Voit E. — Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists :: Электронная библиотека попечительского совета мехмата МГУ

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Voit E. — Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists

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Название: Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists

Автор: Voit E.

Аннотация:

A true understanding of genetic and metabolic function and design is facilitated by mathematical and computational methods for analyzing biochemical systems. This hands-on reference teaches biochemists and molecular biologists the use of modern computational methods for the analysis of complex biomedical systems requiring a modest mathematical background. The book begins with representations of biochemical systems, provides guidelines for setting up models, details mathematical and computational methods of parameter estimation and model analysis, and connects to the modern literature with four detailed case studies. Every step is illustrated with examples and explored with accompanying PLAS software. The volume also features over 250 exercises with about one quarter fully or partially solved.

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Рубрика: Computer science/

Статус предметного указателя: Готов указатель с номерами страниц

ed2k: ed2k stats

Год издания: 2000

Количество страниц: 550

Добавлена в каталог: 19.02.2014

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Предметный указатель

" $\&\&$ " declaration (of independent variable)      121 240 376 393 394
"at" (@) statement      110
$CO_{2}$ production      294 297 298 300 324
$Excel^{\textregistered}$       228
$Gauss^{\textregistered}$       200
$K_{M}$       21 43 64 142 145 159 160 165 169 188 374 418 444
$Maple^{\textregistered}$       200
$MathCad^{\textregistered}$       200
$Mathematica^{\textregistered}$       167 172 200 407
$NAD^{+}$       27 262 263 264 275 283 288 366
$PowerPoint^{\textregistered}$       106 228
$p_{i}$       28 345 346 347 351 353 363 369 370 372
$SAS^{\textregistered}$       178
$Statistica^{\textregistered}$       178 179 180
$\alpha$ -ketoglutarate      31 32 165 299 308 310 313 314 319 443
$\alpha$ -ketoglutarate dehydrogenase      300 314
$\alpha$ -term      52 54 67 70 73 77 78 201 210 219 229 240 277 445 449
$\beta$ -5-phosphoribosyl amine      32 329—330 331
$\beta$ -terms      23 50 51 52 70 73 77—80 82 108 194 201 210 219 229 237 240 244 247 265 267 287 446 450 462 463
$\beta$ -terms aggregation      277—278
3-phosphoglycerate (3PG)      20—21 264
3-phosphohydroxyglycerate      23
3-Phosphohydroxypyruvate      20 22 23
5'(3')-nucleotidase (3NUC)      334 348
5'-nucleotidase (5NUC)      331 334 348
5-adenosylmethionine      32
Absolute change      22 55 68—69 71 225 230
Abstraction      57 326
Accumulation      46 64 77 109 128 132 133 167 262 295 345 402 408
Accuracy      58 59 67 83 92 106 107 148 149 157 158 226 315 319 336 340 357 388 395 398 404—410 419 444 450 461
Acerenza, L.      62 155 157 175 186 190 246 478
Acetate      249
Acetyl-CoA      188 297 308 309 310 311 313 314 320 457
Achs, M.J.      38 469 474
Aconitase      312 314
Activation and activators      54 55 115 126 135 183 215 327 444 see
Activation and activators allosteric      273 275 346
Activation and activators in anaerobic fermentation pathway      262
Activation and activators in maltose catabolic system      401
Activation and activators of carbamoyl phosphate synthetase      153
Activation and activators of degradation      220
Activation and activators of gene regulation      400 401 402 407
Activation and activators of pancreatic zymogen      29—31
Activation and activators of purine metabolism      334 349
Activation and activators of reaction      14 27 28 86 112—113
Activation and activators, branched pathway with      236
Activation and activators, feedback      198 206 220
Activation and activators, feedforward      279
Activation and activators, inhibition compared      4 220
Activation and activators, kinetic orders      145
Activation and activators, notation      14 27 55 349
Activation and activators, phosphorylase cascade      86
Activation and activators, strength of      216 380
Activation and activators, time-dependent      295
Ad hoc models      58
Ad hoc symbols      78
Adams, M.D.      8 473
Additive      3 219 406
Adenine (Ade)      56 146 247 331 333 335 336 338 340 342—345 347 351 352 363
Adenine (Ade) excretion      146 149—150 338 346 364
Adenine (Ade) oxidation      348
Adenine phosphoribosyltransferase (APRT)      328 329 334 341 348 349
Adenosine (Ado)      56 328 333 336 343 347 352
Adenosine deaminase (ADA)      331 334 348
Adenosine diphosphate (ADP)      27 56
Adenosine monophosphate (AMP)      56 90 128 263 271 272 274 275 290 328 330 331 333 335 336 346 347 349 351 352 454
Adenosine triphosphate (ATP)      12 14 27 28 56 90 128 150 152 153 167 168 187 188 247—249 262—264 267 269 270—272 274—278 283 290—292 297 327 328 330 333 336 342 343 346—348 352 362 366 454 458
Adenylate kinase      263
Adenylates      56 128 263 274 283 330 331 335 340 342—346 351 352 354—356 363 454 458
Adenylosuccinate (S-AMP)      56 330 331 333 336 338 346 347 352
Adenylosuccinate lyase (ASLI)      348
Adenylosuccinate synthetase (ASUC)      334 348
Adolph, E.F.      56 469
Adrenaline      6 38
Aerobic ATP formation      247
Affinity      109
Affymetrix      18
Aggregated kinetic order      85 87 267 338 339 342 355 357
Aggregation of fluxes      83 87 91—92 119 288
Aggregation of terms      265 267 272 351 448
Agresar, G.      129 469
Ahmad Mahir, B.R.      411 479
Akaoka, L.      359 474
Akerboom, T.P.M.      162 163 372 475
Akiyama, Y.      16 474
Alanine (ALA)      299 309 310 311 313 315 319 320 322 456
Alanine transaminase      300
Albe, K.R.      171 293 297 298 301 310 315 323 325 469 494
Alcohol      2
Alcon, C.H.      83 223 286 290 396 408 409 490
Algebra      62 167 173 191 200 209 252 391 395 406 407 413 414 426
Algebra Boolean      63
Algebraic analysis      see "Algebraic steady-state evaluation"
Algebraic steady-state evaluation      61
Algebraic steady-state evaluation of glycolytic-glycogenolytic pathway in perfused rat liver      365—398
Algebraic steady-state evaluation of irregular S-systems      206—208
Algebraic steady-state evaluation of linear pathway with feedback      84 212—213
Algebraic steady-state evaluation of pathway with feedback and cross-activation      213—216
Algebraic steady-state evaluation of regular S-systems      83 119 121 201—206
Algebraic steady-state evaluation, branch point constraints      393—395
Algebraic steady-state evaluation, examples      212—216
Algebraic steady-state evaluation, exercises      217—221
Algebraic steady-state evaluation, kinetic order sensitivities      395
Algebraic steady-state evaluation, local stability      208—216
Algebraic steady-state evaluation, log gains of fluxes      385—388
Algebraic steady-state evaluation, log gains of metabolites      384—385
Algebraic steady-state evaluation, matrix notation      200
Algebraic steady-state evaluation, precursor-product relationships      391—393
Algebraic steady-state evaluation, rate constant sensitivities      390—395
Algebraic steady-state evaluation, steady-state equations      193—198 380—384
Algebraic steady-state evaluation, transition time      216—217 389—390
Algebraic steady-state evaluation, two-variable system      212
Algebraic steady-state evaluation, unconstrained parameters      391
Algebraic steady-state evaluation, zero steady states      198—200
Alginate-immobilized cells      260
Alignments, sequence      18
Alippi, C.      174 483
Allele      149
Allometry/allometric relationships      55—56 57 70—73 74
Allopurinol      353 360 361 364
Allosteric activator      273 275 346
Allosteric enzymes      163 271
Allosteric inhibition      76
Allosteric Michaelis-Menten reaction      302
Alphabet      62
Amendment of models      32 81 128 295 297 326 331 343 344 346 351 361
Amidophosphoribosyltransferase (ATASE)      329 334 340 348 361
AMP deaminase (AMPD)      334 340 345 348 355—356 357 363
Amphibolic pathways      25 92
Amplification/amplifiers      86 222 312 314 322
Amplitudes      110 111 116 117 118 121 125 137 409 449
Anaerobic fermentation pathway      260—261
Anaerobic fermentation pathway, activators      262
Anaerobic fermentation pathway, aggregation of $\beta$ -terms      277—278
Anaerobic fermentation pathway, analysis of model      279—284
Anaerobic fermentation pathway, ATP dynamics, constraints      287—289
Anaerobic fermentation pathway, data      268
Anaerobic fermentation pathway, dynamics      282—283
Anaerobic fermentation pathway, enzyme concentrations      287—288
Anaerobic fermentation pathway, exercises      290—292
Anaerobic fermentation pathway, expansion of model      284
Anaerobic fermentation pathway, features      261—262
Anaerobic fermentation pathway, flux maximization      286—290
Anaerobic fermentation pathway, fructose-l,6-diphosphate degradation      273—275
Anaerobic fermentation pathway, glucose-6-phosphate degradation      271—273
Anaerobic fermentation pathway, glycogen synthetase reaction      272—273
Anaerobic fermentation pathway, GMA equations      265—268
Anaerobic fermentation pathway, hexokinase step      269—271
Anaerobic fermentation pathway, linear programming      285—286
Anaerobic fermentation pathway, logarithmic gains      280—282

Anaerobic fermentation pathway, mass conservation      288—289
Anaerobic fermentation pathway, metabolite concentration      288
Anaerobic fermentation pathway, objective function      286—287
Anaerobic fermentation pathway, optimization      284—286 289—290
Anaerobic fermentation pathway, parameter values      268—277
Anaerobic fermentation pathway, phosphofructokinase reaction      271—272
Anaerobic fermentation pathway, properties of model      279—284
Anaerobic fermentation pathway, pyruvate kinase reaction      275
Anaerobic fermentation pathway, robustness of model      283—284
Anaerobic fermentation pathway, S-system representation      277—278
Anaerobic fermentation pathway, sensitivities      282
Anaerobic fermentation pathway, steady state      280 287
Anaerobic fermentation pathway, sugar transport      268—269
Anaerobic fermentation pathway, variables defined      262—265
Analytical evaluation      14 83
Analytical solution      65—66 75 210 350 353 406 410
Anderson, M.L.      315 325 493
Anderson, S.P.      17 472
Animal experiments      8 362 365 401
Antagonistic interactions      11
Anton, H.J.      410 491
Apparent first-order rate constant      308
Appel, R.D.      9 493
Appenzeller, T.      5 474
Approximate character      8 3
Approximation in biochemical system models      37—38 57 88 90 142 144 147 160 164 184 225 226 290 338 357 360 403 404 409 414 417—421 425 426 440 447 448 450 466 467
Approximation of degradation      59
Approximation second-order      406
Approximation theory      56 57
Apweiler, R.      18 469
Arcs      64
Arginine      401
Argonne National Laboratory      16
Aromatic amino acid      20
Arrayer      17
arrows      151 315
Arrows arched      135
Arrows bi-directional      28—29
Arrows curved      349
Arrows dashed      443
Arrows dotted      443
Arrows double-headed      25 26 27 28—29 346
Arrows double-tailed      27 28—29 87 346
Arrows, activation      349
Arrows, feedback control      4 13 251
Arrows, flow      14 20 23 25 27 28—29 31 93 130 133 251 443
Arrows, flux      25 26 27
Arrows, improper diagrams      14 31 443
Arrows, inhibition      349
Arrows, modulation      26 27 31 155
Arrows, signal      443
artificial intelligence      61
Aspartate $\beta$ -semialdehyde      32
Aspartate (ASP)      32 299 300 309 310 315—317 319 325 457 458
Aspartate transaminase      300 308
Aspartyl phosphate      32
Aspergillus niger      162 167—171
Associative      3 23 414 439
assumptions      37 38 39 49 58 72 128 139 144 171 178 241 283 307 322 325 326 330 343 363 379 391 396 406
Assumptions, quasi-steady-state      37
Asymptomatic      364
ATP turnover      187 247 248 249
Auscher, C.      364 472
Australian National Genomic Information Service (ANGIS)      18
Autogenous circuits      400
Automata theory      63
Auxiliary variables      102 138 220 370
Averet, N.      323 483
Ayvazian, J.H.      343 345 469
Backward reaction      98
bacteria      8 11 17 295 327 405
Bailey, J.E.      61 187 260 261 268 269 270 273 396 405 409 474 475 476 487
Bairoch, A.      15 18 469
Baker's yeast      8
balance      52 72 95 195 196 283 296 317 323 333 334 353 370 438
Balance equation      61 93 94 267 371
Balthis, W.L.      140 411 469 491
Bangerter, J.K.      140 469
Barber, J.R.      343 470
Barker, J.L.      63 493
Barker, W.C.      18 470 474
Barrell, B.G.      8 9 475
Barry, C.E., 3rd.      8 471
Bartel, T.      327 470
Bartelmess, I.B.      149 473
Baseline      109 112 114 116 140 141 142 148 228 232
Baseline experiment      52 115
Basmanova, S.      15 487
Bassham, J.A.      367 373 374 470
batch processes      22 23 412
Batschelet, E.      56 470
Battey, J.      8 470
Baxevanis, A.D.      15 470
Becker, M.A.      355 359 364 470 477
Bel-Enguix, G.      62 471
Benson, D.A.      18 470
Berg, P.H.      174 183 470
Bernstein, EC.      18 470
Berry, M.N.      415 421 422 470
Best fit      151 174
Best-case scenario      140
Bhalla, U.S.      3 171 493
Bi bi      301 302
Bi-directional arrows      28—29
Bi-directional processes      315 325
Bi-phasic response      107
Bi-substrate reaction      46 47
Bicyclic glutamine synthase cascade      86
Bimolecular reactions      53 87 88—89 171
Bin Razali, A.M.      175 176 189 404 490
Binns, M.R.      297 484
Biochemical interpretation      8 9
Biochemical map      see "Maps biochemical"
Biochemical parameters      63 see
Biochemical reactions      55
Biochemical signals      9 14 17 47 53 63 86 93 187 248 284 314 320 330—331 397 444
Biochemical system models      7
Biochemical system models, alternatives to S-system models      58—64
Biochemical system models, analytical convenience      58
Biochemical system models, approximations      37—38
Biochemical system models, change in dependent variables      39 41—49 51 56
Biochemical system models, computer simulations      38—39
Biochemical system models, differential equations      42 43 45 47 48 65—67
Biochemical system models, examples      52 54—55
Biochemical system models, exercises      64—65 75
Biochemical system models, integrated      39 40—41
Biochemical system models, kinetic orders      37 53—54 55
Biochemical system models, linear relationships      56
Biochemical system models, mechanistic approach      39
Biochemical system models, networks as languages      62—64
Biochemical system models, parameters      39 51—55
Biochemical system models, power-function representations      59—60
Biochemical system models, rate constants      51—52
Biochemical system models, rate laws in      37—43 47
Biochemical system models, relative changes in flux      73—75
Biochemical system models, S-system form      49—51 55—58 65—75
Biochemical system models, stoichiometric network form      60—62
Biochemical system models, theoretical justification      57—58 60 70—73
Biochemical system models, validity      55—57
Biochemical system models, variables      17 24 25 38 39 48 56
Biochemical time scales      6 209 307 403 404
Bioinformatics      8 9 16 18 19
Biomass allocation      404
Biomolecular structures      18
Biomolecular time scales      6
Biotechnological optimization      83 260 285 390 397
biotechnology      18 22 62 64 223 284 287 290 400
Bish, D.R.      171 470
Bittner, M.      18 473
Blecker, J.      410 491

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