Bioinformatics : the machine learning approach

Bioinformatics : the machine learning approach

  • نوع فایل : کتاب
  • زبان : انگلیسی
  • مؤلف : Pierre Baldi; Søren Brunak
  • ناشر : Cambridge, Mass. : MIT Press
  • چاپ و سال / کشور: 2001
  • شابک / ISBN : 9780262025065

Description

accession number human, 2 active sampling, 97 aging, 300 Alice in Wonderland, 31 alpha-helix, 29, 38, 118, 120, 121, 128, 141, 151, 186, 196, 242, 247 alphabet, 1, 67, 72, 113, 128, 167, 236 merged, 118 reduced, 116 alternative splicing, 4, 43 Altschul, S.F., 35 amino acids, 1, 26, 118, 167, 169 codons, 140 composition, 126, 129, 145 dihedral angle, 120 encoding, 115, 128, 139 genetic code, 26, 137 GES scale, 143 glycosylation, 41 hydrophobicity, 26, 133, 137, 141, 195 in beta-sheets, 115 in helix, 29, 38, 118 in HMM, 195 orthogonal encoding, 121 pathways, 137 substitution matrices, 35, 36, 209, 244, 267, 276 Anastasia, 265 ancestor, 95 Anderson, A., 265 antique DNA (aDNA), 265 Arabidopsis thaliana, 10, 20, 40, 42, 145, 149 archaon, 7 asymmetric window, 114 asymmetric windows, 134 background information, 49, 51, 53 backpropagation, 83, 104, 111, 113, 121, 126, 128, 138, 139, 179, 246, 249 adaptive, 138, 140 learning order, 151 bacteria, 9, 133 bacteriophage, 7 bacteriorhodopsin, 196 Bayes theorem, 52, 249 Bayesian framework, 48 belief, 50, 95 Bellman principle, 82 bendability, 43, 44, 186, 219, 380, 381 beta breakers, 38 beta-sheet, 6, 18, 26, 38, 97, 115, 120, 121, 247 blind prediction, 124, 131 Blobel, G., 143 Bochner’s theorem, 395 Boltzmann–Gibbs distribution, 85, 91, 92, 354, 362, 368 Boltzmann-Gibbs distribution, 73, 74 Boolean algebra, 48 functions, 104 networks, 320 brain content-addressable retrieval, 2 memory, 2 branch length, 266, 273 branch point, 43, 212 C-terminal, 115, 128 C-value, 14 paradox, 14 cancer, 300 capping, 38 Carroll, L., 31 CASP, 124, 131, 262 cat, 7 Cavalier-Smith, T., 143 Chapman–Kolmogorov relation, 267 Chargaff’s parity rules, 230 chimpanzee, 7 Chomsky hierarchy, 277, 279, 280 Chomsky normal form, 279 chromatin, 44, 210 chromosome, 7, 210, 230, 284 components, 8 unstable, 8 classification, 97, 104 classification error, 118 Claverie, J-M., 13 clustering, 44, 186, 191, 313 Cocke–Kasami–Younger-algorithm, 290 codon start, 235 stop, 235 usage, 44, 145, 147, 210 codons, 26, 136, 137, 143, 210, 214 start, 38 stop, 26, 30, 141 coin flip, 67, 71 committee machine, 96 communication, 9 consensus sequences, 37, 165, 212, 236 convolution, 107 correlation coefficient, 122, 158, 209 Matthews, 158 Pearson, 158 Cox–Jaynes axioms, 50, 266 CpG islands, 147 Creutzfeld–Jakob syndrome, 25 Crick, F., 277 cross-validation, 95, 124, 129, 134 crystallography, 5, 120 Cyber-T, 305, 307 Darwin, C., 265 data corpus, 51 overrepresentation, 6 redundancy, 4, 219 storing, 2 database annotation, 2 bias, 129 errors, 6 noise, 2 public, 2, 3 database search iterative, 7 decision theory, 347 deduction, 48 DEFINE program, 120 development, 300 dice, 67 digital data, 1 dinucleotides, 116 Dirichlet distribution, 245 discriminant function, 389 distribution Boltzmann-Gibbs, 73 DNA arrays, 299 bending, 381 binding sites, 320 chip, 300 helix types, 45 library, 299 melting, 14 melting point, 45 periodicity, 44, 212, 216 reading frame, 210 symmetries, 230 DNA chips, 5 DNA renaturation experiments, 27 DNA sequencing, 1 dog, 7 DSSP program, 120, 131 dynamic programming, 81, 172, 175, 240, 246, 249, 289, 290, 295 multidimensional, 184 E. coli, 38, 113, 135, 210 email, 14 encoding adaptive, 128 ensemble, 126, 128, 132 ensembles, 96 entropy, 74 maximum, 129 relative, 54, 69, 78, 109–111, 129 ethics, 1 evidence, 70 evolution, 1, 8, 17, 56, 93, 137, 254 genetic code, 136 protein families, 116 evolutionary information, 124 evolutionary algorithms, 82, 93 evolutionary events, 185, 209, 212 evolutionary relationships, 196 exon assembly, 147 exon shuffling, 196 exon-exon junction, 30 exons, 103, 145, 147, 211 extreme value distribution, 195, 219 feature table, 3 Fisher kernels, 391 FORESST, 189 forward–backward procedure, 83, 172, 174–176, 178, 180, 182, 291 free energy, 73, 77, 85, 178 functional features, 33 fungi, 9 Gamow, G., 17 GenBank, 12, 15, 149, 152, 165, 219 gene, 10 coregulated, 320 number in organism, 11 protein coding, 11 gene pool, 8 GeneMark, 210, 234 GeneParser, 147 genetic code, 136 Genie, 234 genome, 7, 16 circular, 7 diploid, 7 double stranded, 7 haploid, 7, 9 human, 9 mammalian, 15 single stranded, 7 size, 9 GenomeScan, 234 GenScan, 234 Gibbs sampling, 89, 320, 373 glycosylation, 3, 16, 34 GRAIL, 147 Grail, 234 Guigo, R., 153 halting problem, 280 Hansen, J., 325 hidden variables, 78 Hinton, G.E., xviii histone, 44 HMMs used in word and language modeling, 240 Hobohm algorithm, 219 homology, 124, 126, 196, 275 homology building, 33 HSSP, 126, 131 Hugo, V., 14 human, 14 human genome chromosome size, 11 size, 11 hybrid models, 239, 371, 383 hybridization, 5 hydrogen bond, 38, 120, 143 hydrophobicity, 115, 118, 122, 186, 190 signal peptide, 133 hydrophobicity scale, 141 palindrome, 210, 278, 279, 281, 284, 285 PAM matrix, 267, 276 parameters emission, 63, 170, 383 transition, 63, 75 parse tree, 281, 292, 294, 297 partition function, 57, 74, 76, 77, 90, 354, 362 pathway, 320 PDB, 22 perceptron, 113 multilayer, 113 Petersen, T.N., 132 Pfam, 189 phase transition, 76 phonemes, 240 phosphorylation, 16, 119 phylogenetic information, 189, 293 phylogenetic tree, 185, 265, 266, 273 plants, 9 polyadenylation, 147, 210 polymorphism, 1 position-specific scoring matrices, 131 posttranslational modification, 16 prior, 52, 53, 55, 57, 59, 74, 106, 107 conjugate, 56, 303 Dirichlet, 56, 69, 75, 170 gamma, 55 Gaussian, 55, 107 use in hybrid architectures, 243 uniform, 72 profile, 6, 124, 126, 165, 219, 222 bending potential, 219, 381 emission, 214 promoter, 115, 147, 221 propositions, 50 PROSITE, 190, 205 protein beta-sheet, 97 beta-sheet partners, 115 helix, 97 helix periodicity, 120, 128 length, 17 networks, 321 secondary structure, 6, 113, 121, 129, 189, 229 secretory, 16 tertiary structure, 121 Protein Data Bank, 22 protein folding, 73 proteome, 16 pruning, 97 Prusiner, S.B., 25 pseudo-genes, 12 pseudoknots, 284, 288, 297 PSI-BLAST, 7, 131 PSI-PRED, 131 Qian, N., 121 quantum chemistry, 121 reading frame, 29, 43, 145, 210, 214, 217, 218, 286 open, 31 reductionism, 13 redundancy reduction, 4, 219 regression, 104, 308, 349, 387 regularizer, 57, 76, 94, 171, 181, 252, 253 regulatory circuits, 320 relative entropy, 160 renaturation kinetics, 14 repeats, 26, 28, 279, 284 representation orthogonal, 115, 128 semiotic, 2 ribosome, 38, 143, 145 ribosome binding sites, 113 Riis, S., 127 ROC curve, 162, 204 Rost, B., 25, 124 rules, 113, 123, 151 Chou-Fasman, 123 S. solfataricus, 38 Sander, C., 25, 32, 40, 124 Schneider, R., 32 Schneider, T., 37
palindrome, 210, 278, 279, 281, 284,

285

PAM matrix, 267, 276

parameters

emission, 63, 170, 383

transition, 63, 75

parse tree, 281, 292, 294, 297

partition function, 57, 74, 76, 77, 90,

354, 362

pathway, 320

PDB, 22

perceptron, 113

multilayer, 113

Petersen, T.N., 132

Pfam, 189

phase transition, 76

phonemes, 240

phosphorylation, 16, 119

phylogenetic information, 189, 293

phylogenetic tree, 185, 265, 266, 273

plants, 9

polyadenylation, 147, 210

polymorphism, 1

position-specific scoring matrices, 131

posttranslational modification, 16

prior, 52, 53, 55, 57, 59, 74, 106, 107

conjugate, 56, 303

Dirichlet, 56, 69, 75, 170

gamma, 55

Gaussian, 55, 107

use in hybrid architectures, 243

uniform, 72

profile, 6, 124, 126, 165, 219, 222

bending potential, 219, 381

emission, 214

promoter, 115, 147, 221

propositions, 50

PROSITE, 190, 205

protein

beta-sheet, 97

beta-sheet partners, 115

helix, 97

helix periodicity, 120, 128

length, 17

networks, 321

secondary structure, 6, 113, 121,

129, 189, 229

secretory, 16

tertiary structure, 121

Protein Data Bank, 22

protein folding, 73

proteome, 16

pruning, 97

Prusiner, S.B., 25

pseudo-genes, 12

pseudoknots, 284, 288, 297

PSI-BLAST, 7, 131

PSI-PRED, 131

Qian, N., 121

quantum chemistry, 121

reading frame, 29, 43, 145, 210, 214,

217, 218, 286

open, 31

reductionism, 13

redundancy reduction, 4, 219

regression, 104, 308, 349, 387

regularizer, 57, 76, 94, 171, 181, 252,

253

regulatory circuits, 320

relative entropy, 160

renaturation kinetics, 14

repeats, 26, 28, 279, 284

representation

orthogonal, 115, 128

semiotic, 2

ribosome, 38, 143, 145

ribosome binding sites, 113

Riis, S., 127

ROC curve, 162, 204

Rost, B., 25, 124

rules, 113, 123, 151

Chou-Fasman, 123

S. solfataricus, 38

Sander, C., 25, 32, 40, 124

Schneider, R., 32

Schneider, T., 37
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