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Lander E.S., Waterman M.S. (eds.) Calculating the Secrets of Life: Applications of the Mathematical Sciences to Molecular Biology
Lander E.S., Waterman M.S. (eds.)  Calculating the Secrets of Life: Applications of the Mathematical Sciences to Molecular Biology









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: Calculating the Secrets of Life: Applications of the Mathematical Sciences to Molecular Biology

: Lander E.S., Waterman M.S. (eds.)

:

In this first-ever survey of the partnership between mathematics and biology, leading experts look at how mathematical research and methods have made possible important discoveries in biology. Explores how differential geometry, topology, and differential mechanics have allowed researchers to "wind" and "unwind" DNA's double helix to understand the phenomenon of supercoiling. Explains how mathematical tools are revealing the workings of enzymes and proteins. Describes how mathematicians are detecting echoes from the origin of life by applying the stochastic and statictical theory to the study of DNA sequences.


: en

: /

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ed2k: ed2k stats

: 1995

: 285

: 30.11.2005

: | | ID
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$\alpha$-Helix      242248 254
$\beta$-sheet      242248 254
4-plat knots      215216 220 222
Adenine (A)      8 9 99
Algorithms      3536 8486 87
Algorithms, approximate pattern matching      7879
Algorithms, difference measures      7273
Algorithms, dynamic programming      6064 78 82 84 85 86 109
Algorithms, gap cost penalties      7072
Algorithms, global alignment      5864 9499
Algorithms, heuristic      8284
Algorithms, in evolutionary analysis      106 110112
Algorithms, in genetic mapping      3536
Algorithms, in physical mapping      4651
Algorithms, K-best alignments      7678
Algorithms, local alignment      6570 99106
Algorithms, multiple alignments      7376
Alleles      6
Amino acids      4 57 Protein Sequence
Amplification      see Polymerase chain reaction
Ancestry      see Evolutionary analysis
ANREP systems      87
Antidiagonals      62 7980
APC gene      34 3738
Approximate pattern matching      7879 86
Approximate repeats      87
ARIADNE systems      87
Assay techniques      23
Autosomes      26
Base pairs      8 26 48 153 154 163 179 185 188 189 191 194 204 249 Thymine Cystosine Guanine Uracil)
Bayesian statistics      35
Bernoulli random variables      102 125
Biochemistry      25
Biosequences      see Databases of DNA sequences Sequence Sequencing
BLASTA algorithm      8284
Booth Leuker algorithm      5051
BRCAl (breast cancer) gene      33
Cancer      33 34 3742 58 91 183 196
Catenanes      205 212
Cauchys formula      136
Cellular structures      9
Chaperonins      238239
Chen Stein method      102 106 110
Chimeras      51
Chirality      213215
Chromosomal walking      17 18 42 43
Clones and cloning      13 14 26 4243 209
Closed circular DNA      153154 155 156 157 181 204
Coalescent      117 119121
Coalescent, combinatorial structures      119 136148
Coalescent, Ewens sampling formula      119 122124 136139
Coalescent, K-allele model      130132
Coalescent, likelihood methods      146148
Coalescent, tree construction and movement      124127 (see also Finitely-many-sites model Infinitely-manysites
Codons      12 115 239
Colon cancer      34 3742
Combinatorics      119 136148 185
Computing time and memory capacity, algorithmic efficiencies      3536 8486 87
Computing time and memory capacity, approximate pattern matching      79 87
Computing time and memory capacity, dynamic programming, algorithms      6263 64 68 83 84
Computing time and memory capacity, gap cost functions      72
Computing time and memory capacity, heuristic algorithms      8384
Computing time and memory capacity, K-best paths      77
Computing time and memory capacity, multiple alignments      75
Computing time and memory capacity, parallel processing      7981 84
Computing time and memory capacity, sublinear similarity searches      8485
Consecutive ones property      50
Consensus scores      76
Contigs      4750
Crick and Watson model      153 204205
Crossovers      2729
Cruciforms      154
Crystallography      202 203 240
Cystic fibrosis (CF)      1618 2021 26
Cytosine (C)      8 9 99
Databases of DNA sequences      13 17 56 81 87
Databases of DNA sequences, similarity searches in      7879 8286 87 9192 94 BLASTA)
Dayhoff matrix      66 67 83
Diagnostics      see Genetic diagnostics
Difference measures      7273
Diffusion processes      3742 148
Dimers      212
DNA (deoxyribonucleic acid)      89 92
DNA (deoxyribonucleic acid), primers      13 15 16
DNA (deoxyribonucleic acid), protein binding      166167 168 170171 181
DNA (deoxyribonucleic acid), transcription      912 154 179 196198 204205 Protein Sequence Sequencing Strand Supercoiling)
DNA polymerases      8 16 154
DNA polymorphisms and mutations      89 1617 26 30 34 57 106
DNA polymorphisms and mutations, as markers      31 34
DNA polymorphisms and mutations, in evolutionary analysis      114135
DNA polymorphisms and mutations, in mitochondria      115116 117 118 148149
DNA polymorphisms and mutations, minimal cost alignments      7273
DNA polymorphisms and mutations, rates of      66 67 116 117 124125
Dot plots      68 70
Duplex unwinding elements (DUEs)      183 194 195
Dynamic programming algorithm      6064 78 82 84 85 86 109 251
Edit graphs      5961 6870 75
Effective population size      117
Efficient algorithms      3536 8486 87
Electron microscopy      202 211 227
Electrostatic interactions      251
Energetics      154 180 182 186195
Enzymes      3 7 180 238
Eve hypothesis      116
Evolutionary analysis      5758 9094
Evolutionary analysis, coalescent structures      117 119135 148149
Evolutionary analysis, common origins      57 248
Evolutionary analysis, extremal statistical methods      106112
Evolutionary analysis, minimal cost alignments      7273
Evolutionary analysis, multiple alignments      73 76
Evolutionary analysis, random combinatorial structures      136148
Evolutionary analysis, trees      73 76 87 124 129 132 266
Evolutionary analysis, use of mitochondrial DNA      5758 9094 115116 117 148149
Ewens sampling formula (ESF)      119 122124 136139
Extremal statistical methods      106112
Extremal statistical methods, global sequence comparisons      9499
Extremal statistical methods, local sequence comparisons      99106
False negatives and positives      51
Familial adenomatous polyopsis (FAP)      3738
FASTA algorithm      82 83 84
Fingerprinting methods      4247
Finitely-many-sites model      132135
Fleming Viot process      148
Foldases      237238
Fourier transforms, coefficient      240
Fractionation      23
Free energy      154 180 182 186195
Gap costs      7072 7778
Gaussian processes      41
Gel electrophoresis      210211 227
GENBANK database      81
Gene splicing      see Recombinant DNA technology
Gene therapy      18
Generalized Levenshtein measure      73 87
genetic code      12 239
Genetic diagnostics      16 17
Genetic distance      2829
Genetic heterogeneity      34
Genetic maps and mapping      16 1819 26 2730 51
Genetic maps and mapping, and incomplete pedigree information      30 31 3435
Genetic maps and mapping, and maximum likelihood estimation      3442
Genetic maps and mapping, and non-Mendelian genetics      30 31 3334
Genetic maps and mapping, markers in      31
Genetic markers      31 34 42
Genetics      57
Genotype      38 40
Geometry      166 203 210 211 220 223
Geometry, descriptors and methods      155163 (see also Topology)
Global alignment      5 5864 9499
Global alignment, maximum-scoring      63
Graph theory      46 51
Guanine (G)      8 9 99
Haldane mapping function      29 41
Helical periodicity      154
Helix      8 9 153
Helix, destabilization      184 188 196
Heterozygotes      6 16 31
Heuristic algorithms      8284
Hierarchical condensation methods      248251
Histones      154 175
HIV protease structure      254255
Homeomorphisms      212213
Homology modeling      252
Homozygotes      6 31
Human genome project      1822 26
Hydrophilic side chains      244 253 263
Hydrophobic side chains      244 245 253
Hydrophobicity      4
In vitro assays      3
Incomplete penetrance      31 33 34
Independent assortment      29
Indexing, of databases      87
Infmitely-many-sites/alleles model      122 124 125 127130
Isomerases      238
K-allele model      130132
K-best alignments      7678
kDNA (kinetoplast DNA)      231
Kingmans subadditive ergodic theorem      97
Knot theory      212 (see also Tangles and knots)
Large Deviation Theory of Diffusion Processes      3742
Levenshtein measure      73 87
LexA binding sites      198199
Ligases      13
Likelihood methods      3442 146148
Linear DNA      155 156
Linking number (Lk)      155 157158 163164 173174 181
Linking number (Lk), mini chromosomes      175 177
Linking number (Lk), surface      167171 173174
Linking number (Lk), topoisomerase reactions      164166
Local alignment      5 6570 99106
Longest common subsequence      99
Macromolecules      3
Mapping      see Genetic maps and mapping Physical Restriction Sequencing
markers      see Genetic markers
Markov models, processes      36 146147 249
Maximum Likelihood Estimation      3435
Maximum likelihood estimation, and efficient algorithms      3536
Maximum likelihood estimation, and statistical significance      3742
Measure-valued diffusions      148
Membrane-bound transporters      1718 20
Mendelian genetics      57 27 31
Min (multiple intestinal neoplasia) trait      3839
Minichromosomes      174177
Mirror images      213215
Mismatch ratio      86
Mitochondrial DNA (mtDNA)      115116 117 118 135 148149 204
mobius      143 181
Molecular biology, overview      712
Monte Carlo methods      146147 149 241
Morgans      28
mRNA (messenger RNA)      9 12 92
Multiple alignments      7376
Multiple minima problem      241
Mutation      see DNA polymorphisms and mutations
Myoglobin      265266
Native American population studies      116 117
Neighborhood concept      83
Neural networks      259263
Nonadditive scoring schemes      87
Nuclear magnetic resonance (NMR)      203 240
Nucleic acids      3
Nucleosomes      154 166 174177
nucleotides      8 57 118 204
Nucleotides, distances      29 81
Oncogenes      58 91 196
Ornstein Uhlenbeck process      41
Overwinding      154
Packing density      252
Palindromes      87
Papillomavirus      196 199200
Parallel computing      7981 84 87
Penetrance      31 33 35
Phenocopy      34
Phenotype      38 40
Physical maps and mapping      17 19 26 29
Physical maps and mapping, fingerprinting methods      4247
Phytogeny      73 76 87
PIR database      81
PLANS (Pattern Language for Amino and Nucleic Acids Sequences)      263264
Platelet-derived growth factor (PDGF)      9
Plectonemic forms      154 156 169 170 215216
Poisson distributions      144
Poisson distributions, Boltzmann equation      254
Poisson distributions, Dirichlet distribution      144
Poisson distributions, in coalescent trees      121 124127
Poisson distributions, in sequence comparisons      29 100104 108110
Poly-adenylation      196
Polygenic inheritance      34
Polymerase chain reaction (PCR)      13 15 16 46
Polymorphism      see DNA polymorphisms and mutations
Polyoma virus      196
Primers      13 15 16
Principle of optimality      63
Probabilistic combinatorics      136
Processing time      see Computing time and memory capacity
Protein folding      5 12 236248
Protein folding, hierarchical condensation methods      248251 256265
Protein folding, prediction of      5 254255 265266
Protein folding, threading methods      248254
Proteins      35 78 57 92 Protein Sequence
Public databases      see Databases of DNA sequences
Pure breeding      5
Purines (R)      99 117 200
Pyrimidines (Y)      99 117 118 123 128 200
QUEST systems      87
R-group      237
Rational tangles      218221 228229
RecA binding      198199 211 227
Recessive traits      16
Recombinant DNA technology      1316 17
Recombination      2728 205 213 225230
Recombination, frequency      2830 31 35
Recombination, site-specific      207212 222225
Replication processes      92 154 179180 183 204
Resolvase      213 225230
Restriction enzymes      13
Restriction fragment lists      4546
Restriction maps      4445 87
Ribosomes      9 10 12 92
RNA (ribonucleic acid)      9 179 196 237
RNA (ribonucleic acid), evolutionary analysis      9293 106107 110112
RNA (ribonucleic acid), polymerase      9
RNA (ribonucleic acid), rRNA      92 93 106 107 110 112 tRNA)
Rule-based methods      263264
Scoring schemes, gap cost penalties      7072
Scoring schemes, global alignments      5964
Scoring schemes, K-best alignments      7678
Scoring schemes, local alignments      6568
Scoring schemes, minimal cost alignments      7273
Scoring schemes, multiple alignments      7476
Scoring schemes, nonadditive      87
Scoring schemes, unit-cost      5859 86
Sedimentation rate      100
self-replication      92
Sequence similarity, and comparison      5658 8687 91 199
Sequence similarity, approximate pattern matching      7879 86
Sequence similarity, database searches      7879 8286 87 9192 94
Sequence similarity, difference measures      7273
Sequence similarity, gap cost penalties      7072
Sequence similarity, global alignment      5 5864 9499
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