Index

A

Acanthamoeba 196
acquaintance network 2
activation energy 8
adaptation 164
adjacency list 21
adjacency matrix 22
aerobic respiration regulatory protein (ArcA) 101
affinity chromatography 42
aging vertex networks 87
algorithm 18
all pairs docking module 219
all-pairs shortest path problem 18
amino acid composition 239
anabolic pathway 8 anaphase-promoting complex 168
annotation 12
apoptosis 165
apoptosome 195
Arabidopsis 109-110
arginine 239 -biosynthesis 112
Arp 2/3 complex 196, 220
aspartate oxidase 147
association method 60
ATP 115
attractor(s) 107, 109
average-linkage algorithm 113

B

bacterial photosynthesis 174
Barabasi-Albert algorithm 73
Barabasi-Albert model 61
basin of attraction 107
Bayes' theorem 53
Bayesian network(s) 54, 106
betweenness 77
bifurcation 164
big O notation 20
binding constant 8
biochemical pathways 115, 117
BioCyc 118
biological module 82
biological network 2
Biomolecular Interaction Network Database (BIND) 35
Boltzmann constant 249
Boolean networks 106
breadth-first search 22
Brenda 13
Brownian motion 250
brute-force algorithm 72
buzzer 162

C

Cartesian space 128
catabolic pathway 7
Cdc 25
- phosphatase 168
Cdkl kinase 168
cell cycle 11, 168 -division 11
central paradigm 15
checkpoints 11
Chemotaxis 104-105
Cholesky decomposition 125
chromatophore 174
- vesicle 176
clique 71
- problem 72
clustering 76
- algorithm 99
coefficient 69-70
coexpression 44
- networks 105
cofunctionality 48
collaboration network 2
colocalization 199
Combdock 20, 218
combinatorial assembly module 218
community 76
complete graph 71
conditional probability 53
- distribution 52
connected component 17, 72, 140
connected graph 17
constraint-based modeling 146
Consurf 243
continuity equation 169
conversion chain 179
convolution 208
core index 212
core-weighted fitting 212
correlated mutations 243
correlation functions 15
coulombic energy 33
Coulomb law 246
cross-correlation 222
cryo-electron microscopy 194
cut set 141
cycle 17
cyclic AMP receptor protein (CRP) 101
cyclin 11
- dependent kinase 11, 167
- kinase inhibitor 168
cyclin B 168
cytochrome 178
cytochrome bc₁ complex 174
cytochrome c 174
cytoskeleton 7

D

Danielson-Lanczos lemma 209
date hubs 75
degree 68
- distribution 68
delta distribution 225
densely overlapping region (DOR) 112
depth-first search 22
differential equation 15
- models 108
diffusion equation 169
Dijkstra's algorithm 23
dimensions 121
dipole-dipole coupling 202
discrete Fourier transform 207
divide and conquer 20
DNA microarray timeseries 261
Drosophila 86
double description method 128
double description pair 130
duplication-mutation-complementation 86
duplication-random mutations (DMR)
- algorithm 87
dynamic models 106
dynamic Monte Carlo (DMC) 172
dynamic programming 20

E

E-Cell 116
EcoCyc 117
edge 17
- betweenness 77
- clustering coefficient 80
- independent path 77
- relaxation 26
eigenvalue 124
eigenvector 124
electron microscopy 203
electron/proton carrier 174
electron tomography 221
electrospray ionization 44
electrostatic potential 247
elementary flux modes 133, 139
elongation 100
enzyme 8
- classification (EC) 11
equations of motion 15
Ermak-McCammon algorithm 250
Escherichia coli 101, 115, 117, 146
- strain MG 1655 146
essentiality 57, 74
Euler's formula 216
evolutionary trace 243
extreme pathways 133, 137
extreme rays 129
enumeration problem 131

F

factor for inversion stimulation (FIS) 101
false negative 52
false positive 52
Fast Fourier transformation 208
feasible set 126
feed-forward loop (FFL) 5, 111
Fick's first law 170
fluorescence resonance energy transfer 201
flux balance analysis 116, 125, 127
fluxome 150
fly-Base 12
F₀ F₁ , ATPase 174
force-directed layout 32
Forward-Euler integrator 187
Fourier transformation 15, 206
fragility coefficient 145

fumarate and nitrate reductase regulatory protein (FNR) 101

G

G0 phase 11
G1 phase 11
G2 phase 11
Gaussian distribution 226
Gauss-Jordan elimination 125
gel electrophoresis 41
gene cluster method 47
gene neighborhood method 48
gene ontology (GO) 12, 60, 199
generating matrix 131
gene regulatory network 5, 101, 155
genetic algorithm 21, 183
giant component 17, 72
Gillespie algorithm 174
Girven-Newman algorithm 78
global biological network 101
global transcription factors 101, 103
glycolysis 8
Goldbeter-Koshland function 162
gold standard 55
gradient operator 33
graph 21
- theoretical models 105
greedy algorithm 31, 220
greedy method 20
green fluorescent protein 172, 249

H

Haemophilus influenzae 121
Hamming distance 50
harmonics 206
Helicobacter pylori 121
heuristic algorithms 21
hierarchical clustering 76, 103
high-flux backbone 146
high-throughput mass spectrometric protein complex identification 44
histone-like protein or nucleoid-associated protein (Hns) 101
homeostasis 166
homogenous local organization 147
homology 231
hot spots 235
hub 69, 75
human growth hormone (hGH) 235
hydrogen-bond 239
hydrophobic interaction 248
hyperedge 105
hysteresis 165

I

identity matrix 123
induced fit 218
immuno-electron microscopy 201
incidence matrix 22
initiation 100
integrated networks 261
integration host factor (IHF) 101
interaction matrix M 108
interactome 50, 221
intergenic interaction matrix 108
internal substrate 152
intersection points 118
in silico prediction 52
ion screening 247
iPfam 60
iRMSD 233
isoelectric point (pI) 41

J

joint probability 53

K

Katchalski-Katzir algorithm 206, 217
KEGG 13
Kruskal's algorithm 20, 31
Kyoto Encyclopedia of Genes and Genomes (KEGG) 8

L

Laplacian filter 211
leucine-responsive regulatory protein (Lrp) 101
light-harvesting complex (LHC) 174
likelihood function 53
linear algebra 121
linear cross-correlation 205
linear preferential attachment 87
linear programming 20, 128
linear transformations 122
loss-of-function mutant 109

M

macromolecular complexes 254
macromolecules 6 malate dehydrogenase 118
mass conservation 118
mass spectroscopy 44
mathematical graphs 15, 17
mathematical pendulum 156
matrix 121-122 algebra 15
matrix-assisted laser desorption ionization (MALDI) 44
M phase 11
messenger RNA 4
metabolic flux distribution 155
metabolic network 116
metabolic pathway 7
metabolites 115
Methanosarcina barkeri 121
Michaelis-Menten kinetics 162
microarray 5
minimal cut set(s) 140-141
minimum spanning tree 29
MIPS 46, 55, 199
mixed integer linear programming (MILP) 128
modular decomposition 82
modularity 82
module 83, 104, 198
mouse genome database (MGD) 12
mRNA 4
- abundance 46
multiple-input/multiple-output (MIM) 5
multiple sequence alignments (MSAs) 239
mutant phenotype 145

N

neighbor 83
neighborhood 70
network motifs 99, 111
network reconfiguration 140
network theory 1
network topology 4, 68
network verification 145
Newton's second law of motion 155
nonobligate complex 197
NP-complete 20, 72
nuclear magnetic resonance (NMR) spectroscopy 44, 199, 201
nuclear overhauser effect (NOE) 201
nucleoside diphosphate kinase 117
null space 125

O

obligate 197
one-way switch 164
ontology 12
open reading frame 198
operon 49
ordinary differential equation 155
oscillatory response 166

P

parallel module 83
partial differential equation 169
party hubs 75
path 17
pathway length matrix 138
percolation 72
permanent complex 196
phantom cell 222
phylogenetic analysis 86
phylogenetic profiling 49-50
Poisson distribution 69, 73
Poisson-Boltzmann equation 248
polyhedral cone 131
pools-and-proteins model 176
positive feedback 164
posterior probability 53
power law 60
- distribution 75
preferential attachment 3, 73
Prim's algorithm 31
prime module 83
principal component analysis 99
prior probability 53
probabilistic algorithm 21
proteasome 222
protein complex purification (PCP) 84
protein data bank (PDB) 14, 199, 235
protein domain networks 59
protein phosphatase 2A 85
protein-protein docking 216
protein-protein interaction 5, 155
- network 17, 39
proteomics 39
pseudocode 19
psynthesis 141
purine nucleoside Phosphorylase 117
pyruvate dehydrogenase 196

Q

quninol 174
quninone 174
quotient 83

R

Radicchi algorithm 80
random graph 72
random growing networks 87
random networks 2 random static networks 87
rank 123
rate constant 178
reaction center (RC) 174
reaction participation matrix 139
Regulon-DB 101
representation matrix 131
representative vertex 83
response magnitude 159
reverse engineering 99, 107
Rhodobacter sphaeroides 174
ribonucleoprotein 195
ribosome 195
RNA polymerase 4, 100, 194, 220
robustness 74, 145
Rosetta Stone method 48
rotation matrix 124, 130, 205

S

Saccharomyces cerevisiae 121
Saccharomyces Genome Database (SGD) 12
scalar multiplication 122
scale-free 3
- graphs 73
- network 3
Schizosaccharomyces pombe 223
search and enumeration 21
series module 83
shape complementarity 217
shared components 82
shortest path 77
- problem 17
signal transduction 11
- networks 5 signal-to-noise ratio 49
signaling pathway 158
single-input motif (SIM) 112
single-input/multiple-output (SIM) 5 small interfering RNA 99
small worlds 2, 73
- network 87
- phenomenon 1 sniffer 166
socio-affinity index 198
sodium dodecyl sulfate (SDS) 41
solventaccessiblesurfacearea(SASA) 233, 249
spanning tree 29, 219
spatial organization 7
S phase 11
spliceosome 194
square matrix 123
Staphylococcus aureus 121
state transition 107
statistical fluctuation 59
statistical potential 240
steady state 118, 159
stochastic fluctuation 172
stoichiometric analysis 15
stoichiometric matrix 118
stoichiometric modeling 116
Stokes-Einstein relationship 249
structural classification of protein (SCOP) 236
subgraph 17, 87
submatrix 131
succinyl coenzyme A synthetase 147
sum of least squares 205
surface overlap maximization 215
surface plasmon resonance 44
synthetic lethality 44
system of linear equations 124
systemic independence 140
systems biology markup language (SBML) 12

T

tandem affinity purification (TAP) 42, 82
TATA box 100
Taylor expansion 187
technological network 2
termination 100
thermosome 222
Thermus thermophilus 257
three-dimensional structure 39
timer 178
toggle switch 165
trail 17
transformed Shannon entropy 237
translation 4
tree 18, 76, 83
triangle 70
TRIPLES 46, 71
twilight zone 231
two-dimensional electrophoresis 41
tyrosine 239

U

ubiquinol 174
ubiquinone 174
upstream activating sequence 43
underdetermined 125

V

vertex 17
vertex-independent path 76
Vesiweb 181
voxel 178
Virtual Cell 170
vulnerability 74

W

walk 17
weel 168
weighted graph 17

X

X-ray crystallography 199

Y

yeast two-hybrid 18, 42
- method 74

Z

Zachary's karate club 79