Computational methods in cell biology:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2012
|
| Ausgabe: | 1. ed. |
| Schriftenreihe: | Methods in cell biology
110 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XVI, 410 S., [7] Bl. Ill., graph. Darst. |
| ISBN: | 9780123884039 |
Internformat
MARC
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| 008 | 120629s2012 ad|| |||| 00||| eng d | ||
| 020 | |a 9780123884039 |9 978-0-12-388403-9 | ||
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| 245 | 1 | 0 | |a Computational methods in cell biology |c ed. by Anand R. Asthagiri ... |
| 250 | |a 1. ed. | ||
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier, Acad. Press |c 2012 | |
| 300 | |a XVI, 410 S., [7] Bl. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a Methods in cell biology |v 110 | |
| 650 | 0 | 7 | |a Cytologie |0 (DE-588)4070177-3 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Bioinformatik |0 (DE-588)4611085-9 |2 gnd |9 rswk-swf |
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| 700 | 1 | |a Asthagiri, Anand R. |e Sonstige |4 oth | |
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| 999 | |a oai:aleph.bib-bvb.de:BVB01-025138697 | ||
Datensatz im Suchindex
| _version_ | 1804149293615939584 |
|---|---|
| adam_text | CONTENTS
Contributors
■ xi
Preface
xv
1.
Principles of Model Building: An Experimentation-Aided Approach
to Development of Models for Signaling Networks
Ambhighainath Ganesan and Andre Levchenko
I. Introduction
2
II. Signaling Systems and Mathematical Models
3
III. Experimentation-aided Model Development
4
IV Conclusion
· 16
Acknowledgments
16
References
16
2.
Integrated Inference and Analysis of Regulatory Networks from Multi-Level
Measurements
Christopher S. Poultney, Alex Greenfield, and Richard Bonneau
I. Introduction
20
II. Overview of Model/Algorithm
25
III. Biological Insights
33
IV Open Challenges
38
V Computational Methods
40
References
50
3.
Swimming Upstream: Identifying Proteomic Signals that Drive Transcriptional
Changes using the Interactome and Multiple -Omics
Datasets
Shao-shan Carol Huang and Ernest Fraenkel
I. Introduction
58
II. Computational Methods
61
III. Biological Insights
70
IV Open Challenges
74
Acknowledgments
77
References
77
Contents
4.
A
Framework
for Modeling the Relationship between Cellular Steady-state
and Stimulus-responsiveness
Paul M. Loriaux and Alexander Hoffmann
I. Introduction
82
II. Overview of Algorithm
83
III. Biological Insights
91
IV. Open Challenges
95
V Computational Methods
96
Further Reading
107
References
· 108
5.
Stochastic Modeling of Cellular Networks
Jacob Stewart-Ornstein and
Hana El-Samad
I. Introduction
112
II. The Need for a Stochastic Modeling Framework
114
III. Overview of Computational Approach
115
IV. Biological Insights from Computational Approaches
116
V Computational Methods
117
VI. Open Challenges
129
VII.
Conclusions
134
References
134
Further Reading
137
6.
Quantifying Traction Stresses in Adherent Cells
Casey M. Kraning-Rush, Shawn P. Carey, Joseph P. Califano,
and Cynthia
A. Reinhart-King
I. Introduction
140
II. Overview of Method
142
III. Biological Insights from Traction Methods
155
IV Open Challenges
159
V Methods
160
VI. Summary
172
Acknowledgments
172
References
172
Further Reading
177
7.
CellOrganizer: Image-Derived Models of Subcellular Organization
and Protein Distribution
Robert F. Murphy
I. Introduction
180
II. Components of a Model of Subcellular Organization
and Protein Distribution
181
III. Models of Subcellular Organization
181
Contents
IV
Protein
Distributions
Across Subcellular Structures
190
V Use of Models for Testing Algorithms
191
VI. Conclusion
191
Acknowledgments
192
References
192
Spatial Modeling of Cell Signaling Networks
Ann E. Cowan, Ion I. Moraru, James C.
Schaff,
Boris M. Slepchenko,
and Leslie M. Loew
I. Introduction
196
II. Overview of Spatial Modeling
197
III. Building a Spatial Model
202
IV Running Spatial Simulations with VCell: Numerical Method
and Simulation Parameters
209
V Application to a Specific Example: cAMP Signaling
in
Neuronal
Cells
213
Acknowledgments
218
References
218
Further Reading
220
9.
Stochastic Models of Cell Protrusion Arising from Spatiotemporal
Signaling and Adhesion Dynamics
Erik S.
Welf
and Jason M. Haugh
I. Introduction
224
II. Model Synthesis
224
III. Model Analysis
228
IV Biological Insights from the Modeling Approach
232
V Open Challenges
234
VI. Computational Methods
235
Acknowledgments
239
References
239
10.
Nonparametric Variable Selection and Modeling for Spatial
and Temporal Regulatory Networks
Anil Aswani, Mark D. Biggin, Peter Bickel, and Claire
Tomiin
I. Introduction
244
II. Overview of the NODE Model
246
III. Biological Insights
252
IV Open Challenges
256
V Computational Methods
256
VI. Building a NODE Model
256
VII.
Building a Comb Diagram with the NALEDE Extension
258
Further Reading
259
Acknowledgments
259
References
260
Contents
11. Quantitative Models
of the Mechanisms that Control Genome-Wide Patterns
of Animal Transcription Factor Binding
Tommy Kaplan and Mark D. Biggin
I. Introduction
■ 264
II. Overview of Model/Algorithm
265
III. Biological Insights
270
IV Open Challenges
. 275
V Computational Methods
276
VI. Glossary
279
Further Reading
280
References
280
12.
Computational Analysis of Live Cell Images of the Arabidopsis thaliana Plant
Alexandre
Cunha,
Paul
T.
Tarr,
Adrienne
Н.К.
Roeder,
Alphan
Aitinole,
Eric Mjolsness,
and Elliot
M.
Meyerowitz
I. Introduction
286
II. Overview of Systems and Methods
288
III. Biological Insights
299
IV Open Computational Challenges
300
V Imaging and Computational Methods
302
VI. Further Reading
319
Acknowledgments
320
References
320
13.
Multi-Scale Modeling of Tissues Using CompuCelBD
Maciej
H.
Swat,
Gilberto
L.
Thomas, Julio
M.
Belmonte,
Abbas Shirinifard,
Dimitrij Hmelj
ak,
and James A. Glazier
I. Introduction
326
II. Glazier-Graner-Hogeweg (GGH) Modeling
326
III. CompuCelBD
331
IV Building CC3D Models
333
V Conclusion
362
Acknowledgments
362
References
363
14.
Multiscale Model of Fibrin Accumulation on the Blood Clot Surface
and Platelet Dynamics
Zhiliang Xu, Scott Christley, Joshua Lioi,
Oleg
Kim, Cameron Harvey,
Wenzhao Sun, Elliot D. Rosen, and Mark
Al ber
I. Introduction
368
II. Biological Background
370
III. Overview of the Modeling Approach
372
IV Study of the Role of the Fibrin Network
373
Contents ix
V
Multiscale
Model of
Thrombus
Development with Fibrin
Network Formation
377
VI. GPU Implementation of the Simulation of the Platelet-Blood
Flow Interaction
381
VII.
Concluding Remarks
385
Acknowledgments
386
References
386
Index
389
Volumes in Series
401
|
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| discipline | Biologie |
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| indexdate | 2024-07-10T00:20:44Z |
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| isbn | 9780123884039 |
| language | English |
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| series | Methods in cell biology |
| series2 | Methods in cell biology |
| spelling | Computational methods in cell biology ed. by Anand R. Asthagiri ... 1. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2012 XVI, 410 S., [7] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in cell biology 110 Cytologie (DE-588)4070177-3 gnd rswk-swf Bioinformatik (DE-588)4611085-9 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Bioinformatik (DE-588)4611085-9 s Cytologie (DE-588)4070177-3 s b DE-604 Asthagiri, Anand R. Sonstige oth Methods in cell biology 110 (DE-604)BV002534878 110 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025138697&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Computational methods in cell biology Methods in cell biology Cytologie (DE-588)4070177-3 gnd Bioinformatik (DE-588)4611085-9 gnd |
| subject_GND | (DE-588)4070177-3 (DE-588)4611085-9 (DE-588)4143413-4 |
| title | Computational methods in cell biology |
| title_auth | Computational methods in cell biology |
| title_exact_search | Computational methods in cell biology |
| title_full | Computational methods in cell biology ed. by Anand R. Asthagiri ... |
| title_fullStr | Computational methods in cell biology ed. by Anand R. Asthagiri ... |
| title_full_unstemmed | Computational methods in cell biology ed. by Anand R. Asthagiri ... |
| title_short | Computational methods in cell biology |
| title_sort | computational methods in cell biology |
| topic | Cytologie (DE-588)4070177-3 gnd Bioinformatik (DE-588)4611085-9 gnd |
| topic_facet | Cytologie Bioinformatik Aufsatzsammlung |
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