777968 aut Eichelberger, Christopher N. Verfasser (DE-588)1107779499 aut Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018673063&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Najarian, Kayvan Najarian, Siamak Gharibzadeh, Shahriar Eichelberger, Christopher N. Systems biology and bioinformatics a computational approach Includes bibliographical references and index Bio-informatique Biologie systémique Bioinformatics Systems biology Computational biology Computational Biology Systems Biology Mathematische Methode (DE-588)4155620-3 gnd Systembiologie (DE-588)4809615-5 gnd Bioinformatik (DE-588)4611085-9 gnd |
| subject_GND | (DE-588)4155620-3 (DE-588)4809615-5 (DE-588)4611085-9 |
| title | Systems biology and bioinformatics a computational approach |
| title_auth | Systems biology and bioinformatics a computational approach |
| title_exact_search | Systems biology and bioinformatics a computational approach |
| title_full | Systems biology and bioinformatics a computational approach Kayvan Najarian, Siamak Najarian, Shahriar Gharibzadeh, Christopher N. Eichelberger |
| title_fullStr | Systems biology and bioinformatics a computational approach Kayvan Najarian, Siamak Najarian, Shahriar Gharibzadeh, Christopher N. Eichelberger |
| title_full_unstemmed | Systems biology and bioinformatics a computational approach Kayvan Najarian, Siamak Najarian, Shahriar Gharibzadeh, Christopher N. Eichelberger |
| title_short | Systems biology and bioinformatics |
| title_sort | systems biology and bioinformatics a computational approach |
| title_sub | a computational approach |
| topic | Bio-informatique Biologie systémique Bioinformatics Systems biology Computational biology Computational Biology Systems Biology Mathematische Methode (DE-588)4155620-3 gnd Systembiologie (DE-588)4809615-5 gnd Bioinformatik (DE-588)4611085-9 gnd |
| topic_facet | Bio-informatique Biologie systémique Bioinformatics Systems biology Computational biology Computational Biology Systems Biology Mathematische Methode Systembiologie Bioinformatik Einführung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018673063&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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