Systems biology and bioinformatics: a computational approach
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Hauptverfasser: | , , , |
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Format: | Buch |
Sprache: | English |
Veröffentlicht: |
Boca Raton ; London ; New York
CRC Press, Taylor & Francis Group
[2009]
|
Schlagworte: | |
Online-Zugang: | Inhaltsverzeichnis |
Beschreibung: | xxiii, 166 Seiten Diagramme |
ISBN: | 9781420046502 |
Internformat
MARC
LEADER | 00000nam a2200000 c 4500 | ||
---|---|---|---|
001 | BV035814196 | ||
003 | DE-604 | ||
005 | 20160722 | ||
007 | t | ||
008 | 091107s2009 |||| |||| 00||| eng d | ||
010 | |a 2009009352 | ||
020 | |a 9781420046502 |c hardcover : alk. paper |9 978-1-4200-4650-2 | ||
035 | |a (OCoLC)312625448 | ||
035 | |a (DE-599)BVBBV035814196 | ||
040 | |a DE-604 |b ger |e rda | ||
041 | 0 | |a eng | |
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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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999 | |a oai:aleph.bib-bvb.de:BVB01-018673063 |
Datensatz im Suchindex
_version_ | 1804140767097126912 |
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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 |
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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 | 2024-07-09T22:05:12Z |
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 Systembiologie (DE-588)4809615-5 gnd rswk-swf Mathematische Methode (DE-588)4155620-3 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 Systembiologie (DE-588)4809615-5 gnd Mathematische Methode (DE-588)4155620-3 gnd Bioinformatik (DE-588)4611085-9 gnd |
subject_GND | (DE-588)4809615-5 (DE-588)4155620-3 (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 Systembiologie (DE-588)4809615-5 gnd Mathematische Methode (DE-588)4155620-3 gnd Bioinformatik (DE-588)4611085-9 gnd |
topic_facet | Bio-informatique Biologie systémique Bioinformatics Systems biology Computational biology Computational Biology Systems Biology Systembiologie Mathematische Methode 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 |
work_keys_str_mv | AT najariankayvan systemsbiologyandbioinformaticsacomputationalapproach AT najariansiamak systemsbiologyandbioinformaticsacomputationalapproach AT gharibzadehshahriar systemsbiologyandbioinformaticsacomputationalapproach AT eichelbergerchristophern systemsbiologyandbioinformaticsacomputationalapproach |