Computational Systems Biology Methods and Protocols.7z

INDEX

A

Accuracy (ACC)..................................................4, 40, 55,
57, 59, 79, 86, 89, 116, 120, 140, 188, 192, 198,
215, 225, 230, 242, 244, 249, 250, 253, 254,
258, 273, 276, 312, 313, 401
Acute lymphoblastic leukemia (ALL)................387–392,
394–401, 403–406
Adverse drug reactions (ADR)...........................388, 392,
398, 399
Alternative splicing modules (ASM)............................351
Area under the curve (AUC)..............................217, 230
Artificial neural network.....................191, 228, 238, 243
A* search algorithm.............................................147, 148

B

Basic local alignment search tool (BLAST).......... 10, 226
Betweenness centrality (BC)...............................160, 227
Binary tree (BT)............................................................252
Biological general repository for interaction
datasets (BioGRID).................................112, 113
Bottom-up integration.......................................110, 116,
117, 119–121, 126

C

Cancer stem cells (CSCs)....................................312, 314,
323, 324
Cell-free tumour DNA (cfDNA) ............................45–59,
67, 68, 71–73, 76, 86, 88, 91, 92
Central nervous system (CNS)............................. 60,375,
381, 390
Chromatin immunoprecipitation followed by
sequencing (ChIP-seq)....................................126,
333, 401
Chromosomal confirmation capture (3C)..................112,
333, 392, 398, 399
Circulating tumour cells (CTCs) .............................45–47
Clathrin-mediated endocytosis (CME) .......................190
Composition moment vector (CMV)..........................242
Conditional mutual information (CMI).............139, 140
Convolutional neural networks (CNNs).............. 89, 196
Copy number alterations (CNA) .......................119, 392,
396, 397, 400, 403
Copy number variants (CNV).................................73–75,
90–92, 101, 360, 393–395, 402

D

Detection of acid fast bacilli (AFB)..............................376

Di-deoxynucleotidetriphosphates (ddNTPs) ..............2, 3

Differential coexpression network analysis.........155–164

Differentially expressed genes (DEGs) .........................17,

22–24, 171, 175–179, 213, 342, 356

Dijkstra’s algorithm......................................................147

DNA sequencing.................................................1–12, 30,

42, 47, 57, 67–70, 72–76, 78, 79, 81–89, 91, 92,

114, 361

E

Escherichia coli.........................................31, 42,185, 270

Expression Atlas............................................................137

Extracellular RNA (exRNA).........................................205

F

False negatives (FN)........................................56, 81,102,

218, 230, 243, 360, 362

False positives (FP)................................................. 69, 70,

74, 81, 85, 89, 91, 102–106, 139, 175, 218, 230,

243, 316, 333, 359, 379

Fluorescence-activated cell sorting (FACS)................311,

313, 329

F-measure (F1)..............................................................230

Fragments per kilobase per million fragments

mapped (FPKM) ...............................................352

G

Galeopterus variegatus..................................................... 32

Gas chromatography (GC) coupled with mass

spectrometry (MS)............................................266

gDNA-mRNA sequencing (DR-seq)...........................334

Gene Expression Omnibus (GEO).............................112,

137, 172, 217

Gene ontology (GO)..........................................145, 158,

171, 175, 177

Gene regulatory networks (GRNs)....................137–139,

141–150

Generalized singular value decomposition

(GSVD).....................................................122, 123

Genetic Association Database (GAD).................207, 208

Genome & transcriptome sequencing

(G&T-seq) .........................................................334

Tao Huang (ed.),Computational Systems Biology: Methods and Protocols, Methods in Molecular Biology, vol. 1754,
https://doi.org/10.1007/978-1-4939-7717-8,©Springer Science+Business Media, LLC, part of Springer Nature 2018

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