Systems Biology (Methods in Molecular Biology)

Epithelial-Mesenchymal Transition (EMT).........99–101,
103–105, 107, 108, 112, 115, 118, 121, 152
Extracellular matrix (ECM)..............................7, 23,100,
107, 151, 206

F

Feedback loops...........................................128, 217, 227,
234–236, 252, 254, 255
Fingerprint
biochemical..............................................................328
“First order” phase transition..............................163, 164
Fisher Information Matrix (FIM)...............57, 58,75–77
Fluctuation analysis..............................................277–289
Fluorescence correlation spectroscopy (FCS) ....278, 284
Fluorophores (GFP-tagged)................................278, 288
Force-fields ...................................................308–314, 325
Fractal dimension (FD)............................... 98,105, 106,
109, 111, 132, 134, 136, 137, 143–145, 164,
346, 348

G

Gene expressions..............................9, 11,28–37, 63, 64,
67, 68, 96, 97, 99, 129, 198, 199, 219, 221, 224,
227, 234, 237, 258, 264, 265, 291, 292, 298,
299, 304
Gene set variation analysis (GSVA)....................292, 293,
299, 300
Gene targeting......................................................258, 266
Genetic mutation patterns...................................217, 227
Genetic switch.....................................217, 219, 225, 241
Genomes............................... 3, 8, 9, 23, 29, 33, 36,129,
154, 216, 217, 230, 234, 237, 239, 264,
291–293, 338, 350
Genotype.....................................................217, 237, 264
Genotyping..................................................217, 237, 264
Gibbs free energy...........................................96,109, 149
Glycolitic oscillations....................................................131
Growth (tumor)..................................... 7,129, 132–146,
158, 159, 164

H

HeLa tumor cells........................................149, 151, 153,
156, 159, 164
Hepatocellular carcinoma (HCC)......................217, 219,
222, 223, 225, 227, 228, 230, 232, 234–238,
240, 241
Heterogeneity........................8,133, 173, 188, 196–198,
210, 228, 278, 339, 340
High-speed single-particle tracking (SPT)..................277
Hysteresis........................................................33,100, 236

I

Identifiability (of systems) ..................................... 71, 128
ImageJ.........................................346–348, 352, 354, 357

Inducible systems..........................................................190

Inflammation......................................186, 216–218, 220,

234–236, 239, 240, 328

Intracellular signaling pathways ...................................129

Invariants...................................... 20,45–47, 73, 84, 310

Ising models.........................................................319–323

Isogenic DNA

K

Kreb’s cycle.....................................................35,173, 182

L

Lacunarity.............................................................108, 346

Landscape ................................30, 96, 97,112, 126–136,

138–140, 142–144, 146–154, 156, 157, 159,

161, 162, 164, 198, 237–240, 307

Linear discriminant analysis (LDA).....................332, 333

Linear stability analysis.....................................84–88, 173

Lyapunov function..............................................118, 132,

133, 144, 145, 163

LZ complexity..............................................138, 160–162

M

Mass action kinetics............................174, 175, 177, 179

Mathematical modeling............................. 17, 20, 21, 23,

41–54, 61, 71, 77, 79, 83, 95–121, 126, 129, 200,

205, 206, 209, 211, 248, 251, 255–258, 260,

261, 324, 337, 338

Mathematics.........................................16, 17,19–21, 23,

41–54, 61, 81, 101, 126, 128, 129, 173, 174,

200, 203–207, 209–211, 220, 225, 240, 241,

248, 251, 255–258, 260, 261, 264, 324, 328,

335, 337, 338

Maximum Entropy (Principle of)........................150, 163

Membrane heterogeneity.............................................278

Metabolic rates.............................................131, 143–145

Metabolism........................................ 7, 33, 37,144, 146,

148–150, 152, 156, 158, 163, 173, 196, 218,

219, 221, 223, 234, 334

Metabolomics.............................258, 328–335, 350, 352

Metastasis...........................................133, 134, 136, 144,

148, 151, 152, 158, 159, 248–250

Metastatic cells.....................................................141, 216

Microenvironment..........................................7–9, 11, 24,

36, 99, 100, 129, 151, 157, 216, 346

MicroRNAs (miRNAs)................................ 11,219, 222,

249, 252, 255, 264–266, 268, 269, 272

Model analysis..................................................49–52, 257

Modeling....................................... 17, 20, 21, 23,41–54,

57, 59, 61, 63, 67, 126, 128, 129, 139, 160, 172,

174–177, 179, 181, 190, 200, 203–211, 220,

225, 248–251, 255–258, 260, 261, 263, 264,

272, 278, 308, 311, 312, 319, 338

Modular....................179, 217, 218, 222, 224, 225, 240

362
SYSTEMSBIOLOGY
Index